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WO2025184125A1 - Lambda n-based compositions and methods for nucleic acids editing - Google Patents

Lambda n-based compositions and methods for nucleic acids editing

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Publication number
WO2025184125A1
WO2025184125A1 PCT/US2025/017272 US2025017272W WO2025184125A1 WO 2025184125 A1 WO2025184125 A1 WO 2025184125A1 US 2025017272 W US2025017272 W US 2025017272W WO 2025184125 A1 WO2025184125 A1 WO 2025184125A1
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Prior art keywords
peptide
deaminase
amino acid
seq
nucleotide
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French (fr)
Inventor
Andrew W. Fraley
Stephen Su
Duncan Brown
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Korro Bio Inc
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Korro Bio Inc
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Publication of WO2025184125A1 publication Critical patent/WO2025184125A1/en
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y305/00—Hydrolases acting on carbon-nitrogen bonds, other than peptide bonds (3.5)
    • C12Y305/04—Hydrolases acting on carbon-nitrogen bonds, other than peptide bonds (3.5) in cyclic amidines (3.5.4)
    • C12Y305/04005—Cytidine deaminase (3.5.4.5)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/102—Mutagenizing nucleic acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/78—Hydrolases (3) acting on carbon to nitrogen bonds other than peptide bonds (3.5)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y305/00—Hydrolases acting on carbon-nitrogen bonds, other than peptide bonds (3.5)
    • C12Y305/04—Hydrolases acting on carbon-nitrogen bonds, other than peptide bonds (3.5) in cyclic amidines (3.5.4)
    • C12Y305/04004—Adenosine deaminase (3.5.4.4)
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/85—Fusion polypeptide containing an RNA binding domain
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/50—Physical structure
    • C12N2310/53—Physical structure partially self-complementary or closed
    • C12N2310/531—Stem-loop; Hairpin

Definitions

  • the present disclosure relates to the field of nucleic acid editing. Specifically, the present disclosure provides, in part, compositions and methods comprising nucleic acid editing complexes and uses thereof, as well as methods of treatment for diseases, conditions and disorders originating from genetic mutations.
  • RNA editing alters the nucleotide sequences of RNA transcripts (e.g., messenger RNAs) once they are synthesized and thereby changes the coded message the mRNA transcript carries.
  • RNA transcripts e.g., messenger RNAs
  • mRNA editing In animals, two principal types of mRNA editing occur: the deamination of adenosine to produce inosine (A-to-I editing) and, less frequently, the deamination of cytosine to produce uracil (C-to-U editing). In the former, the resulting inosine is read as guanosine by translation machinery. If the edit occurs in a coding region, it can have a profound impact on downstream processes, such as changing the amino acids of the protein or producing a truncated protein by creating a premature stop codon, thereby affecting the protein’s structure and function.
  • Edits that occur outside coding sequences can affect the pattern of pre-mRNA splicing, the transport of mRNA from the nucleus to the cytosol, the efficiency with which the RNA is translated, or the base-pairing between microRNAs (miRNAs) and their mRNA targets.
  • miRNAs microRNAs
  • the process of A-to-I editing is particularly prevalent in humans, where it occurs in approximately 1,000 genes.
  • Enzymes called ADARs adenosine deaminases acting on RNA
  • these enzymes recognize double-stranded RNA structures that are formed through base-pairing between the site to be edited and a complementary sequence located elsewhere on the same RNA molecule, typically in an intron.
  • RNA The structure of the double-stranded RNA specifies whether the mRNA is to be edited, and if so, where the edit should be made.
  • C-to-U editing which is carried out by a different set of enzymes is also crucial in mammals.
  • Attorney Docket No.: 33791/41005 [0005] Advances in the field have led to the development of technologies that harness the power of nucleic acid-editing enzymes by way of editing or altering specific nucleobases in RNA and DNA of cells. However, there is still a need in the field for gene editing strategies for the purpose of therapeutically targeting and correcting genetic mutations that give rise to genetic diseases, conditions and disorders.
  • RNA editing processes that yield lower off-target mutations, such as those resulting from technologies involving nuclease activities (e.g., CRISPR).
  • CRISPR nuclease activities
  • site-specific RNA editing strategies have progressed in the field and look promising, challenges remain with regards to various RNA editing systems known in the art. See, Vogel and Stafforst, “Critical review on engineering deaminases for site-directed RNA editing,” Current Opinion in Biotech 55 (2019) at 75-76. Accordingly, there remains the need for enhanced RNA-editing systems.
  • compositions and methods for site- specific editing of a target nucleotide e.g., within an RNA molecule
  • Such compositions and methods provide increased efficiency and/or specificity of nucleic acid editing than which is provided in present systems.
  • compositions and methods in various embodiments, provide for nucleotide changes which are reversible and tunable in nature. Without wishing to be bound by theory, this limited duration of effect reduces a likelihood of danger related to harmful off- site editings, and tunability allows continuous adjustment of the effect in a dose-dependent manner, to mitigate or eliminate adverse effects.
  • the present disclosure allows for manipulation of cellular pathways and processes of which permanent manipulation would have serious health consequences.
  • the present disclosure allows for genetic manipulation that is nuclease-free and spares the genetic information encoded in DNA.
  • the present disclosure allows for genetic manipulation that is not DNA level and therefore less likely to cause a permanent effect (e.g. avoids an adverse outcome at the DNA level).
  • the present compositions and methods provide for targeted enzymatic functionality that supports editing of a target nucleotide combined with targeted nucleic acid specificity that locates the enzymatic functionality to the target nucleotide.
  • fusion proteins of a deaminase linked to a mutant ⁇ also referred to as “lambda” herein
  • these fusion proteins find use in efficient and/or specific base editing.
  • the present disclosure relates to a fusion protein between a deaminase, such as an ADAR, or the catalytic domain thereof, linked to a mutant ⁇ N-peptide, a lamboid P22 bacteriophage N-peptide, or a lamboid P21 bacteriophage N-peptide.
  • the fusion protein is capable of specifically interacting with a hairpin (e.g., a hairpin RNA) oligonucleotide.
  • methods described herein comprise contacting a cell with a deaminase linked to a mutant ⁇ N-peptide, a lamboid P22 bacteriophage N-peptide, or a lamboid P21 bacteriophage N-peptide, and an antisense RNA oligonucleotide linked to a hairpin (e.g., a hairpin RNA) oligonucleotide.
  • the hairpin RNA oligonucleotide is the cognate hairpin oligonucleotide of the mutant ⁇ N- peptide.
  • the cognate hairpin oligonucleotide can be a BoxB hairpin RNA oligonucleotide.
  • the antisense RNA oligonucleotide comprises a region complementary to an RNA molecule comprising the target nucleotide.
  • the mutant N-peptide and hairpin oligonucleotide interact, and the deaminase domain causes editing of the target nucleotide to induce a base change.
  • the disclosure also provides methods for treating diseases, conditions and/or disorders that manifest from genetic mutation(s).
  • methods of treating a disorder, condition or disease by editing a target nucleotide within an RNA molecule in a cell include contacting a cell with a deaminase linked to a mutant ⁇ N-peptide, a lamboid P22 bacteriophage N-peptide, or a lamboid P21 bacteriophage N- peptide, and an antisense RNA oligonucleotide linked to a hairpin (e.g., a hairpin RNA) oligonucleotide.
  • the hairpin RNA oligonucleotide is the cognate hairpin of the mutant ⁇ N-peptide.
  • the cognate hairpin can be a BoxB hairpin RNA oligonucleotide.
  • the antisense RNA oligonucleotide comprises a region complementary to an RNA molecule comprising the target nucleotide.
  • the mutant ⁇ N-peptide, a lamboid P22 bacteriophage N- peptide, or a lamboid P21 bacteriophage N-peptide and hairpin interact, and the deaminase domain causes editing of the target nucleotide to induce a base change.
  • Methods described herein further contemplate adenosine or cytidine deaminases, wherein a cytidine deaminase may yield a uridine nucleotide upon inducing a cytidine (C) to uridine (U) nucleotide change.
  • an adenosine deaminase induces a cytidine (C) to uridine (U) nucleotide change.
  • the adenosine or cytidine deaminase is a fragment comprising the catalytic domain of the adenosine or cytidine deaminase.
  • the fragment comprises Attorney Docket No.: 33791/41005 a catalytic domain and one or more mutations.
  • the adenosine deaminase is selected from ADAR1 and ADAR2, or fragments or variants thereof.
  • the mutant ⁇ N-peptide is derived from the ⁇ lambdoid bacteriophage N protein.
  • the ⁇ N-peptide is the wild-type amino-terminal domain ⁇ N-peptide and comprises the amino acid sequence of SEQ ID NO: 1.
  • the ⁇ N-peptide is a mutant of the wild-type amino-terminal domain ⁇ N-peptide and comprises at least one mutation as compared to the wild-type amino-terminal domain ⁇ N-peptide (SEQ ID NO: 1).
  • the mutant ⁇ N-peptide can comprise from 1 to 21 amino acid residue substitutions, as compared to the wild-type ⁇ N-peptide.
  • such mutations increase the binding affinity of the mutant ⁇ N-peptide to its hairpin, as compared to the binding affinity of the wild-type ⁇ N-peptide to its hairpin.
  • the mutant ⁇ N-peptide can comprise from 1 to 21 amino acid residue substitutions, as compared to the wild-type ⁇ N-peptide.
  • such mutations increase the binding affinity of the mutant ⁇ N-peptide to its hairpin, as compared to the binding affinity of the wild- type ⁇ N-peptide to its hairpin.
  • the deaminase and the mutant ⁇ N-peptide are a fusion protein, optionally connected by a chemical linker.
  • the deaminase can be linked to at least 2, at least 3, at least 4, at least 5, at least 6, or at least 7 mutant ⁇ N-peptides.
  • the deaminase and the mutant ⁇ N-peptide comprise a nuclear localization signal, optionally wherein the RNA molecule comprising the target nucleotide is in the nucleus of the cell.
  • the nuclear localization signal is the SV40 Large T-antigen nuclear localization signal.
  • the P22 N-peptide is a variant that is the wild-type amino-terminal domain P22 N-peptide and comprises the amino acid sequence of SEQ ID NO: 2.
  • the amino-terminal domain P22 N-peptide comprises an arginine-rich motif.
  • the amino-terminal domain P22 N-peptide comprises an Ala at position 5 and an arginine at each of positions 8, 12, and 13 of SEQ ID NO: 2.
  • the amino-terminal domain P22 N-peptide variant comprises at least one mutation as compared to the wild type amino-terminal domain P22 N-peptide.
  • the amino-terminal domain P22 N-peptide variant comprises from 1 to 21 amino acid residue substitutions.
  • the amino acid substitution takes place at one or more of amino acid residue positions 1 to 21, relative to the wild type amino-terminal domain P22 N-peptide sequence (SEQ ID NO: 2).
  • the amino-terminal domain P22 N-peptide variant Attorney Docket No.: 33791/41005 comprises the amino acid sequence of any one of SEQ ID NO: 10 to SEQ ID NO: 34.
  • such mutations increase the binding affinity of the P22 N-peptide variant for the BoxB hairpin RNA, as compared to the binding affinity of the wild type P22 N-peptide for the BoxB hairpin RNA.
  • the P12 N-peptide is the wild-type amino-terminal domain P21 N- peptide and comprises the amino acid sequence of SEQ ID NO: 3.
  • the amino- terminal domain P21 N-peptide comprises an arginine-rich motif.
  • the amino- terminal domain P21 N-peptide comprises an Ala at position 5 and an arginine at each of positions 8, 12, and 13 of SEQ ID NO: 3.
  • the amino-terminal domain P21 N-peptide variant comprises at least one mutation as compared to the wild type amino-terminal domain P21 N-peptide.
  • the amino-terminal domain P21 N-peptide variant comprises from 1 to 21 amino acid residue substitutions.
  • the amino acid substitution takes place at one or more of amino acid residue positions 1 to 21, relative to the wild type amino-terminal domain P21 N-peptide sequence (SEQ ID NO: 3).
  • the amino-terminal domain P21 N-peptide variant comprises one or more mutations at positions R13 and I17 of SEQ ID NO: 3. In various embodiments, such mutations increase the binding affinity of the P21 N-peptide variant for the BoxB hairpin RNA, as compared to the binding affinity of the wild type P21 N-peptide for the BoxB hairpin RNA.
  • Methods described herein further contemplate an antisense RNA oligonucleotide that hybridizes with a wild-type or mutant target sequence in an endogenous RNA molecule that comprises a target nucleotide to be edited. In some embodiments of the present disclosure, the target nucleotide to be edited induces a beneficial mutation in the wild-type target sequence.
  • the target nucleotide to be edited eliminates a detrimental mutation in the mutant target sequence.
  • the target nucleotide can be a genetic mutation associated with a genetic disease, condition or disorder.
  • the mutant ⁇ N-peptide interacts with a hairpin (e.g., a hairpin RNA, where there is hairpin recognition of the ⁇ N-peptide) oligonucleotide.
  • the hairpin RNA oligonucleotide is the cognate hairpin of ⁇ N-peptide.
  • the cognate hairpin can be a BoxB hairpin RNA oligonucleotide.
  • the BoxB hairpin RNA oligonucleotide is located from about 2-20 nucleotide residues 5’ of the target mutation. In some embodiments, the BoxB hairpin RNA oligonucleotide is located from about 2-20 nucleotide residues 3’ of the target mutation.
  • such components described herein are synthetically generated or generated from a plasmid. In still further embodiments, the components are contained within a plasmid or Attorney Docket No.: 33791/41005 vector, optionally wherein the vector is a viral vector.
  • Such viral vectors can include, but are not limited to, adeno-associated viruses (AAVs), adenoviruses, retroviruses, and lentiviruses.
  • AAVs adeno-associated viruses
  • the present disclosure contemplates the use of mRNA and/or lipid nanoparticles for delivery of the components of the nucleic acid-editing system to a cell.
  • Figure 1 is a schematic that depicts an illustrative, non-limiting example of the embodiments of the present disclosure.
  • FIG. 1 depicts editing of a target nucleotide within an RNA molecule, mediated by (i) a deaminase linked to a lambdoid bacteriophage N-peptide, and (ii) an antisense RNA oligonucleotide linked to a hairpin RNA oligonucleotide, wherein the lambdoid bacteriophage N-peptide interacts with the hairpin RNA oligonucleotide.
  • Figure 2 is a schematic that depicts an illustrative, non-limiting example of the embodiments of the present disclosure.
  • the figure depicts editing of a target nucleotide within a disease target, mediated by (i) a deaminase domain linked to a lambdoid bacteriophage N-peptide, and (ii) an antisense 2boxB guide RNA oligonucleotide linked to a hairpin RNA oligonucleotide, wherein the lambdoid bacteriophage N- peptide interacts with the hairpin RNA oligonucleotide.
  • a target nucleotide e.g., within an endogenous RNA molecule
  • the fusion of a deaminase, such as (without limitation) an ADAR, or the catalytic domain thereof, with a mutant ⁇ N-peptide allows for nucleic acid editing that is specific and not substantially hindered by off-target effects, while also allowing for a transient and tunable effect.
  • a deaminase such as (without limitation) an ADAR
  • the catalytic domain thereof allows for nucleic acid editing that is specific and not substantially hindered by off-target effects, while also allowing for a transient and tunable effect.
  • methods described herein comprise (a) contacting a cell with (i) a deaminase linked to a mutant ⁇ N-peptide, and (ii) an antisense RNA oligonucleotide linked to a hairpin (e.g., a hairpin RNA) oligonucleotide.
  • a hairpin e.g., a hairpin RNA
  • the hairpin RNA oligonucleotide is the cognate hairpin of the ⁇ N- peptide.
  • the cognate hairpin can be a BoxB hairpin RNA oligonucleotide.
  • methods described herein comprise (a) contacting a cell with (i) a deaminase linked to a lambdoid bacteriophage N-peptide, and (ii) an antisense RNA oligonucleotide linked to a hairpin (e.g., a hairpin RNA) Attorney Docket No.: 33791/41005 oligonucleotide.
  • the hairpin RNA oligonucleotide is the cognate hairpin of the N- peptide.
  • the cognate hairpin can be a BoxB hairpin RNA oligonucleotide.
  • the lambdoid bacteriophage is P22 or P21.
  • the antisense RNA oligonucleotide comprises a region complementary to an RNA molecule comprising the target nucleotide.
  • the N-peptide and hairpin interact, and the deaminase domain causes editing of the target nucleotide.
  • the antisense RNA oligonucleotide comprises a region complementary to an RNA molecule comprising the target nucleotide.
  • the ⁇ N-peptide and hairpin interact, and the deaminase domain causes editing of the target nucleotide.
  • the disclosure further provides methods for treating diseases, conditions and/or disorders that manifest from genetic mutation(s).
  • methods of treating a disorder, conditions or disease by editing a target nucleotide within an RNA molecule in a cell include contacting a cell with a deaminase linked to a mutant ⁇ N-peptide, lamboid P21 N-peptide, or lamboid P22 N-peptide, and an antisense RNA oligonucleotide linked to a hairpin (e.g., hairpin RNA) oligonucleotide.
  • the hairpin RNA oligonucleotide is the cognate hairpin of the ⁇ N-peptide, lamboid P21 N-peptide, or lamboid P22 N- peptide.
  • the cognate hairpin can be a BoxB hairpin RNA oligonucleotide sequence.
  • the antisense RNA oligonucleotide comprises a region complementary to an RNA molecule comprising the target nucleotide.
  • the ⁇ N-peptide, lamboid P21 N-peptide, or lamboid P22 N-peptide and hairpin interact, and the deaminase domain causes editing of the target nucleotide to induce a base change.
  • the disclosure provides a method of site-specific editing of a target nucleotide within an RNA molecule in a cell comprising: (a) contacting the cell with: (i) a deaminase linked to a mutant ⁇ N-peptide, lamboid P21 N-peptide, or lamboid P22 N-peptide, and (ii) an antisense RNA oligonucleotide linked to a BoxB hairpin RNA oligonucleotide, the BoxB hairpin RNA oligonucleotide being the cognate hairpin oligonucleotide of the ⁇ N-peptide, lamboid P21 N-peptide, or lamboid P22 N-peptide, and wherein: the antisense RNA oligonucleotide comprises a region complementary to an RNA molecule comprising the target nucleotide; the ⁇ N-peptide, lamboid P21 N-peptide, or
  • the present disclosure contemplates a method of treating a disease, condition or disorder by editing of a target nucleotide within an RNA molecule in a cell comprising: (a) contacting the cell with: (i) a deaminase linked to a mutant ⁇ N-peptide, lamboid P21 N-peptide, or lamboid P22 N-peptide, and (ii) an antisense RNA oligonucleotide linked to a BoxB hairpin RNA oligonucleotide, the BoxB hairpin RNA oligonucleotide being the cognate hairpin of the ⁇ N-peptide, lamboid P21 N-peptide, or lamboid P22 N-peptide, and wherein: the antisense RNA oligonucleotide comprises a region complementary to an RNA molecule comprising the target nucleotide; the ⁇ N-peptide
  • nucleic Acid-Editing Enzymes and Deaminase Domains [0031] Some embodiments of this disclosure provide strategies, systems, reagents, and methods that are useful for the targeted editing of nucleic acids, including editing a single site within a subject's genome, e.g., the human genome.
  • nucleic acid editing enzymes or enzyme domains e.g., deaminase domains.
  • Methods of the present disclosure further contemplate the use of adenosine and/or cytidine deaminases, wherein a cytidine deaminase may yield a uridine nucleotide upon inducing a cytidine (C) to uridine (U) nucleotide change.
  • an adenosine deaminase induces a cytidine (C) to uridine (U) nucleotide change.
  • the nucleic acid-editing domain is an RNA-editing domain.
  • the nucleic acid-editing domain is a deaminase domain.
  • the deaminase is an adenosine deaminase.
  • the deaminase can be selected from adenosine deaminase, RNA specific (ADAR), adenosine deaminase, RNA specific 2 (ADAR2), adenosine deaminase, RNA specific B1 (ADARB1), adenosine deaminase like (ADAL), adenosine deaminase 2 (ADA2), adenosine monophosphate deaminase 1 (AMPD1), adenosine monophosphate deaminase 2 (AMPD2), adenosine monophosphate deaminase 3 (AMPD3), adenosine deaminase domain containing 1 (ADAD1), adenosine deaminase domain containing 2 (ADAD2), adenosine deaminaminaminas
  • the deaminase is an AD AT family deaminase.
  • adenosine deaminase of the present disclosure is a fragment comprising the catalytic domain of the adenosine deaminase. In further embodiments, the fragment comprises a catalytic domain and one or more mutations.
  • the fragment or variant of the adenosine deaminase can Attorney Docket No.: 33791/41005 comprise an amino acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity with the adenosine deaminase amino acid sequences provided herein.
  • the fragment is the catalytic domain of the deaminase.
  • the deaminase comprises any isoform thereof, such as those known in the art (e.g., ADAR comprises two isoforms: ADAR1p150 and ADAR1p110).
  • the adenosine deaminase comprises an amino acid sequence modified by one or more mutations at one or more positions selected from E396, C451, V351, R455, T375, K376, S486, Q488, R510, K594, R348, G593, S397, H443, L444, Y445, F442, E438, T448, A353, V355, T339, P539, V525 and I520.
  • the adenosine deaminase comprises an amino acid sequence modified by one or more mutations at one or more positions selected from E396X, C451X, V351X, R455X, T375X, K376X, S486X, Q488X, R510X, K594X, R348X, G593X, S397X, H443X, L444X, Y445X, F442X, E438X, T448X, A353X, V355X, T339X, P539X, V525X and I520X, wherein X is selected from arginine (R), lysine (K), asparagine (N), glutamine (Q), serine (S), threonine (T), proline (P), cysteine (C), aspartate (D), glutamate (E), histidine (H), glycine (G), alanine (A), leucine (L),
  • a substituted amino acid residue is any naturally-occurring amino acid, such as a hydrophilic, hydrophobic, or non-classical amino acid.
  • the hydrophilic amino acid can be selected from a polar and positively charged hydrophilic amino acid, a polar and neutral of charge hydrophilic amino acid, and polar and negatively charged hydrophilic amino acid, and an aromatic, polar and positively charged hydrophilic amino acid.
  • a polar and positively charged hydrophilic amino acid can be selected from arginine (R) and lysine (K).
  • a polar and neutral of charge hydrophilic amino acid can be selected from asparagine (N), glutamine (Q), serine (S), threonine (T), proline (P), and cysteine (C).
  • a polar and negatively charged hydrophilic amino acid can be selected from aspartate (D) and glutamate (E).
  • An aromatic, polar and positively charged hydrophilic amino acid can be histidine (H).
  • a hydrophobic amino acid can be selected from a hydrophobic, aliphatic amino acid and a hydrophobic, aromatic amino acid.
  • the hydrophobic, aliphatic amino acid can be glycine (G), alanine (A), leucine (L), isoleucine (I), methionine (M), or valine (V).
  • a hydrophobic, aromatic amino acid can be phenylalanine (F), tryptophan (W), or tyrosine (Y).
  • a non-classical amino acid can be selected from selenocysteine, pyrrolysine, N- formylmethionine ⁇ -alanine, GABA, ⁇ -Aminolevulinic acid, 4-Aminobenzoic acid (PABA), D-isomers of the Attorney Docket No.: 33791/41005 common amino acids, 2,4-diaminobutyric acid, ⁇ -amino isobutyric acid, 4-aminobutyric acid, Abu, 2-amino butyric acid, ⁇ -Abu, ⁇ -Ahx, 6-amino hexanoic acid, Aib, 2-amino isobutyric acid, 3-amino propionic acid, ornithine, norleucine, norvaline, hydroxyproline, sarcosme, citrulline,
  • an adenosine deaminase induces a cytidine (C) to uridine (U) nucleotide change.
  • the adenosine deaminase of the present disclosure is adenosine deaminase, RNA specific 2 (ADAR2).
  • the ADAR2 deaminase can comprise a fragment that comprises a catalytic domain, wherein the catalytic domain is the deaminase domain of human ADAR2 (SEQ ID NO: 18), shown below: LHLDQTPSRQPIPSEGLQLHLPQVLADAVSRLVLGKFGDLTDNFSSPHA RRKVLAGVVMTTGTDVKDAKVISVSTGTKCINGEYMSDRGLALNDCHAE IISRRSLLRFLYTQLELYLNNKDDQKRSIFQKSERGGFRLKENVQFHLY ISTSPCGDARIFSPHEPILEEPADRHPNRKARGQLRTKIESGEGTIPVR SNASIQTWDGVLQGERLLTMSCSDKIARWNVVGIQGSLLSIFVEPIYFS SIILGSLYHGDHLSRAMYQRISNIEDLPPLYTLNKPLLSGISNAEARQP GKAPNFSVNWTVGDSAIEVINATTGKDELGRASRLCKHALYCRWMRVHG KVP
  • the ADAR2 fragment comprises a catalytic domain and one or more mutations.
  • the fragment or variant of ADAR2 can comprise an amino acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity with the amino acid sequence of SEQ ID NO: 18.
  • the catalytic domain is the deaminase domain of human ADAR2 comprising an amino acid sequence having at least 90% sequence identity with the amino acid sequence of SEQ ID NO: 18.
  • the ADAR2 comprises the amino acid sequence of SEQ ID NO: 18.
  • the ADAR2 comprises an amino acid sequence comprising a mutation of V351G with respect to SEQ ID NO: 18.
  • the V351G mutation allows the ADAR2 to induce a cytidine (C) to uridine (U) nucleotide change.
  • the fragment or Attorney Docket No.: 33791/41005 variant of ADAR2 comprises an amino acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity with the amino acid sequence of SEQ ID NO: 19, as shown below: LHLDQTPSRQPIPSEGLQLHLPQVLADAVSRLVLGKFGDLTDNFSSPHA RRKGLAGVVMTTGTDVKDAKVISVSTGTKCINGEYMSDRGLALNDCHAE IISRRSLLRFLYTQLELYLNNKDDQKRSIFQKSERGGFRLKENVQFHLY ISTSPCGDARIFSPHEPILEEPADRHPNRKARGQLRTKIESGEGTIPVR SNASIQTWDGVLQGERLLTMSCSDKIARWNVVGIQGSLLSIFVEPIYFS SIILGSLYHGDHLSRAMYQRISNIEDLPPLYTLNKPL
  • the catalytic domain is a variant deaminase domain of human ADAR2 comprising an amino acid sequence having at least 90% sequence identity with the amino acid sequence of SEQ ID NO: 19.
  • the ADAR2 comprises the amino acid sequence of SEQ ID NO: 19.
  • the ADAR2 comprising the amino acid sequence of SEQ ID NO: 19 induces a cytidine (C) to uridine (U) nucleotide change.
  • the ADAR2 comprises an amino acid sequence comprising an addition of amino acid residues LV with respect to SEQ ID NO: 18.
  • the fragment or variant of ADAR2 comprises an amino acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity with the amino acid sequence of SEQ ID NO: 38, as shown below: LHLDQTPSRQPIPSEGLQLHLPQVLADAVSRLVLGKFGDLTDNFSSPHA RRKVLAGVVMTTGTDVKDAKVISVSTGTKCINGEYMSDRGLALNDCHAE IISRRSLLRFLYTQLELYLNNKDDQKRSIFQKSERGGFRLKENVQFHLY ISTSPCGDARIFSPHEPILEEPADRHPNRKARGQLRTKIESGEGTIPVR SNASIQTWDGVLQGERLLTMSCSDKIARWNVVGIQGSLLSIFVEPIYFS SIILGSLYHGDHLSRAMYQRISNIEDLPPLYTLNKPLLSGISNAEARQP GKAP
  • the catalytic domain is a variant deaminase domain of human ADAR2 comprising an amino acid sequence having at least 90% sequence identity with the amino acid sequence of SEQ ID NO: 38.
  • the ADAR2 comprises the amino acid sequence of SEQ ID NO: 38.
  • the ADAR induces a cytidine (C) to uridine (U) nucleotide mutation.
  • the ADAR comprises one or more mutations that allow it to induce the C to U nucleotide mutation.
  • the ADAR mutation is selected from a substitution at one or more positions E396, C451, V351, R455, T375, K376, S486, Q488, R510, K594, R348, G593, S397, H443, L444, Y445, F442, E438, T448, A353, V355, T339, P539, V525 and I520 relative to SEQ ID NO: 18 or SEQ ID NO: 19.
  • the nucleic acid-editing domain is an RNA-editing domain. In some embodiments, the nucleic acid-editing domain is a deaminase domain.
  • the deaminase is a cytidine deaminase.
  • the deaminase is an apolipoprotein B niRNA- editing complex (APOBEC) family deaminase.
  • APOBEC apolipoprotein B niRNA- editing complex
  • the cytidine deaminase can be selected from APOBEC1, activation-induced cytidine deaminase (AID), APOBEC2, APOBEC3A, APOBEC3B, APOBEC3C, APOBEC3D, APOBEC3E, APOBEC3F, APOBEC3G, and APOBEC3H, or fragments or variants thereof.
  • the deaminase is an APOBEC 1 family deaminase. In some embodiments, the deaminase is pmCDA1, or fragments or variants thereof. In some embodiments, the deaminase is an ACF1/ASE deaminase, or fragments or variants thereof. In some embodiments, the deaminase is an activation-induced cytidine deaminase (AID), or fragments or variants thereof. In various embodiments, cytidine deaminase of the present disclosure is a fragment comprising the catalytic domain of the cytidine deaminase. In further embodiments, the fragment comprises a catalytic domain and one or more mutations.
  • the fragment or variant of the cytidine deaminase can comprise an amino acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the cytidine deaminase amino acid sequences provided herein.
  • the fragment is the catalytic domain of the cytidine deaminase.
  • the cytidine deaminase comprises any isoform thereof, such as those known in the art.
  • the adenosine or cytidine deaminase is a fragment comprising the catalytic domain of the adenosine or cytidine deaminase.
  • the fragment comprises a catalytic domain and one or more mutations.
  • deaminase enzyme or deaminase domain amino acid sequences of the present disclosure are variants having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the amino acid sequences provided herein.
  • the adenosine deaminase is ADAR2, or fragments or variants thereof. Additional suitable deaminase enzymes or domains will be apparent to the skilled artisan based on this disclosure.
  • the present compositions comprise a nucleic acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the nucleic acid sequences SEQ ID NOs: 39, 41, 43, 45-52, provided in Table 4, or a codon-optimized version thereof.
  • the present compositions comprise a nucleic acid, or a codon- optimized version thereof, encoding a protein having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the amino acid sequences SEQ ID NOs: 40, 42, 44, provided in Table 4.
  • the present compositions comprise an amino acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the amino acid sequences SEQ ID NOs: 40, 42, 44, provided in Table 4.
  • the present compositions comprise a nucleic acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the nucleic acid sequences SEQ ID NOs: 98, 100, 102, 104, 106, or 108, provided in Table 8, or a codon-optimized version thereof.
  • the present compositions comprise a nucleic acid, or a codon- optimized version thereof, encoding a protein having at least 70%, at least 75%, at least 80%, at least 85%, Attorney Docket No.: 33791/41005 at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the amino acid sequences SEQ ID NOs: 99, 101, 103, 105, or 107 provided in Table 8.
  • the present compositions comprise an amino acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the amino acid sequences SEQ ID NOs: 99, 101, 103, 105, or 107 provided in Table 8.
  • the present compositions comprise a nucleic acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the nucleic acid sequences SEQ ID NOs: 98, 100, 102, 104, 106, or 108, provided in Table 8, or a codon-optimized version thereof.
  • the present compositions comprise a nucleic acid, or a codon- optimized version thereof, encoding a protein having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the amino acid sequences SEQ ID NOs: 99, 101, 103, 105, 107, or 109 provided in Table 8.
  • the present compositions comprise an amino acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the amino acid sequences SEQ ID NOs: 99, 101, 103, 105, 107, or 109 provided in Table 8.
  • the present compositions comprise a nucleic acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the nucleic acid sequences SEQ ID NOs: 81, 83, 85, 87, 89, 91, provided in Table 12, or a codon-optimized version thereof.
  • the present compositions comprise a nucleic acid, or a codon- optimized version thereof, encoding a protein having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the amino acid sequences SEQ ID NOs: 82, 84, 86, 88, 90, or 92, provided in Table 12.
  • the present compositions comprise an amino acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least Attorney Docket No.: 33791/41005 97%, at least 98%, or at least 99% similarity to the amino acid sequences SEQ ID NOs: 82, 84, 86, 88, 90, or 92, provided in Table 12.
  • B. ⁇ Bacteriophage N-Peptide contemplates a N-peptide linked to a deaminase domain, or variant thereof.
  • the N-peptide comprises a helical structure.
  • the helical peptide is a ⁇ lambdoid bacteriophage N-peptide.
  • the present disclosure contemplates at least 2, at least 3, at least 4, at least 5, at least 6, or at least 7 N-peptides linked to a deaminase domain.
  • the mutant ⁇ N-peptide of the present disclosure is derived from the ⁇ lambdoid bacteriophage N protein.
  • the lambdoid bacteriophage N proteins comprise arginine-rich motifs (ARMs) necessary for transcription antitermination that can bind to and/or interact with hairpin sequences.
  • an arginine-rich motif can bind to and/or interact with a RNA hairpin sequence (e.g., boxB RNA hairpin) with a characteristic induced ⁇ -induced helical structure.
  • a RNA hairpin sequence e.g., boxB RNA hairpin
  • variants and/or mutant lambdoid bacteriophage N-peptides e.g., mutant ⁇ N-peptide
  • the ⁇ N-peptide is the wild-type amino-terminal domain ⁇ N-peptide and comprises the amino acid sequence of SEQ ID NO: 1: M DAQTRRRERR AEKQAQWK (SEQ ID NO: 1).
  • a ⁇ N-peptide, and/or mutants thereof comprises an arginine-rich motif (ARM).
  • an amino-terminal domain ⁇ N-peptide of the present disclosure comprises an Alanine (Ala) at position 3 (respective of wild-type ⁇ N-peptide of SEQ ID NO: 1) and an Arginine (Arg) at each of positions 6, 10, and 11 (respective of wild-type ⁇ N-peptide of SEQ ID NO: 1).
  • the amino-terminal domain ⁇ N-peptide is a mutant of the wild-type amino-terminal domain ⁇ N-peptide and comprises at least one mutation as compared to the wild-type amino-terminal domain ⁇ N- peptide. Such a mutation can be selected from one or more of an amino acid substitution, amino acid deletion, and amino acid addition.
  • a mutant amino-terminal domain ⁇ N-peptide can comprise from 1 to 19 amino acid residue substitutions, as compared to the wild-type ⁇ N-peptide (SEQ ID NO: 1).
  • the mutant amino-terminal domain ⁇ N-peptide comprises at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, or at least 19 amino acid residue substitutions, as compared to the wild-type amino-terminal domain ⁇ N-peptide (SEQ ID NO: 1).
  • an amino acid substitution of the mutant amino-terminal domain ⁇ N-peptide takes place at one or more of amino acid residue positions 1 to 19, relative to the wild-type amino-terminal domain ⁇ N- peptide (SEQ ID NO: 1).
  • the mutant amino-terminal domain ⁇ N-peptide comprises an amino acid substitution that takes place at one or more of amino acid residue positions 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or 19, as compared to the wild-type amino-terminal domain ⁇ N- peptide (SEQ ID NO: 1).
  • a mutant amino-terminal domain ⁇ N-peptide of the present disclosure comprises the amino acid sequence of any one of SEQ ID NO: 2 to SEQ ID NO: 9.
  • the mutant amino-terminal domain ⁇ N-peptide of the present disclosure can comprise the amino acid sequence of M NAQTRRRERR AEKQAQWK (SEQ ID NO: 2), M NAKTRRRERR AEKQAQWK (SEQ ID NO: 3), M NARTRRRERR AEKQAQWK (SEQ ID NO: 4), G NAKTRRRERR AEKQAQWK (SEQ ID NO: 5), G NARTRRRERR AEKQAQWK (SEQ ID NO: 6), M NAQTRRRLRR AEKQAQWK (SEQ ID NO: 7), M DAQTRARERR AEKQAQWK (SEQ ID NO: 8), or M DAQTRRRERK AEKQAQWK (SEQ ID NO: 9).
  • one or more amino acids of SEQ ID NO: 1 is substituted with a naturally occurring amino acid, such as a hydrophilic amino acid (e.g. a polar and positively charged hydrophilic amino acid, such as arginine (R) or lysine (K); a polar and neutral of charge hydrophilic amino acid, such as asparagine (N), glutamine (Q), serine (S), threonine (T), proline (P), and cysteine (C), a polar and negatively charged hydrophilic amino acid, such as aspartate (D) or glutamate (E), or an aromatic, polar and positively charged hydrophilic amino acid, such as histidine (H)) or a hydrophobic amino acid (e.g.
  • a hydrophilic amino acid e.g. a polar and positively charged hydrophilic amino acid, such as arginine (R) or lysine (K)
  • a polar and neutral of charge hydrophilic amino acid such as asparagine (N), glut
  • a hydrophobic, aliphatic amino acid such as glycine (G), alanine (A), leucine (L), isoleucine (I), methionine (M), or valine (V)
  • a hydrophobic, aromatic amino acid such as phenylalanine (F), tryptophan (W), or tyrosine (Y) or a non-classical amino acid (e.g.
  • the amino-terminal domain ⁇ N-peptide is a mutant of the wild-type amino-terminal domain ⁇ N-peptide and comprises at least one mutation as compared to the wild-type amino-terminal domain ⁇ N-peptide (SEQ ID NO: 1).
  • the at least one mutation to SEQ ID NO: 1 comprises an amino acid substitution selected from any one of the following amino acid substitutions: Met1Ala; Met1Cys; Met1Asp; Met1Glu; Met1Phe; Met1Gly; Met1His; Met1Ile; Met1Lys; Met1Leu; ; Met1Asn; Met1Pro; Met1Gln; Met1Arg; Met1Ser; Met1Thr; Met1Val; Met1Trp; Met1Tyr; Asp2Ala; Asp2Cys; ; Asp2Glu; Asp2Phe; Asp2Gly; Asp2His; Asp2Ile; Asp2Lys; Asp2Leu; Asp2Met; Asp2Asn; Asp2Pro; Asp2Gln; Asp2Arg; Asp2Ser; Asp2Thr; Asp2Val; Asp2Trp; Asp2Tyr; ; Ala3C
  • the amino acid substitution is selected from any one of the amino acid substitutions listed in Table 1.
  • the mutant ⁇ N-peptide sequence comprises an amino acid substitution selected from Table 1, with respect to SEQ ID NO: 1.
  • the mutant ⁇ N- peptide sequence comprises 1, or 2, or 3, or 4, or 5, or 6, or 7, or 8, or 9, or 10, or 11, or 12, or 13, or 14, or 15, or 16, or 17, or 18, or 19 amino acid substitutions selected from Table 1, with respect to SEQ ID NO: 1.
  • the mutant ⁇ N-peptide sequence comprises 1-9, or 1-8, or 1-7, or 1-6, or 1-5, or 1-4, or 1-3, or 1-2 amino acid substitutions selected from Table 1, with respect to SEQ ID NO: 1.
  • Table 1 1-9, or 1-8, or 1-7, or 1-6, or 1-5, or 1-4, or 1-3, or 1-2 amino acid substitutions selected from Table 1, with respect to SEQ ID NO: 1.
  • such mutations increase the binding affinity of the mutant ⁇ N-peptide to its respective hairpin RNA oligonucleotide, as compared to the binding affinity of the wild-type ⁇ N- peptide to its respective hairpin RNA oligonucleotide.
  • the binding affinity of the inventive contemplated mutant ⁇ N-peptide for its hairpin RNA oligonucleotide is greater than the affinity of the wild-type ⁇ N-peptide for its hairpin RNA oligonucleotide (e.g., wild-type ⁇ BoxB hairpin RNA oligonucleotide).
  • mutant ⁇ bacteriophage amino-terminal domain N-peptides having binding affinities for respective hairpin oligonucleotides that are greater than the wild-type ⁇ bacteriophage N-peptide binding affinities for respective hairpin oligonucleotides by at least 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10- fold, 15-fold, 20-fold, 25-fold, 30-fold, 35-fold, 40-fold, 45-fold, 50-fold, or 100-fold.
  • the present disclosure contemplates a N-peptide linked to a deaminase domain, or variant thereof.
  • the N-peptide comprises a helical structure.
  • the helical peptide is a lambdoid bacteriophage N-peptide.
  • the present disclosure contemplates at least 2, at least 3, at least 4, at least 5, at least 6, or at least 7 N- peptides linked to a deaminase domain.
  • the lambdoid bacteriophage N-peptide of the present disclosure is derived from the P22 or lambdoid bacteriophage.
  • the lambdoid bacteriophage N- peptide of the present disclosure is not the wild-type ⁇ N-peptide (SEQ ID NO: 1).
  • the lambdoid bacteriophages comprise arginine-rich motifs (ARMs) necessary for transcription antitermination that can bind to and/or interact with hairpin oligonucleotides.
  • an arginine-rich motif can bind to and/or Attorney Docket No.: 33791/41005 interact with a hairpin RNA oligonucleotide (e.g., BoxB hairpin RNA oligonucleotide) with a characteristic induced ⁇ -induced helical structure.
  • a hairpin RNA oligonucleotide e.g., BoxB hairpin RNA oligonucleotide
  • variants and/or mutant lambdoid bacteriophage N-peptides can exhibit enhanced binding affinity properties for their respective hairpins compared to the wild-type phage N-peptides.
  • the lambdoid bacteriophage N-peptide is the wild-type amino-terminal domain P22 N-peptide and comprises the amino acid sequence of SEQ ID NO: 53: FAG NAKTRRHERR RKLAIERD (SEQ ID NO: 53).
  • a P22 N-peptide, and/or variants thereof comprises an arginine-rich motif (ARM).
  • an amino-terminal domain P22 N-peptide of the present disclosure comprises an Alanine (Ala) at position 5 (respective of wild-type P22 N-peptide of SEQ ID NO: 53) and an Arginine (Arg) at each of positions 8,12, and 13 (respective of wild-type P22 N-peptide of SEQ ID NO: 53).
  • the amino-terminal domain P22 N-peptide is a variant of the wild-type amino- terminal domain P22 N-peptide and comprises at least one mutation as compared to the wild-type amino- terminal domain P22 N-peptide. Such a mutation can be selected from one or more of an amino acid substitution, amino acid deletion, and amino acid addition.
  • a variant amino-terminal domain P22 N-peptide can comprise from 1 to 21 amino acid residue substitutions, as compared to the wild-type P22 N-peptide (SEQ ID NO: 53).
  • the variant amino-terminal domain P22 N-peptide comprises at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 amino acid residue substitutions, as compared to the wild-type amino- terminal domain P22 N-peptide (SEQ ID NO: 53).
  • an amino acid substitution of the variant amino-terminal domain P22 N-peptide takes place at one or more of amino acid residue positions 1 to 21, relative to the wild-type amino-terminal domain P22 N-peptide (SEQ ID NO: 53).
  • the variant amino-terminal domain P22 N-peptide comprises an amino acid substitution that takes place at one or more of amino acid residue positions 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21, as compared to the wild-type amino-terminal domain P22 N-peptide (SEQ ID NO: 53).
  • an amino-terminal domain P22 N-peptide variant of the present disclosure comprises the amino acid sequence of any one of SEQ ID NO: 54 to SEQ ID NO: 78.
  • the amino-terminal domain P22 N-peptide variant of the present disclosure can comprise the amino acid sequence of FAG Attorney Docket No.: 33791/41005 TAKTRRHERR RKLAIERD (SEQ ID NO: 54), FAG NARTRRHERR RKLAIERD (SEQ ID NO: 55), FAG NAKSRRHERR RKLAIERD (SEQ ID NO: 56), FAG NAKWRRHERR RKLAIERD (SEQ ID NO: 57), FAG NAKYRRHERR RKLAIERD (SEQ ID NO: 58), FAG NAKARRHERR RKLAIERD (SEQ ID NO: 59), FAG NAKRRRHERR RKLAIERD (SEQ ID NO: 60), FAG NAKTRRFERR RKLAIERD (SEQ ID NO: 61), FAG NAKTRRWERR RKLAIERD (SEQ ID NO: 62), FAG NAKTRRHLRR RKLAIERD (SEQ ID NO: 63), FAG NAKTRRHERR RQ
  • one or more mutations of the wild- type amino-terminal domain P22 N-peptide do not yield the wild-type amino-terminal domain ⁇ N-peptide (SEQ ID NO: 1).
  • one or more amino acids of SEQ ID NO: 53 is substituted with a naturally occurring amino acid, such as a hydrophilic amino acid (e.g.
  • a polar and positively charged hydrophilic amino acid such as arginine (R) or lysine (K); a polar and neutral of charge hydrophilic amino acid, such as asparagine (N), glutamine (Q), serine (S), threonine (T), proline (P), and cysteine (C), a polar and negatively charged hydrophilic amino acid, such as aspartate (D) or glutamate (E), or an aromatic, polar and positively charged hydrophilic amino acid, such as histidine (H)) or a hydrophobic amino acid (e.g.
  • a hydrophobic, aliphatic amino acid such as glycine (G), alanine (A), leucine (L), isoleucine (I), methionine (M), or valine (V)
  • a hydrophobic, aromatic amino acid such as phenylalanine (F), tryptophan (W), or tyrosine (Y) or a non-classical amino acid (e.g.
  • the amino-terminal domain P22 N-peptide is a variant of the wild-type amino-terminal domain P22 N-peptide and comprises at least one mutation as compared to the wild-type amino-terminal domain P22 N-peptide (SEQ ID NO: 53).
  • the at least one mutation to SEQ ID NO: 53 comprises an amino acid substitution selected from any one of the following amino acid substitutions: Phe1Ala; Phe1Cys; Phe1Asp; Phe1Glu; Phe1Phe; Phe1Gly; Phe1His; Phe1Ile; Phe1Lys; Phe1Leu; Phe1Met; Phe1Asn; Phe1Pro; Phe1Gln; Phe1Arg; Phe1Ser; Phe1Thr; Phe1Val; Phe1Trp; Phe1Tyr; Ala2Ala; Ala2Cys; Ala2Asp; Ala2Glu; Ala2Phe; Ala2Gly; Ala2His; Ala2Ile; Ala2Lys; Ala2Leu; Ala2Met; Ala2Asn; Ala2Pro; Ala2Gln; Ala2Arg; Ala2Ser; Ala2
  • the amino acid substitution is selected from any one of the amino acid substitutions listed in Table 2.
  • the P22 N-peptide sequence comprises an amino acid substitution selected from Table 2, with respect to SEQ ID NO: 53.
  • the P22 N-peptide sequence comprises 1, or 2, or 3, or 4, or 5, or 6, or 7, or 8, or 9, or 10, or 11, or 12, or 13, or 14, or 15, or 16, or 17, or 18, or 19, or 20, or 21 amino acid substitutions selected from Table 2, with respect to SEQ ID NO: 53.
  • the P22 N-peptide sequence comprises 1-20, or 1-10, or 1-5, or 1-4, or 1-3, or 1-2 amino acid substitutions selected from Table 2, with respect to SEQ ID NO: 53. Table 2.
  • the affinity of any one of the inventive contemplated P22 N-peptide variants for their hairpin RNA oligonucleotide is greater than the affinity of the wild-type P22 N-peptide for its hairpin RNA oligonucleotide (e.g., wild-type P22 BoxB hairpin RNA oligonucleotide).
  • the present disclosure contemplates variant bacteriophage amino-terminal domain N-peptides having binding affinities for respective hairpin oligonucleotides that are greater than the wild-type bacteriophage N-peptide binding affinities for respective hairpin oligonucleotides by at least 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 15-fold, 20-fold, 25-fold, 30-fold, 35-fold, 40-fold, 45-fold, 50-fold, or 100-fold.
  • the lambdoid bacteriophage N-peptide of the present disclosure is derived from the P21 (a.k.a.
  • the lambdoid bacteriophage N-peptide of the present disclosure is not the wild-type ⁇ N-peptide (SEQ ID NO: 1).
  • the lambdoid bacteriophages comprise arginine-rich motifs (ARMs) necessary for transcription antitermination that can bind to and/or interact with hairpin oligonucleotides.
  • an arginine-rich motif can bind to Attorney Docket No.: 33791/41005 and/or interact with a hairpin RNA oligonucleotide (e.g., BoxB hairpin RNA oligonucleotide) with a characteristic induced ⁇ -induced helical structure.
  • a hairpin RNA oligonucleotide e.g., BoxB hairpin RNA oligonucleotide
  • variants and/or mutant lambdoid bacteriophage N-peptides can exhibit enhanced binding affinity properties for their respective hairpins compared to the wild-type phage N-peptides.
  • the lambdoid bacteriophage N-peptide is the wild-type amino-terminal domain P21 N-peptide and comprises the amino acid sequence of SEQ ID NO: 95: SKG TAKSRYKARR AELIAERR (SEQ ID NO: 95).
  • a P21 N-peptide, and/or variants thereof comprises an arginine-rich motif (ARM).
  • an amino-terminal domain P21 N-peptide of the present disclosure comprises an Alanine (Ala) at position 5 (respective of wild-type P21 N-peptide of SEQ ID NO: 95) and an Arginine (Arg) at each of positions 8,12, and 13 (respective of wild-type P21 N-peptide of SEQ ID NO: 95).
  • the amino-terminal domain P21 N-peptide is a variant of the wild-type amino- terminal domain P21 N-peptide and comprises at least one mutation as compared to the wild-type amino- terminal domain P21 N-peptide. Such a mutation can be selected from one or more of an amino acid substitution, amino acid deletion, and amino acid addition.
  • a variant amino-terminal domain P21 N-peptide can comprise from 1 to 21 amino acid residue substitutions, as compared to the wild-type P21 N-peptide (SEQ ID NO: 95).
  • the variant amino-terminal domain P21 N-peptide comprises at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 amino acid residue substitutions, as compared to the wild-type amino- terminal domain P21 N-peptide (SEQ ID NO: 95).
  • an amino acid substitution of the variant amino-terminal domain P21 N-peptide takes place at one or more of amino acid residue positions 1 to 21, relative to the wild-type amino-terminal domain P21 N-peptide (SEQ ID NO: 95).
  • the variant amino-terminal domain P21 N-peptide comprises an amino acid substitution that takes place at one or more of amino acid residue positions 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21, as compared to the wild-type amino-terminal domain P21 N-peptide (SEQ ID NO: 95).
  • the variant amino-terminal domain P21 N-peptide comprises one or more mutations at position R13 and/or I17, with respect to SEQ ID NO: 95.
  • the variant amino-terminal domain P21 N-peptide is not mutated at position R13 and/or I17, with respect to SEQ ID Attorney Docket No.: 33791/41005 NO: 95.
  • one or more mutations of the wild-type amino-terminal domain P21 N- peptide do not yield the wild-type amino-terminal domain ⁇ N-peptide (SEQ ID NO: 1).
  • one or more amino acids of SEQ ID NO: 95 is substituted with a naturally occurring amino acid, such as a hydrophilic amino acid (e.g.
  • a polar and positively charged hydrophilic amino acid such as arginine (R) or lysine (K); a polar and neutral of charge hydrophilic amino acid, such as asparagine (N), glutamine (Q), serine (S), threonine (T), proline (P), and cysteine (C), a polar and negatively charged hydrophilic amino acid, such as aspartate (D) or glutamate (E), or an aromatic, polar and positively charged hydrophilic amino acid, such as histidine (H)) or a hydrophobic amino acid (e.g.
  • a hydrophobic, aliphatic amino acid such as glycine (G), alanine (A), leucine (L), isoleucine (I), methionine (M), or valine (V)
  • a hydrophobic, aromatic amino acid such as phenylalanine (F), tryptophan (W), or tyrosine (Y) or a non-classical amino acid (e.g.
  • the amino-terminal domain P21 N-peptide is a variant of the wild-type amino-terminal domain P21 N-peptide and comprises at least one mutation as compared to the wild-type amino-terminal domain P21 N-peptide (SEQ ID NO: 95).
  • the at least one mutation to SEQ ID NO: 95 comprises an amino acid substitution selected from any one of the following amino acid substitutions: Ser1Ala; Ser1Cys; Ser1Asp; Ser1Glu; Ser1Phe; Ser1Gly; Ser1His; Ser1Ile; Ser1Lys; Ser1Leu; Ser1Met; Ser1Asn; Ser1Pro; Ser1Gln; Ser1Arg; Ser1Thr; Ser1Val; Ser1Trp; Ser1Tyr; Lys2Ala; Lys2Cys; Lys2Asp; Lys2Glu; Lys2Phe; Lys2Gly; Lys2His; Lys2Ile; Lys2Leu; Lys2Met; Lys2Asn; Lys2Pro; Lys2Gln; Lys2Arg; Lys2Ser; Lys2Thr; Lys2Val; Lys2Trp; Lys2Tyr; Gly3Ala; Gly3Cy
  • the amino acid substitution is selected from any one of the amino acid substitutions listed in Table 3.
  • the P21 N-peptide sequence comprises an amino acid substitution selected from Table 3, with respect to SEQ ID NO: 95.
  • the P21 N-peptide sequence comprises 1, or 2, or 3, or 4, or 5, or 6, or 7, or 8, or 9, or 10, or 11, or 12, or 13, or 14, or 15, or 16, or 17, or 18, or 19, or 20, or 21 amino acid substitutions selected from Table 3, with respect to SEQ ID NO: 95.
  • the P21 N-peptide sequence comprises 1-20, or 1-10, or 1-5, or 1-4, or 1-3, or 1-2 amino acid substitutions selected from Table 3, with respect to SEQ ID NO: 95. Table 3.
  • the affinity of any one of the inventive contemplated P21 N-peptide variants for their hairpin RNA oligonucleotides is greater than the affinity of the wild-type P21 N-peptide for its hairpin RNA oligonucleotide (e.g., wild-type P21 BoxB hairpin RNA oligonucleotide).
  • the present disclosure provides v ariant bacteriophage amino-terminal domain N-peptides having binding affinities for respective hairpin oligonucleotides that are greater than the wild-type bacteriophage N-peptide binding affinities for respective hairpin oligonucleotides by at least 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10- fold, 15-fold, 20-fold, 25-fold, 30-fold, 35-fold, 40-fold, 45-fold, 50-fold, or 100-fold.
  • a high affinity interaction between the variant N- peptides described herein and the respective hairpin oligonucleotide allows for low dose uses of the present agents. Further, without wishing to be bound by theory, such high affinity interaction allows for reduced frequency of dosing and reduced off-target effects. Stated another way the tight interaction between the present mutant ⁇ N-peptides and respective hairpin oligonucleotides favors the occurrence of the beneficial interaction which drives editing and disfavors interactions that do not support, or even hinder, a therapeutic effect. [0080] Methods of assaying binding affinity are known in the art.
  • Non-limiting examples include optical assays, such as monitoring the change in fluorescence of a 2-aminopurine (2AP) base analogue substituted at different adenine positions within the target hairpin in order to measure kinetics; chemical assays, such as gel electrophoresis, ELISA, and immunoblots; and other methods studying RNA-protein interactions, such as electrophoretic mobility shift assay (EMSA), systematic evolution of ligands by exponential enrichment (SELEX), RNA pull-down assay, RNA footprinting, RNA immunoprecipitation (RIP), UV-induced crosslinking immunoprecipitation (CLIP). Pollard, Mol Biol Cell. (2010) 21(23): 4061-4067 and Popova et al. Mol. Biol.
  • ESA electrophoretic mobility shift assay
  • SELEX systematic evolution of ligands by exponential enrichment
  • RIP RNA pull-down assay
  • CLIP UV-induced crosslinking immunoprecipitation
  • the target RNA sequence comprises a sequence associated with a disease, condition or disorder, and wherein the deamination of the nucleotide base results in an RNA sequence that is not associated with a disease, condition or disorder.
  • the target RNA sequence Attorney Docket No.: 33791/41005 comprises a wild-type sequence, wherein the deamination of a particular nucleotide base therein results in a mutation that induces a beneficial and/or therapeutic effect.
  • methods of the present disclosure further contemplate an antisense RNA oligonucleotide that hybridizes with a wild-type or mutant target sequence in an endogenous RNA molecule that comprises a target nucleotide to be edited.
  • the target nucleotide to be edited eliminates a detrimental mutation in the mutant target sequence.
  • the target nucleotide can be a genetic mutation associated with a genetic disease, condition or disorder.
  • a genetic mutation of the target nucleotide may cause a premature termination codon (PTC) or an in-frame stop codon.
  • the genetic disorder or condition is caused by a substitution of C from U nucleotides so that C-to-U editing would correct the mutation.
  • the present disclosure contemplates a nucleic acid-editing system that can edit any target nucleotide and/or genetic mutation (e.g., by facilitating splice modulation).
  • the target RNA sequence relates to a target gene of interest.
  • the target gene of interest can include, but is not limited to, Human SerpinA1 E342K gene (NM_000295.4) and human IDUA gene (NM_000203.5) that contains the W402X mutation.
  • the antisense RNA oligonucleotide hybridizes with an RNA molecule comprising the target nucleotide in endogenous RNA of the cell. In some embodiments, the antisense RNA oligonucleotide has perfect base-pairing complementarity with the RNA molecule comprising the target nucleotide. In various embodiments, the antisense RNA oligonucleotide comprises one or more mismatches with the RNA molecule comprising the target nucleotide.
  • the antisense RNA oligonucleotide sequence can comprise from 1 to 15 mismatches, e.g., about 1, or about 2, or about 3, or about 4, or about 5, or about 6, or about 7, or about 8, or about 9, or about 10, or about 11, or about 12, or about 13, or about 14, or about 15 mismatches.
  • a mismatch is a non-complementary match hybridization between the antisense RNA oligonucleotide and the RNA molecule comprising the target nucleotide.
  • the present disclosure further contemplates an antisense RNA oligonucleotide that hybridizes with a wild-type target sequence in an endogenous RNA molecule that comprises a target nucleotide to be edited.
  • the target nucleotide to be edited induces a beneficial mutation in the wild-type target sequence.
  • an antisense RNA oligonucleotide hybridizes with a target sequence comprising a target nucleotide to be edited under stringent conditions.
  • the present disclosure contemplates methods of editing RNA in any cell type of a subject.
  • the cell containing RNA to be edited can be a cell of the central nervous system (e.g., neurons) or a liver cell.
  • the cells to be edited are in a subject so that the methods of the present disclosure are in vivo methods of editing.
  • cells may be edited in vitro and subsequently delivered to a subject as ex vivo treatment.
  • hairpin refers to a particular oligonucleotide and/or nucleic acid structure (e.g., RNA oligonucleotide and/or RNA structure) that is recognized by and interacts with a lambdoid bacteriophage N-peptide (e.g., amino-terminal domain N-peptide derived from ⁇ N protein; amino-terminal domain N-peptide derived from P21; or amino-terminal domain N-peptide derived from P22) or other helical peptide.
  • a lambdoid bacteriophage N-peptide e.g., amino-terminal domain N-peptide derived from ⁇ N protein; amino-terminal domain N-peptide derived from P21; or amino-terminal domain N-peptide derived from P22
  • a lambdoid bacteriophage N-peptide e.g., amino-terminal domain N-peptide derived from ⁇ N protein; amino-terminal domain N-peptide derived from P21
  • a particular example of such a hairpin is a BoxB hairpin RNA oligonucleotide that is the cognate hairpin of the lamboid bacteriophage N-peptide, or mutant thereof.
  • the lamboid bacteriophage N-peptide, or mutant thereof interacts with a hairpin RNA (e.g., there is hairpin recognition of the lamboid bacteriophage N-peptide) oligonucleotide.
  • the hairpin RNA oligonucleotide is the cognate hairpin of the lamboid bacteriophage N-peptide.
  • the cognate hairpin can be a boxB hairpin RNA oligonucleotide.
  • the boxB hairpin RNA oligonucleotide is located from about 2-20 nucleotide residues 5’ of the target mutation.
  • the boxB hairpin RNA oligonucleotide is located from about 2-20 nucleotide residues 3’ of the target mutation.
  • the antisense RNA oligonucleotide of the present disclosure (described herein) is linked to one or more hairpin RNA oligonucleotides.
  • the antisense RNA oligonucleotide is linked to 1, 2, 3, or 4 hairpin RNA oligonucleotides. In some embodiments, the antisense RNA oligonucleotide is linked to at least 2, at least 3, or at least 4 hairpin RNA oligonucleotides.
  • a BoxB hairpin RNA oligonucleotide of the present disclosure comprises a nucleic acid sequence of SEQ ID NO: 10 or SEQ ID NO: 11, or mutants thereof.
  • a BoxB hairpin RNA oligonucleotide can comprise a nucleic acid sequence selected from the wild-type ⁇ BoxB hairpin RNA oligonucleotide (e.g., nutR ⁇ BoxB hairpin RNA oligonucleotide), right: GCCCUGAAAAAGGGC (SEQ ID NO: 10), and the wild-type ⁇ BoxB hairpin RNA oligonucleotide (e.g., nutL ⁇ BoxB hairpin RNA oligonucleotide), left:GCCCUGAAGAAGGGC (SEQ ID NO: 11).
  • wild-type ⁇ BoxB hairpin RNA oligonucleotide e.g., nutR ⁇ BoxB hairpin RNA oligonucleotide
  • wild-type ⁇ BoxB hairpin RNA oligonucleotide e.g., nutL ⁇ BoxB
  • the ⁇ N-peptide, or mutant thereof interacts with a ⁇ BoxB hairpin RNA oligonucleotide comprising the nucleotide sequence of SEQ ID NO: 10 or SEQ ID NO: 11, or mutant thereof.
  • the ⁇ N-peptide, or mutant thereof interacts with a mutant ⁇ BoxB hairpin RNA oligonucleotide comprising a nucleotide sequence of any one of SEQ ID NOs: 12-17.
  • the ⁇ N-peptide, or mutant thereof, and ⁇ BoxB hairpin RNA oligonucleotide, or mutant thereof interaction adopts a 4-out GNRA-like pentaloop.
  • a tetraloop is a type of four-base hairpin loop motif in RNA secondary structures that cap many double helices.
  • the N could be either uracil, adenine, cytosine, or guanine
  • the R is either guanine or adenine.
  • the GNRA tetraloop specifically, has a guanine-adenine base pair, where the guanine is 5’ to the helix and the adenine is 3’ to the helix.
  • a hairpin oligonucleotide of the present disclosure comprises at least one mutation selected from missense mutation, nonsense mutation, insertion, deletion, duplication, frameshift mutation, and repeat expansion.
  • such mutations can be made with respect to a hairpin oligonucleotide comprising one or more of SEQ ID NO: 10 or SEQ ID NO: 11.
  • the ⁇ BoxB hairpin RNA oligonucleotide comprises a nucleic acid sequence having sequence identity to SEQ ID NO: 10 or SEQ ID NO: 11, and further comprises from 1 to 15 nucleotide mutations selected from one or more of nucleotide substitutions, nucleotide deletions, and nucleotide additions.
  • a mutant ⁇ BoxB hairpin RNA oligonucleotide comprises a nucleotide sequence of any one of SEQ ID NOs: 12-17: SEQ ID NO: 12:GCCCUAAAAAAGGGC ( ⁇ boxBR:G6A); SEQ ID NO: 13:GCCCUGAUAAAGGGC ( ⁇ boxBR:A8U); SEQ ID NO: 14:GCCCGGAAAACGGGC ( ⁇ boxBR:U5G,A11C); Attorney Docket No.: 33791/41005 SEQ ID NO: 15:GCCCUGAACAAGGGC ( ⁇ boxBR:A9C); SEQ ID NO: 16:GCCCUGAAACAGGGC ( ⁇ boxBR:A10C); and SEQ ID NO: 17:GCCCUGAAAAGGGGC
  • a BoxB hairpin RNA oligonucleotide of the present disclosure comprises a nucleic acid sequence of any one of SEQ ID NOs: 79-80, or variants thereof.
  • a BoxB hairpin RNA oligonucleotide comprises a nucleic acid sequence selected from the wild-type P22 BoxB RNA hairpin, right:ACCGCCGACAACGCGGU (SEQ ID NO: 79); the wild-type P22 BoxB RNA hairpin, left:UGCGCUGACAAAGCGCG (SEQ ID NO: 80).
  • the P22 N-peptide, or variant thereof interacts with a P22 BoxB hairpin RNA oligonucleotide comprising the nucleic acid sequence of SEQ ID NO: 79 or SEQ ID NO: 80, or variant thereof.
  • the P22 N-peptide and P22 BoxB hairpin RNA oligonucleotide interaction adopts a 3-out GNRA-like pentaloop.
  • a tetraloop is a type of four-base hairpin loop motif in RNA secondary structures that cap many double helices.
  • a hairpin oligonucleotide of the present disclosure comprises at least one mutation selected from missense mutation, nonsense mutation, insertion, deletion, duplication, frameshift mutation, and repeat expansion.
  • such mutations can be made with respect to a hairpin oligonucleotide comprising one or more of nucleic acid sequences selected from SEQ ID NOs: 70-80.
  • the P22 BoxB hairpin RNA oligonucleotide comprises the nucleic acid sequence of SEQ ID NO: 70 or SEQ ID NO: 80, and further comprises from 1 to 17 nucleotide mutations selected from one or more of nucleotide substitutions, nucleotide deletions, and nucleotide additions.
  • a BoxB hairpin RNA oligonucleotide of the present disclosure comprises a nucleic acid sequence of any one of SEQ ID NOs: 96-97, or variants thereof.
  • a BoxB hairpin RNA oligonucleotide comprises a nucleic acid sequence selected from the wild-type P21 BoxB RNA hairpin, right:UUCACCUCUAACCGGGUGAG (SEQ ID NO: 96); and the wild-type P21 BoxB RNA hairpin, left:UCUCAACCUAACCGUUGAGA (SEQ ID NO: 97).
  • Attorney Docket No.: 33791/41005 [0096]
  • the P21 N-peptide, or variant thereof interacts with a P21 BoxB hairpin RNA oligonucleotide comprising the nucleic acid sequence of SEQ ID NO: 96 or SEQ ID NO: 97, or variant thereof.
  • the P21 N-peptide and P21 BoxB hairpin RNA oligonucleotide interaction adopts a non-GNRA U-turn with respect to the apical four nucleotides of the P21 BoxB hairpin RNA oligonucleotide.
  • a tetraloop is a type of four-base hairpin loop motif in RNA secondary structures that cap many double helices.
  • the N could be either uracil, adenine, cytosine, or guanine
  • the R is either guanine or adenine.
  • a hairpin oligonucleotide of the present invention comprises at least one mutation selected from missense mutation, nonsense mutation, insertion, deletion, duplication, frameshift mutation, and repeat expansion.
  • mutations can be made with respect to a hairpin oligonucleotide comprising one or more of nucleic acid sequences selected from SEQ ID NOs: 96-97.
  • the P21 BoxB hairpin RNA oligonucleotide comprises the nucleic acid sequence of SEQ ID NO: 96 or SEQ ID NO: 97, and further comprises from 1 to 20 nucleotide mutations selected from one or more of nucleotide substitutions, nucleotide deletions, and nucleotide additions.
  • the one or more nucleotide mutations take(s) place at one or more of nucleotide residue positions 1 to 20, relative to wild-type P21 BoxB hairpin RNA oligonucleotide.
  • fusion proteins comprising a deaminase, or fragment thereof, and a bacteriophage N-peptide, optionally connected by a chemical linker.
  • the deaminase, or fragment thereof can be linked to at least 2, at least 3, or at least 4 N-peptides.
  • the N-peptide can be linked to at least 2, at least 3, or at least 4 deaminases, or fragments thereof.
  • Some aspects of the disclosure provide fusion proteins that comprise one or more deaminase domains (e.g., adenosine deaminase and/or cytidine deaminase).
  • the fusion protein comprises at least two deaminase domains.
  • dimerization of deaminases may improve the ability (e.g., efficiency) of the fusion protein to edit a nucleic acid base and/or nucleotide, for example to deaminate adenosine and/or cytidine.
  • any of the fusion proteins may comprise at least 2, at least 3, at least 4 or at least 5 adenosine deaminase domains.
  • any of the fusion proteins provided herein comprise two deaminases.
  • any of the fusion proteins provided herein contain only two deaminases.
  • the deaminases are the same.
  • the deaminases are any of the deaminases provided herein.
  • the deaminases are different.
  • the first deaminase is any of the adenosine or cytidine deaminases provided herein
  • the second deaminase is any of the adenosine or cytidine deaminases provided herein, but is not identical to the first deaminase.
  • the deaminase and bacteriophage N-peptide fusion protein comprises one or more nuclear localization signals (NLS), optionally wherein the RNA molecule comprising the target nucleotide to be edited is located in the nucleus of the cell.
  • the fusion protein of the present disclosure comprises 1, 2, 3, 4, or 5 nuclear localization signals (e.g., nuclear localization sequences).
  • the nuclear localization signal is the SV40 Large T-antigen nuclear localization signal (SEQ ID NO: 21).
  • SEQ ID NO: 21 SV40 Large T-antigen nuclear localization signal
  • Nuclear localization sequences are known in the art and would be apparent to the skilled artisan. For example, NLS sequences are described in Plank et al., International PCT application, PCT/EP2000/011690, filed November 23, 2000, published as WO/2001/038547 on May 31, 2001; and in Kosugi et al., J. Biol. Chem. (2009) 284: 478-485, the contents of which are incorporated herein by reference for their disclosure of exemplary nuclear localization sequences.
  • Nuclear localization sequences can include the nuclear localization sequence of the SV40 virus large T-antigen the minimal functional unit of which is the seven amino acid sequence PKKKRKV (SEQ ID NO: 22).
  • nuclear localization sequences include the nucleoplasmin bipartite NLS with the sequence NLSKRPAAIKKAGQAKKKK (SEQ ID NO: 23); the c-myct nuclear localization sequence having the amino acid sequence PAAKRVKLD (SEQ ID NO: 24) or RQRRNELKRSF (SEQ ID NO: 25); and the hRNPAI M9 NLS having the sequence NQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGY (SEQ ID NO: 26).
  • nuclear localization sequences are: the sequence RMRKFKNKGKDTAELRRRRVEVSVELRKAKKDEQILKRRNV (SEQ ID NO: 27) of the IBB domain from importin-alpha; the sequences VSRKRPRP (SEQ ID NO: 28) and PPKKARED (SEQ ID NO: 29) of the myoma T protein; the sequence PQPKKKPL (SEQ ID NO: 30) of human p53; the sequence SALIKKKKKMAP (SEQ ID NO: 31) of mouse c-abl IV; the sequences DRLRR (SEQ ID NO: 32) and PKQKKRK (SEQ ID NO: 33) of the influenza virus NS1; the sequence RKLKKKIKKL (SEQ ID NO: 34) of Attorney Docket No.: 33791/41005 the Hepatitis virus delta antigen; and the sequence REKKKFLKRR (SEQ ID NO: 35) of the mouse Mx1 protein.
  • a NLS of the present disclosure comprises the amino acid sequence SV40 Large T-antigen NLS comprising the amino acid sequence: DPKKKRKVDPKKKRKVDPKKKRKV (SEQ ID NO: 21).
  • the NLS contemplated by the present disclosure comprises one or more mutations (e.g., amino acid substitutions, deletions, and/or insertions) with respect to any one of SEQ ID NOs: 21-37.
  • the fusion proteins provided herein further comprise one or more nuclear targeting sequences, for example, a nuclear localization signal/sequence (NLS).
  • NLS nuclear localization signal/sequence
  • a NLS comprises an amino acid sequence that facilitates the importation of a protein, that comprises an NLS, into the cell nucleus.
  • the NLS is fused to the N-terminus of the fusion protein.
  • the NLS is fused to the C-terminus of the fusion protein.
  • the NLS is fused to the N-terminus of the deaminase. In some embodiments, the NLS is fused to the C-terminus of the deaminase. In some embodiments, the NLS is fused to the N-terminus of the ⁇ N-peptide. In some embodiments, the NLS is fused to the C-terminus of the ⁇ N-peptide. In some embodiments, the NLS is fused to the fusion protein via one or more linkers. In some embodiments, the NLS is fused to the fusion protein without a linker. In some embodiments, the NLS comprises an amino acid sequence of any one of the NLS sequences provided or referenced herein.
  • the NLS comprises an amino acid sequence as set forth in SEQ ID NO: 21-37, or variants thereof. Additional nuclear localization sequences are known in the art and would be apparent to the skilled artisan. For example, NLS sequences are described in Plank et al., PCT/EP2000/011690, the contents of which are incorporated herein by reference for their disclosure of illustrative nuclear localization sequences. G.
  • components (i) a deaminase linked to a mutant ⁇ N-peptide, and (ii) an antisense RNA oligonucleotide linked to a hairpin (e.g., a BoxB hairpin RNA) oligonucleotide, of the present disclosure are contained within various delivery vehicles.
  • Attorney Docket No.: 33791/41005 [00104]
  • the components of the present disclosure are contained within a plasmid or vector.
  • components (i) and (ii) of the present disclosure are contained within a viral vector.
  • such components of the present disclosure as previously described are synthetically generated or generated from a plasmid.
  • the components are contained within a plasmid or vector, optionally wherein the vector is a viral vector.
  • viral vectors can include, but are not limited to, adeno-associated viruses (AAVs), adenoviruses, retroviruses, and lentiviruses.
  • AAV adeno-associated virus
  • the AAV can be selected from AAV1, or AAV2, or AAV3, or AAV4, or AAV5, or AAV6, or AAV7, or AAV8, or AAV9, or AAV10, or AAV11, and AAV12.
  • AAV adeno-associated virus
  • components of the present disclosure are contained within mRNA for delivery.
  • a synthetic oligonucleotide encoding the present compositions is provided.
  • the synthetic oligonucleotide can have non-canonical nucleotides that, without wishing to be bound by theory, reduce innate immune responses.
  • the synthetic oligonucleotide is an mRNA comprising one or more non-canonical nucleotides.
  • the mRNA comprises one or more non-canonical nucleotides found in U.S. Patent No.8,278,036, the entire contents of which are hereby incorporated by reference.
  • the mRNA comprises one or more of m5C, m5U, m6A, s2U, ⁇ , and 2′-O-methyl-U.
  • the components of the present disclosure are contained in lipid nanoparticles for gene delivery.
  • an excipient may be used that aids in enhancing the stability, solubility, absorption, bioavailability, activity, pharmacokinetics, pharmacodynamics and/or delivery of the components of the present disclosure to a cell and into a cell.
  • particular excipients capable of forming complexes, vesicles, nanoparticles, microparticles, nanotubes, nanogels, hydrogels, poloxamers or pluronics, polymersomes, colloids, microbubbles, vesicles, micelles, lipoplexes and/or liposomes, that deliver components complexed or trapped in the vesicles or liposomes through a cell membrane find use.
  • nanoparticles that are useful in various emobodiments include gold nanoparticles, magnetic nanoparticles, silica nanoparticles, lipid nanoparticles, sugar particles, protein nanoparticles and peptide nanoparticles.
  • polycations such like diethyl amino ethyl amino ethyl (DEAE)-dextran, which are well known as DNA transfection Attorney Docket No.: 33791/41005 reagent can be combined with butylcyanoacrylate (PBCA) and hexylcyanoacrylate (PHCA) to formulate cationic nanoparticles that can deliver said compound across cell membranes into cells), butylcyanoacrylate (PBCA), hexylcyanoacrylate (PHCA), poly(lactic-co-gly colic acid) (PLGA), polyamines (e.g.
  • PBCA butylcyanoacrylate
  • PHCA hexylcyanoacrylate
  • PLGA poly(lactic-co-gly colic acid)
  • polyamines e.g.
  • spermine spermidine, putrescine, cadaverine), chitosan, poly(amido amines) (PAMAM), poly(ester amine), polyvinyl ether, polyvinyl pyrrolidone (PVP), polyethylene glycol (PEG) cyclodextrins, hyaluronic acid, colominic acid, and derivatives thereof), dendrimers (e.g.
  • poly(amidoamine), lipids e.g.1,2-dioleoyl-3- dimethylammonium propane (DODAP), dioleoyldimethylammonium chloride (DODAC), phosphatidylcholine derivatives (e.g 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC)), lyso-phosphatidylcholine derivatives (e.g.1-stearoyl-2-lyso-sn-glycero-3-phosphocholine (S-LysoPC)), sphingomyeline, 2- ⁇ 3-[bis-(3-amino- propyl)-amino]-propylamino ⁇ -N-ditetracedyl carbamoyl methylacetamide (RPR209120), phosphoglycerol derivatives (e.g.1,2-dipalmitoyl-sn-glycero-3-phosphoglycerol, sodium salt (DPPG
  • dioleoyl-J-R-phosphatidylethanolamine DOPE
  • 1,2-distearoyl-sn-glycero-3- phosphoethanolamine DSPE
  • 2-diphytanoyl-sn-glycero-3-phosphoethanolamine DPhyPE
  • JV-[1-(2,3- dioleoyloxy)propyl]-N,N,N-trimethyl ammonium DOTAP
  • 1,3-di-oleoyloxy-2-(6-carboxy-spermyl)- propylamid DOSPER
  • DMRIE 1,2-dimyristyolxypropyl-3-dimethylhydroxy ethyl ammonium
  • DMRIE dimethyldioctadecylammonium bromide
  • CD AN dimethyldioctadecylammonium bromide
  • DDAB dimethyldioctadecylammonium bromide
  • Lipofectin is an illutrative liposomal transfection agent that finds use in various embodiments. It consists of at least two lipid components, a cationic lipid N-[1-(2,3-dioleoyloxy)propyl]-N,N,N- trimethylammonium chloride (DOTMA) (cp.
  • DOTMA cationic lipid N-[1-(2,3-dioleoyloxy)propyl]-N,N,N- trimethylammonium chloride
  • DOTAP which is the methylsulfate salt
  • DOPE neutral lipid dioleoylphosphatidylethanolamine
  • the neutral component mediates the intracellular release.
  • the cationic peptide protamine offers an alternative approach to formulate components of the present disclosure as colloids.
  • This colloidal nanoparticle system can form so called proticles, which can be prepared by a simple self-assembly process to package and mediate intracellular release of a component as defined herein.
  • the skilled person may select and adapt any of the above or other commercially available or not commercially available alternative excipients and delivery systems.
  • the components of the present disclosure are contained within the same or separate vectors, plasmids, mRNAs, and/or lipid nanoparticles, thus allowing for consecutive (e.g., before or after) or concurrent (e.g., at the same time) delivery to the target cells in the same composition or in separate compositions.
  • the deaminase and lambdoid bacteriophage N-peptide are not linked and/or fused.
  • the present disclosure contemplates the use of an endogenous deaminase.
  • the deaminase may be recruited by the nucleic acid-editing system that includes some or all of the previously mentioned components. H.
  • compositions of the present disclosure e.g., compositions comprising plasmids and/or viral vectors
  • compositions of the present disclosure further comprise a pharmaceutically acceptable carrier.
  • the composition is formulated in appropriate pharmaceutical vehicles for administration to human or animal subjects.
  • Some examples of materials which can serve as pharmaceutically-acceptable carriers include: (1) sugars, such as lactose, glucose and sucrose; (2) starches, such as corn starch and potato starch; (3) cellulose, and its derivatives, such as sodium carboxymethyl cellulose, methylcellulose, ethyl cellulose, microcrystalline cellulose and cellulose acetate; (4) powdered tragacanth; (5) malt; (6) gelatin; (7) lubricating agents, such as magnesium stearate, sodium lauryl sulfate and talc; (8) excipients, such as cocoa butter and suppository waxes; (9) oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; (10) glycols, such as propylene glycol; (11) polyols, such as glycerin, sorbitol, mannitol and polyethylene glycol (PEG); (12) esters, such as
  • compositions and methods find use in various embodiments in altering nucleotides within an RNA molecule to provide a medically-beneficial effect.
  • the present compositions and methods are useful in reducing the prevalence of, or ablating, a mutation.
  • the present compositions and methods are useful in introducing a mutation that beneficially affects a subject’s health.
  • compositions and methods described herein for the purpose of site-specific editing of a target nucleotide (e.g., within an RNA molecule) in a cell may be administered to a subject in need thereof in a therapeutically effective amount to treat and/or prevent a disease, condition or disorder the subject is suffering from.
  • the subject may not be suffering from a disease, condition or disorder, and the site-specific editing of a target nucleotide (e.g., within an RNA molecule) in a cell may induce a beneficial mutation in the wild-type target sequence.
  • the present disclosure contemplates a method of site-specific base editing of a target nucleotide within a SerpinA1 gene in a cell using the compositions and methods described herein (including, without limitation, a wild-type ⁇ N-peptide).
  • the present disclosure contemplates a method of site-specific base editing of a target nucleotide within a SerpinA1 gene in a cell comprising: (a) contacting the cell with: (i) a deaminase linked to a mutant or wild-type ⁇ N- peptide, and (ii) an antisense RNA oligonucleotide linked to a BoxB hairpin RNA oligonucleotide, the BoxB hairpin RNA oligonucleotide being the cognate hairpin oligonucleotide of the ⁇ N-peptide, and wherein: the antisense RNA oligonucleotide comprises a region complementary to an RNA molecule comprising the target nucleotide; the ⁇ N-peptide and BoxB hairpin RNA oligonucleotide interact; and the deaminase domain causes editing of the target nucleotide to induce a base change.
  • the present disclosure contemplates a method of site-specific base editing of a target nucleotide within an IDUA gene in a cell using the compositions and methods described herein (including, without limitation, a wild-type lamboid bacteriophage N-peptide).
  • the present disclosure contemplates a method of site-specific base editing of a target nucleotide within an Attorney Docket No.: 33791/41005 IDUA gene in a cell comprising: (a) contacting the cell with: (i) a deaminase linked to a mutant or wild-type lamboid bacteriophage N-peptide, and (ii) an antisense RNA oligonucleotide linked to a BoxB hairpin RNA oligonucleotide, the BoxB hairpin RNA oligonucleotide being the cognate hairpin oligonucleotide of the ⁇ N- peptide, and wherein: the antisense RNA oligonucleotide comprises a region complementary to an RNA molecule comprising the target nucleotide; the lamboid bacteriophage N-peptide and BoxB hairpin RNA oligonucleotide interact; and the deaminase domain causes editing of
  • compositions of this disclosure may be administered or packaged as a unit dose, for example.
  • unit dose when used in reference to a pharmaceutical composition of the present disclosure refers to physically discrete units suitable as unitary dosage for the subject, each unit containing a predetermined quantity of active material calculated to produce the desired therapeutic effect in association with the required diluent, i.e., a carrier or vehicle.
  • Treatment of a disease, condition or disorder includes delaying the development or progression of the disease, or reducing disease severity. Treating the disease or condition does not necessarily require curative results.
  • "delaying" the development of a disease means to defer, hinder, slow, retard, stabilize, and/or postpone progression of the disease.
  • This delay can be of varying lengths of time, depending on the history of the disease and/or individuals being treated.
  • a method that "delays" or alleviates the development of a disease, or delays the onset of the disease is a method that reduces probability of developing one or more symptoms of the disease in a given time frame and/or reduces extent of the symptoms in a given time frame, when compared to not using the method. Such comparisons are typically based on clinical studies, using a number of subjects sufficient to give a statistically significant result.
  • "Development” or "progression" of a disease means initial manifestations and/or ensuing progression of the disease. Development of the disease can be detectable and assessed using standard clinical techniques as well known in the art.
  • development also refers to progression that may be undetectable.
  • development or progression refers to the biological course of the symptoms.
  • “Development” includes occurrence, recurrence, and onset.
  • "onset” or “occurrence” of a disease includes initial onset and/or recurrence.
  • Conventional methods known to those of ordinary skill in the art of medicine, can be used to administer the Attorney Docket No.: 33791/41005 isolated polypeptide or pharmaceutical composition to the subject, depending upon the type of disease to be treated or the site of the disease.
  • J. Host Cells [00121] Cells that may contain any of the compositions described herein include prokaryotic cells and eukaryotic cells.
  • a eukaryotic cell e.g., a mammalian cell, such as a human cell.
  • the cell is in vitro (e.g., cultured cell).
  • the cell is in vivo (e.g., in a subject such as a human subject).
  • the cell is ex vivo (e.g., isolated from a subject and may be administered back to the same or a different subject).
  • Mammalian cells of the present disclosure include human cells, primate cells (e.g., vero cells), rat cells (e.g., GH3 cells, OC23 cells) or mouse cells (e.g., MC3T3 cells).
  • primate cells e.g., vero cells
  • rat cells e.g., GH3 cells, OC23 cells
  • mouse cells e.g., MC3T3 cells.
  • human cell lines including, without limitation, human embryonic kidney (HEK) cells, HeLa cells, cancer cells from the National Cancer Institute's 60 cancer cell lines (NCI60), DU145 (prostate cancer) cells, Lncap (prostate cancer) cells, MCF-7 (breast cancer) cells, MDA-MB-438 (breast cancer) cells, PC3 (prostate cancer) cells, T47D (breast cancer) cells, THP-1 (acute myeloid leukemia) cells, U87 (glioblastoma) cells, SHSY5Y human neuroblastoma cells (cloned from a myeloma) and Saos-2 (bone cancer) cells.
  • HEK human embryonic kidney
  • HeLa cells cancer cells from the National Cancer Institute's 60 cancer cell lines (NCI60)
  • DU145 (prostate cancer) cells Lncap (prostate cancer) cells
  • MCF-7 breast cancer
  • MDA-MB-438 breast cancer
  • PC3 prostate cancer
  • T47D
  • plasmids or viral vectors are delivered into human embryonic kidney (HEK) cells (e.g., HEK 293 or HEK 293T cells).
  • AAV vectors are delivered into stem cells (e.g., human stem cells) such as, for example, pluripotent stem cells (e.g., human pluripotent stem cells including human induced pluripotent stem cells (hiPSCs)).
  • stem cell refers to a cell with the ability to divide for indefinite periods in culture and to give rise to specialized cells.
  • a pluripotent stem cell refers to a type of stem cell that is capable of differentiating into all tissues of an organism, but not alone capable of sustaining full organismal development.
  • a human induced pluripotent stem cell refers to a somatic (e.g., mature or adult) cell that has been reprogrammed to an embryonic stem cell-like state by being forced to express genes and factors important for maintaining the defining properties of embryonic stem cells (see, e.g., Takahashi and Yamanaka, Cell 126 (4): 663-76, 2006, incorporated by reference herein).
  • Human induced pluripotent stem cell cells express stem cell markers and are capable of generating cells characteristic of all three germ layers (ectoderm, endoderm, mesoderm).
  • kits comprising nucleic acid vectors for the expression of the components of the nucleic acid-editing systems described herein.
  • the kit described herein may include one or more containers housing components for performing the methods described herein and optionally instructions for use. Any of the kit described herein may further comprise components needed for performing the assay methods.
  • Each component of the kits, where applicable, may be provided in liquid form (e.g., in solution) or in solid form, (e.g., a dry powder).
  • kits may optionally include instructions and/or promotion for use of the components provided.
  • "instructions” can define a component of instruction and/or promotion, and typically involve written instructions on or associated with packaging of the disclosure. Instructions also can include any oral or electronic instructions provided in any manner such that a user will clearly recognize that the instructions are to be associated with the kit, for example, audiovisual (e.g., videotape, DVD, etc.), Internet, and/or web-based communications, etc.
  • the written instructions may be in a form prescribed by a governmental agency regulating the manufacture, use, or sale of pharmaceuticals or biological products, which can also reflect approval by the agency of manufacture, use or sale for animal administration.
  • "promoted” includes all methods of doing business including methods of Attorney Docket No.: 33791/41005 education, hospital and other clinical instruction, scientific inquiry, drug discovery or development, academic research, pharmaceutical industry activity including pharmaceutical sales, and any advertising or other promotional activity including written, oral and electronic communication of any form, associated with the disclosure.
  • the kits may include other components depending on the specific application, as described herein. [00127]
  • the kits may contain any one or more of the components described herein in one or more containers.
  • kits may be prepared sterilely, packaged in a syringe and shipped refrigerated. Alternatively, it may be housed in a vial or other container for storage. A second container may have other components prepared sterilely. Alternatively, the kits may include the active agents premixed and shipped in a vial, tube, or other container. [00128] The kits may have a variety of forms, such as a blister pouch, a shrink wrapped pouch, a vacuum sealable pouch, a sealable thermoformed tray, or a similar pouch or tray form, with the accessories loosely packed within the pouch, one or more tubes, containers, a box or a bag.
  • kits may be sterilized after the accessories are added, thereby allowing the individual accessories in the container to be otherwise unwrapped.
  • the kits can be sterilized using any appropriate sterilization techniques, such as radiation sterilization, heat sterilization, or other sterilization methods known in the art.
  • the kits may also include other components, depending on the specific application, for example, containers, cell media, salts, buffers, reagents, syringes, needles, a fabric, such as gauze, for applying or removing a disinfecting agent, disposable gloves, a support for the agents prior to administration, etc. [00129] Without further elaboration, it is believed that one skilled in the art can, based on the above description, utilize the present disclosure to its fullest extent.
  • nucleic acid-editing system of the present disclosure was constructed.
  • a nucleic acid construct e.g., a plasmid, was created composed of a nucleic acid sequence encoding a mutant ⁇ N- peptide, a P21 N-peptide, or a P22 N-peptide linked to a deaminase domain, described herein, according to methods known to those skilled in the art.
  • a further nucleic acid construct e.g., the same plasmid or a different plasmid, composed of a nucleic acid sequence encoding an antisense RNA oligonucleotide, which is complementary to a targeted nucleic acid allele sequence, linked to a hairpin RNA oligonucleotide, as described herein.
  • the deaminase domain is the human ADAR2 catalytic domain, optionally mutated (e.g., without limitation, with one or more mutations at one or more positions selected from E396, C451, V351, R455, T375, K376, S486, Q488, R510, K594, R348, G593, S397, H443, L444, Y445, F442, E438, T448, A353, V355, T339, P539, V525 and I520).
  • the construct can be modified to include a NLS sequence (e.g. SV40).
  • the antisense oligonucleotide linked to a hairpin RNA oligonucleotide was made by obtaining a DNA oligonucleotide encoding a U6 (RNA Polymerase III) promoter at the 5′ end followed by a sequence comprising the antisense oligonucleotide linked to the hairpin RNA oligonucleotide.
  • a U6 RNA polymerase promoter from the pENTR plasmid was used for plasmids that encode the antisense RNA oligonucleotide used for substrate specificity and selectivity because a U6 promoter gives a very defined 5’-end transcription start site that confers the editing specificity and selectivity.
  • the antisense oligonucleotide sequence corresponds to a variable length of antisense sequence, complementary to the RNA molecule that was targeted.
  • a hairpin RNA oligonucleotide of the present disclosure was used.
  • An antisense version of the same DNA oligonucleotide was also synthesized. The two were then hybridized together and used as a template to make RNA with an RNA polymerase (e.g. U6).
  • Human SerpinA1 E342K gene (NM_000295.4) was synthesized and cloned into pcDNA3.1 plasmid under the control of the CMV promoter using BamHI and XbaI restriction sites (Quintara Bio, Berkeley, CA) and the correct insert was sequence verified.
  • This plasmid henceforth will be denoted as “SerpinA1/E342K/pcDNA3.1” and is nucleic acid sequence is SEQ ID NO: 45.
  • the heterologous IDUA genetic fusion was designed to express Td Tomato gene fused a 2A peptide that was fused in frame to a small region of the human IDUA gene (NM_000203.5) that contains the W402X mutation. This was then fused in frame to eGFP.
  • This entire genetic sequence was synthesized and cloned into pcDNA3.1 plasmid under the control of the CMV promoter using BamHI and XbaI restriction sites (Life Technologies). This plasmid henceforth will be denoted as “Td_IDUA W402X_eGFP/pcDNA3.1” and the correct insert was sequence verified as SEQ ID NO: 46.
  • the sequence for bacteriophage lambda 2boxBLambda guide RNA designed for the SerpinA1 E342K allele is SEQ ID NO: 47 and was cloned into pENTR/U6 plasmid. The correct insert was sequence verified. This plasmid is denoted as “2boxBLambda SerpinA1 E342K.”
  • the sequence for bacteriophage lambda 2boxBLambda guide RNA designed for the Td_IDUA W402X_eGFP mRNA is SEQ ID NO: 48 and was cloned into pENTR/U6 plasmid. The correct insert was sequence verified.
  • This plasmid is denoted as “2boxBLambda IDUA W402X.”
  • AAV vectors containing the plasmids and/or synthetic oligonucleotides are then prepared according to knowledge of those skilled in the art.
  • the proper construction of the nucleic acid-editing system is verified via sequence analysis.
  • the following tables provides the above-mentioned nucleic acid and/or amino acid sequences: Table 4.
  • a further nucleic acid construct e.g., the same plasmid or a different plasmid, composed of a nucleic acid sequence encoding an antisense RNA oligonucleotide, which is complementary to a targeted nucleic acid allele sequence, linked to a hairpin RNA oligonucleotide, as described herein.
  • the deaminase domain is the human ADAR2 catalytic domain, optionally mutated (e.g., without limitation, with one or more mutations at one or more positions selected from E396, C451, V351, R455, T375, K376, Attorney Docket No.: 33791/41005 S486, Q488, R510, K594, R348, G593, S397, H443, L444, Y445, F442, E438, T448, A353, V355, T339, P539, V525 and I520).
  • the construct can be modified to include a NLS sequence (e.g. SV40).
  • the antisense oligonucleotide linked to a hairpin RNA oligonucleotide was made by obtaining a DNA oligonucleotide encoding a U6 (RNA Polymerase III) promoter at the 5′ end followed by a sequence comprising the antisense oligonucleotide linked to the hairpin RNA oligonucleotide.
  • a U6 RNA polymerase promoter from the pENTR plasmid was used for plasmids that encode the antisense RNA oligonucleotide used for substrate specificity and selectivity because a U6 promoter gives a very defined 5’-end transcription start site that confers the editing specificity and selectivity.
  • the antisense oligonucleotide sequence corresponds to a variable length of antisense sequence, complementary to the RNA molecule that was targeted.
  • a hairpin RNA oligonucleotide of the present invention was used.
  • An antisense version of the same DNA oligonucleotide was also synthesized. The two were then hybridized together and used as a template to make RNA with an RNA polymerase (e.g. U6).
  • Human SerpinA1 E342K gene (NM_000295.4) was synthesized and cloned into pcDNA3.1 plasmid under the control of the CMV promoter using BamHI and XbaI restriction sites (Quintara Bio, Berkeley, CA) and the correct insert was sequence verified. This plasmid henceforth will be denoted as “SerpinA1/E342K/pcDNA3.1” and is nucleic acid sequence is SEQ ID NO: 45.
  • the heterologous IDUA genetic fusion was designed to express Td Tomato gene fused a 2A peptide that was fused in frame to a small region of the human IDUA gene (NM_000203.5) that contains the W402X mutation.
  • This plasmid is denoted as “2boxBP21 SerpinA1 E342K.”
  • the sequence for bacteriophage P212boxB guide RNA designed for the Td_IDUA W402X_eGFP mRNA was cloned into pENTR/U6 plasmid. The correct insert was sequence verified.
  • This plasmid is denoted as “2boxBP21 IDUA W402X.”
  • AAV vectors containing the plasmids and/or synthetic oligonucleotides are then prepared according to knowledge of those skilled in the art. Attorney Docket No.: 33791/41005 [00146] The proper construction of the nucleic acid-editing system is verified via sequence analysis.
  • a further nucleic acid construct e.g., the same plasmid or a different plasmid, composed of a nucleic acid sequence encoding an antisense RNA oligonucleotide, which is complementary to a targeted nucleic acid allele sequence, linked to a hairpin RNA oligonucleotide, as described herein.
  • the deaminase domain is the human ADAR2 catalytic domain, optionally mutated (e.g., without limitation, with one or more mutations at one or more positions selected from E396, C451, V351, R455, T375, K376, S486, Q488, R510, K594, R348, G593, S397, H443, L444, Y445, F442, E438, T448, A353, V355, T339, P539, V525 and I520).
  • the construct can be modified to include a NLS sequence (e.g. SV40).
  • the antisense oligonucleotide linked to a hairpin RNA oligonucleotide was made by obtaining a DNA oligonucleotide encoding a U6 (RNA Polymerase III) promoter at the 5′ end followed by a sequence comprising the antisense oligonucleotide linked to the hairpin RNA oligonucleotide.
  • U6 RNA Polymerase III
  • a U6 RNA polymerase promoter from the pENTR plasmid was used for plasmids that encode the antisense RNA oligonucleotide used for substrate specificity and selectivity because a U6 promoter gives a very defined 5’-end transcription start site that confers the editing specificity and selectivity.
  • the antisense oligonucleotide sequence corresponds to a variable length of antisense sequence, complementary to the RNA molecule that was targeted.
  • a hairpin RNA oligonucleotide of the present invention was used.
  • An antisense version of the same DNA oligonucleotide was also synthesized. The two were then hybridized together and used as a template to make RNA with an RNA polymerase (e.g. U6).
  • Human SerpinA1 E342K gene (NM_000295.4) was synthesized and cloned into pcDNA3.1 plasmid under the control of the CMV promoter using BamHI and XbaI restriction sites (Quintara Bio, Berkeley, CA) and the correct insert was sequence verified. This plasmid henceforth will be denoted as “SerpinA1/E342K/pcDNA3.1” and is nucleic acid sequence is SEQ ID NO: 45.
  • the heterologous IDUA genetic fusion was designed to express Td Tomato gene fused a 2A peptide that was fused in frame to a small region of the human IDUA gene (NM_000203.5) that contains the W402X mutation.
  • the correct insert was sequence verified. This plasmid is denoted as “2boxBP22 SerpinA1 E342K.”
  • the sequence for bacteriophage lambda 2boxBP22 guide RNA designed for the Td_IDUA W402X_eGFP mRNA is SEQ ID NO: 94 and was cloned into pENTR/U6 plasmid. The correct insert was sequence verified. This plasmid is denoted as “2boxBP22 IDUA W402X.”
  • AAV vectors containing the plasmids and/or synthetic oligonucleotides are then prepared according to knowledge of those skilled in the art.
  • the proper construction of the nucleic acid-editing system is verified via sequence analysis.
  • the samples are treated with TURBO DNase (Life Technologies) prior to elution.
  • the resultant isolated mRNA is used for cDNA synthesis using SuperScript IV Vilo according the manufacturer’s instructions (Life Technologies).
  • Two to six ⁇ l of the cDNA is used for as template for PCR (Platinum II Hot-Start PCR Master Mix; Life Technologies) using gene specific primers to generate an amplicon for Sanger sequencing (SEQ ID NOs: 49-52 are used for primers in RT PCR).
  • Sanger sequencing is performed by QuintaraBio (USA) or Psomagen (USA).
  • RNA oligonucleotide linked to a hairpin RNA oligonucleotide is combined with a test gene mRNA Attorney Docket No.: 33791/41005 in vitro and a bacteriophage N-peptide linked to a deaminase domain protein, where they are expressed via the same or a separate plasmid promotor system, and brought in contact with the cell. After incubation, the test gene mRNA is converted into cDNA.
  • Direct sequencing of RT-PCR products is undertaken to reveal editing at the specific nucleotide positions previously mentioned, directed by the antisense oligonucleotide and adjacent hairpin RNA oligonucleotide.
  • Control experiments that lack either the antisense oligonucleotide linked to the hairpin RNA oligonucleotide or the ⁇ N-peptide linked to a deaminase domain protein are expected to show no editing.
  • a further control is to incorporate scrambled RNA sequence in place of the antisense sequence, which would be expected to show no editing and further demonstrates specificity.
  • RNA oligonucleotide- ⁇ N-peptide interaction is required to target the catalytic domain of the deaminase to the nucleotide positions to be edited.
  • the system is further tested to correct a genetic mutation or sequence expressed endogenously in vitro (the type of genetic mutation described herein is illustrative of any of the various genetic mutations or wild type nucleotide that can be edited).
  • a specific nucleotide of an mRNA is targeted in a human disease model (e.g. cell line).
  • a mutation can cause codons to change so that instead of an mRNA encoding and translating to an amino acid, a premature termination codon (PTC) is read, which can lead to these humans developing a disease or condition.
  • PTC premature termination codon
  • a specific cytidine is converted to uracil by the acting deamination domain, thereby converting the PTC to a codon encoding tryptophan.
  • the ⁇ N- peptide linked to a deaminase domain protein will edit at a specific position based on being guided by the antisense RNA oligonucleotide linked to an inserted hairpin RNA oligonucleotide.
  • construction of the antisense oligonucleotide linked to a hairpin RNA oligonucleotide will include selecting a sequence complementary to site to be edited with various lengths of nucleotides 5’ of the position.
  • this antisense oligonucleotide linked to the hairpin RNA oligonucleotide is combined with the ⁇ N-peptide linked to a deaminase domain protein and the mutated mRNA in vitro, a percentage of the mutant mRNA is corrected, with the cytidine nucleotide being changed to uracil and thus correcting the codon. Editing is expected to be specific to the cytidine.
  • Example 3 In vivo RNA editing in various genetic disorder models corrects mutation and recovers wild-type Attorney Docket No.: 33791/41005 [00161]
  • the system and methods of Examples 1 and 2 can be tested in living cells or cell lysates. Any suitable model for the desired editing may be used. For instance, if genetically altered mice (e.g. wild type mice in which the target mutation is knocked in) are available, cells or tissues from such mice can be used to study the editing (either in vivo or ex vivo, e.g. by harvesting cells from the mice). Secondly, primary diseased human cell models in which the cells are procured from a human patient afflicted with the disease can be used to study the editing.
  • genetically altered mice e.g. wild type mice in which the target mutation is knocked in
  • cells or tissues from such mice can be used to study the editing (either in vivo or ex vivo, e.g. by harvesting cells from the mice).
  • primary diseased human cell models
  • in vivo model can be employed to examine editing using wild type mice when targeting a wild type mRNA.
  • Other suitable methods that may be employed in these Examples are described in PNAS November 5, 2013110 (45) 18285-18290; PNAS October 31, 2017114 (44) E9395-E9402; and Nature Methods February 8, 201916:239-242, the entire contents of which are incorporated by reference in their entireties.
  • DEFINITIONS [00163] The following definitions are used in connection with the disclosure disclosed herein. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood to one of skill in the art to which this disclosure belongs. [00164] As used herein, “a,” “an,” or “the” can mean one or more than one.
  • the term “about” when used in connection with a referenced numeric indication means the referenced numeric indication plus or minus up to 10% of that referenced numeric indication.
  • the language “about 50” covers the range of 45 to 55.
  • the term "deaminase” refers to an enzyme that catalyzes a deamination reaction.
  • the deaminase is a cytidine deaminase, catalyzing the hydrolytic deamination of cytidine or deoxycytidine to uracil or deoxyuracil, respectively.
  • an “effective amount,” when used in connection with medical uses is an amount that is effective for providing a measurable treatment, prevention, or reduction in the rate of pathogenesis of a disease of interest, or optionally “effective amount” refers to an amount of a biologically active agent that is sufficient to elicit a desired biological response.
  • an effective amount of a nuclease may refer to the amount of the nuclease that is sufficient to induce cleavage of a target site specifically bound and cleaved by the nuclease.
  • an effective amount of a fusion protein provided herein e.g., of a fusion protein comprising a deaminase (e.g., a nucleic acid-editing Attorney Docket No.: 33791/41005 domain) and a lambdoid bacteriophage N-peptide may refer to the amount of the fusion protein that is sufficient to induce editing of a target site specifically bound and edited by the fusion protein.
  • a deaminase e.g., a nucleic acid-editing Attorney Docket No.: 33791/41005 domain
  • a lambdoid bacteriophage N-peptide may refer to the amount of the fusion protein that is sufficient to induce editing of a target site specifically bound and edited by the fusion protein.
  • an agent e.g., a fusion protein, a deaminase, a recombinase, a hybrid protein, a protein dimer, a complex of a protein (or protein dimer) and a polynucleotide, or a polynucleotide
  • an agent e.g., a fusion protein, a deaminase, a recombinase, a hybrid protein, a protein dimer, a complex of a protein (or protein dimer) and a polynucleotide, or a polynucleotide
  • all compositional percentages are by weight of the total composition, unless otherwise specified.
  • the word “include,” and its variants, is intended to be non- limiting, such that recitation of items in a list is not to the exclusion of other like items that may also be useful in the compositions and methods of this technology.
  • the terms “can” and “may” and their variants are intended to be non-limiting, such that recitation that an embodiment can or may comprise certain elements or features does not exclude other embodiments of the present technology that do not contain those elements or features.
  • the term “hairpin” refers to a particular RNA oligonucleotide and/or RNA structure that is recognized by and interacts with a bacteriophage N-peptide as disclosed herein (e.g., amino-terminal domain ⁇ N-peptide derived from the ⁇ N protein).
  • a particular example of such a hairpin is a BoxB hairpin RNA oligonucleotide that is the cognate hairpin of the N- peptide.
  • “Homology” or “identity” or “similarity” refers to sequence similarity between two peptides or between two nucleic acid molecules. Homology can be determined by comparing a position in each sequence that may be aligned for purposes of comparison. When a position in the compared sequence is occupied by the same base or amino acid, then the molecules are homologous at that position. A degree of homology between sequences is a function of the number of matching or homologous positions shared by the sequences.
  • “unrelated” or “non-homologous” sequence shares less than 40% identity, or alternatively less than 25% identity, with one of the sequences of the present disclosure.
  • Attorney Docket No.: 33791/41005 [00172] “Homology” or “identity” or “similarity” can also refer to two nucleic acid molecules that hybridize under stringent conditions. [00173] “Hybridization” refers to a reaction in which one or more polynucleotides react to form a complex that is stabilized via hydrogen bonding between the bases of the nucleotide residues. The hydrogen bonding may occur by Watson-Crick base pairing, Hoogstein binding, or in any other sequence- specific manner.
  • the complex may comprise two strands forming a duplex structure, three or more strands forming a multi-stranded complex, a single self-hybridizing strand, or any combination of these.
  • a hybridization reaction may constitute a step in a more extensive process, such as the initiation of a PCR reaction, or the enzymatic cleavage of a polynucleotide by a ribozyme.
  • Examples of stringent hybridization conditions include: incubation temperatures of about 25° C. to about 37° C.; hybridization buffer concentrations of about 6 ⁇ SSC to about 10 ⁇ SSC; formamide concentrations of about 0% to about 25%; and wash solutions from about 4 ⁇ SSC to about 8 ⁇ SSC.
  • Examples of moderate hybridization conditions include: incubation temperatures of about 40° C. to about 50° C.; buffer concentrations of about 9 ⁇ SSC to about 2 ⁇ SSC; formamide concentrations of about 30% to about 50%; and wash solutions of about 5 ⁇ SSC to about 2 ⁇ SSC.
  • Examples of high stringency conditions include: incubation temperatures of about 55° C. to about 68° C.; buffer concentrations of about 1 ⁇ SSC to about 0.1 ⁇ SSC; formamide concentrations of about 55% to about 75%; and wash solutions of about 1 ⁇ SSC, 0.1 ⁇ SSC, or deionized water.
  • hybridization incubation times are from 5 minutes to 24 hours, with 1, 2, or more washing steps, and wash incubation times are about 1, 2, or 15 minutes.
  • SSC is 0.15 M NaCl and 15 mM citrate buffer. It is understood that equivalents of SSC using other buffer systems can be employed.
  • specifically binds refers to the binding specificity of a specific binding pair. Hybridization by a target-specific nucleic acid sequence of a particular target polynucleotide sequence in the presence of other potential targets is one characteristic of such binding. Specific binding involves two different nucleic acid molecules wherein one of the nucleic acid molecules specifically hybridizes with the second nucleic acid molecule through chemical or physical means. The two nucleic acid molecules are related in the sense that their binding with each other is such that they are capable of distinguishing their binding partner from other assay constituents having similar characteristics.
  • linker refers to a chemical group or a molecule linking two molecules or moieties, e.g., two domains of a fusion protein, such as, for example, a deaminase domain (e.g., a nucleic acid-editing domain) and lambdoid bacteriophage N-peptide.
  • a linker joins an antisense RNA oligonucleotide and a hairpin RNA oligonucleotide.
  • the linker is positioned between, or flanked by, two groups, molecules, or other moieties and connected to each one via a covalent bond, thus connecting the two.
  • the linker is an amino acid or a plurality of amino acids (e.g., a peptide or protein).
  • the linker is an organic molecule, group, polymer, or chemical moiety.
  • the linker is 5-100 amino acids in length, for example, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 30-35, 35-40, 40-45, 45-50, 50-60, 60-70, 70-80, 80-90, 90-100, 100-150, or 150-200 amino acids in length.
  • a mismatch is found at any position where no direct Watson-Crick base pair (A/T, G/C, C/G, T/A) correspondence exists between the oligonucleotide and the target in the region of complementarity between the two strands.
  • An artificial mismatch is typically provided at one or more single nucleotide positions in an oligonucleotide, but can include more extensive changes.
  • a true mismatch in a duplex formed between an oligonucleotide and a variant target can include a substitution, an insertion, a deletion, and a rearrangement of oligonucleotide nucleic acid relative to the target.
  • Substitution can be at one or more positions in the oligonucleotide.
  • the term "mutation,” as used herein, refers to a substitution of a residue within a sequence, e.g., a nucleic acid or amino acid sequence, with another residue, or a deletion or insertion of one or more residues within a sequence. Mutations are typically described herein by identifying the original residue followed by the position of the residue within the sequence and by the identity of the newly substituted residue. Various methods for making the amino acid substitutions (mutations) provided herein are well known in the art, and are provided by, for example, Green and Sambrook, Molecular Cloning: A Laboratory Manual (4th ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (2012)).
  • a substituted amino acid residue is any naturally-occurring amino acid, such as a hydrophilic, hydrophobic, or non-classical amino acid.
  • the hydrophilic amino acid can be selected from a polar and positively charged hydrophilic amino acid, a polar and neutral of charge hydrophilic amino acid, and polar and negatively charged hydrophilic amino acid, and an aromatic, polar and positively charged hydrophilic amino acid.
  • a polar and positively charged hydrophilic amino acid can be selected from arginine (R) and lysine (K).
  • a polar and neutral of charge hydrophilic amino acid can be Attorney Docket No.: 33791/41005 selected from asparagine (N), glutamine (Q), serine (S), threonine (T), proline (P), and cysteine (C).
  • a polar and negatively charged hydrophilic amino acid can be selected from aspartate (D) and glutamate (E).
  • An aromatic, polar and positively charged hydrophilic amino acid can be histidine (H).
  • a hydrophobic amino acid can be selected from a hydrophobic, aliphatic amino acid and a hydrophobic, aromatic amino acid.
  • the hydrophobic, aliphatic amino acid can be glycine (G), alanine (A), leucine (L), isoleucine (I), methionine (M), or valine (V).
  • a hydrophobic, aromatic amino acid can be phenylalanine (F), tryptophan (W), or tyrosine (Y).
  • a non-classical amino acid can be selected from selenocysteine, pyrrolysine, N- formylmethionine ⁇ -alanine, GABA, ⁇ -Aminolevulinic acid, 4-Aminobenzoic acid (PABA), D-isomers of the common amino acids, 2,4-diaminobutyric acid, ⁇ -amino isobutyric acid, 4-aminobutyric acid, Abu, 2-amino butyric acid, ⁇ -Abu, ⁇ -Ahx, 6-amino hexanoic acid, Aib, 2-amino isobutyric acid, 3-amino propionic acid, ornithine, norleucine, norvaline, hydroxyproline, sarcosme, citrulline, homocitrulline, cysteic acid, t- butylglycine, t-butylalanine, phenylglycine, cyclohexylalanine,
  • nuclear localization signal refers to an amino acid sequence that promotes import of a protein into the cell nucleus, for example, by nuclear transport.
  • Nuclear localization sequences are known in the art and would be apparent to the skilled artisan. For example, NLS sequences are described in Plank et al., international PCT application, PCT/EP2000/011690, filed November 23, 2000, published as WO/2001/038547 on May 31, 2001, the contents of which are incorporated herein by reference for their disclosure of exemplary nuclear localization sequences.
  • nucleic acid and “nucleic acid molecule,” as used herein, refer to a compound comprising a nucleobase and an acidic moiety, e.g., a nucleoside, a nucleotide, or a polymer of nucleotides.
  • polymeric nucleic acids e.g., nucleic acid molecules comprising three or more nucleotides are linear molecules, in which adjacent nucleotides are linked to each other via a phosphodiester linkage.
  • nucleic acid refers to individual nucleic acid residues (e.g. nucleotides and/or nucleosides).
  • nucleic acid refers to an oligonucleotide chain comprising three or more individual nucleotide residues.
  • oligonucleotide and “polynucleotide” can be used interchangeably to refer to a polymer of nucleotides (e.g., a string of at least three nucleotides).
  • nucleic acid encompasses RNA as well as single- and/or double-stranded DNA.
  • Nucleic acids may be naturally occurring, for example, in the context of a genome, a transcript, an mRNA, tRNA, rRNA, siRNA, snRNA, a plasmid, cosmid, chromosome, chromatid, or other Attorney Docket No.: 33791/41005 naturally occurring nucleic acid molecule.
  • a nucleic acid molecule may be a non-natural occurring molecule, e.g., a recombinant DNA or RNA, an artificial chromosome, an engineered genome, or fragment thereof, or a synthetic DNA, RNA, DNA/RNA hybrid, or including non-naturally occurring nucleotides or nucleosides.
  • nucleic acid examples include nucleic acid analogs, e.g., analogs having other than a phosphodiester backbone.
  • Nucleic acids can be purified from natural sources, produced using recombinant expression systems and optionally purified, chemically synthesized, etc. Where appropriate, e.g., in the case of chemically synthesized molecules, nucleic acids can comprise nucleoside analogs such as analogs having chemically modified bases or sugars, and backbone modifications. A nucleic acid sequence is presented in the 5' to 3' direction unless otherwise indicated.
  • a nucleic acid is or comprises natural nucleosides (e.g.
  • nucleoside analogs e.g., 2-aminoadenosine, 2-thiothymidine, inosine, pyrrolo-pyrimidine, 3-methyl adenosine, 5-methylcytidine, 2-aminoadenosine, C5-bromouridine, C5-fluorouridine, C5- iodouridine, C5-propynyl-uridine, C5-propynyl-cytidine, C5-methylcytidine, 2-aminoadenosine, 7- deazaadenosine, 7-deazaguanosine, 8-oxoadenosine, 8-oxoguanosine, 0(6)-methylguanine, and 2- thioc
  • nucleoside analogs e.g., 2-aminoadenosine, 2-thiothymidine, inosine, pyrrolo-pyrimidine, 3-methyl adenosine, 5-methylc
  • methylated bases e.g., methylated bases
  • intercalated bases e.g., modified sugars (e.g., 2'-fluororibose, ribose, 2'-deoxyribose, arabinose, and hexose); and/or modified phosphate groups (e.g., phosphorothioates and 5'-N-phosphoramidite linkages).
  • modified sugars e.g., 2'-fluororibose, ribose, 2'-deoxyribose, arabinose, and hexose
  • modified phosphate groups e.g., phosphorothioates and 5'-N-phosphoramidite linkages.
  • pharmaceutically-acceptable carrier means a pharmaceutically-acceptable material, composition or vehicle, such as a liquid or solid filler, diluent, excipient, manufacturing aid (e.g., lubricant, talc magnesium, calcium or zinc stearate, or steric acid), or solvent encapsulating material, involved in carrying or transporting the compound from one site (e.g., the delivery site) of the body, to another site (e.g., organ, tissue or portion of the body).
  • a pharmaceutically acceptable carrier is "acceptable” in the sense of being compatible with the other ingredients of the formulation and not injurious to the tissue of the subject (e.g., physiologically compatible, sterile, physiologic pH, etc.).
  • the words “preferred” and “preferably” refer to embodiments of the technology that afford certain benefits, under certain circumstances. However, other embodiments may also be preferred, under the same or other circumstances. Furthermore, the recitation of one or more preferred embodiments does not imply that other embodiments are not useful, and is not intended to exclude other embodiments from the scope of the technology.
  • Attorney Docket No.: 33791/41005 [00183]
  • the subject is a rodent. In some embodiments, the subject is a sheep, a goat, cattle, a cat, or a dog. In some embodiments, the subject is a vertebrate, an amphibian, a reptile, a fish, an insect, a fly, or a nematode. In some embodiments, the subject is a research animal. In some embodiments, the subject is genetically engineered, e.g., a genetically engineered non-human subject. The subject may be of either sex and at any stage of development.
  • the effect will result in a quantifiable change of at least about 10%, at least about 20%, at least about 30%, at least about 50%, at least about 70%, or at least about 90%. In some embodiments, the effect will result in a quantifiable change of about 10%, about 20%, about 30%, about 50%, about 70%, or even about 90% or more. In certain embodiments, the effect will result in a quantifiable change of two-fold, or three-fold, or four-fold, or five-fold, or ten-fold. Therapeutic benefit also includes halting or slowing the progression of the underlying disease or disorder or reduction in toxicity, regardless of whether improvement is realized.
  • a method of site-specific editing of a target nucleotide within an RNA molecule in a cell comprising: (a) contacting the cell with: (i) a deaminase linked to a mutant ⁇ bacteriophage N-peptide, a lamboid P22 bacteriophage N-peptide, and (ii) an antisense RNA oligonucleotide linked to a hairpin RNA oligonucleotide, wherein: the antisense RNA oligonucleotide comprises a region complementary to an RNA molecule comprising the target nucleotide; the N-peptide and hairpin interact; and the deaminase domain causes editing of the target nucleotide to induce a base change.
  • a method of treating a disease or disorder by editing a target nucleotide within an RNA molecule in a cell comprising contacting the cell with: (i) a deaminase linked to a mutant ⁇ bacteriophage N-peptide, a lamboid P22 bacteriophage N-peptide, and (ii) an antisense RNA oligonucleotide linked to a hairpin RNA oligonucleotide, wherein: the antisense RNA oligonucleotide comprises a region complementary to an RNA molecule comprising the target nucleotide; the N-peptide and hairpin interact; and the deaminase domain causes editing of the target nucleotide to induce a base change.
  • adenosine deaminase is selected from adenosine deaminase RNA specific 1 (ADAR1), adenosine deaminase RNA specific 2 (ADAR2), adenosine deaminase RNA specific B1 (ADARB1), adenosine deaminase like (ADAL), adenosine deaminase 2 (ADA2), adenosine monophosphate deaminase 1 (AMPD1), adenosine monophosphate deaminase 2 (AMPD2), adenosine monophosphate deaminase 3 (AMPD3), adenosine deaminase domain containing 1 (ADAD1), adenosine deaminase domain containing 2 (ADAD2), adenosine deaminase tRNA specific 1 (ADAT1),
  • ADAR1 adenosine dea
  • the ADAR1 or ADAR2 comprises a fragment that comprises a catalytic domain.
  • the catalytic domain is the deaminase domain of human ADAR2, comprising an amino acid sequence having at least 90% amino acid sequence identity with SEQ ID NO: 18.
  • the ADAR2 comprises the amino acid sequence of SEQ ID NO: 19.
  • 12A The method of any one of the preceding paragraphs, wherein the ADAR2 comprises the amino acid sequence of SEQ ID NO: 19.
  • the ADAR induces a cytidine (C) to uridine (U) nucleotide mutation
  • the ADAR comprises one or more mutations that allow the ADAR to induce the C to U nucleotide mutation
  • the ADAR mutation(s) is selected from a substitution at one or more positions E396, C451, V351, R455, T375, K376, S486, Q488, R510, K594, R348, G593, S397, H443, L444, Y445, F442, E438, T448, A353, V355, T339, P539, V525 and I520, optionally relative to SEQ ID NO: 18 or SEQ ID NO: 19.
  • mutant amino-terminal domain ⁇ N-peptide comprises an arginine-rich motif.
  • mutant amino-terminal domain ⁇ N-peptide comprises an Ala at position 3 and an arginine at each of positions 6, 10, and 11 of SEQ ID NO: 1.
  • mutant amino-terminal domain ⁇ N-peptide variant comprises at least one mutation as compared to the wild-type amino- terminal domain ⁇ N-peptide (SEQ ID NO: 1).
  • mutant mutant amino- terminal domain ⁇ N-peptide comprises a mutation selected from one or more of an amino acid substitution, deletion, and addition.
  • mutant amino-terminal domain ⁇ N-peptide comprises from 1 to 19 amino acid residue substitutions.
  • amino acid substitution takes place at one or more of amino acid residue positions 1 to 19, relative to the wild-type amino- terminal domain ⁇ N-peptide sequence (SEQ ID NO: 1).
  • any one of the preceding paragraphs wherein the amino acid substitution is selected from any one of the amino acid substitutions listed in Table 1.
  • 25A The method of any one of the preceding paragraphs, wherein the mutant amino-terminal domain ⁇ N-peptide comprises the amino acid sequence of any one of SEQ ID NO: 2 to SEQ ID NO: 9.
  • 26A The method of any one of the preceding paragraphs, wherein the affinity of the mutant ⁇ N-peptide for the BoxB hairpin RNA oligonucleotide is greater than the affinity of the wild-type ⁇ N- peptide for the BoxB hairpin RNA oligonucleotide.
  • the affinity is greater by at least 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 15-fold, 20-fold, 25-fold, 30-fold, 35-fold, 40-fold, 45-fold, 50-fold, or 100-fold.
  • 28A The method of any one of the preceding paragraphs, wherein the mutant ⁇ N-peptide comprises a substituted amino acid residue that is any naturally-occurring amino acid.
  • 29A The method of any one of the preceding paragraphs, wherein the naturally-occurring amino acid is hydrophilic, hydrophobic, or non-classical.
  • 30A The method of any one of the preceding paragraphs, wherein the naturally-occurring amino acid is hydrophilic, hydrophobic, or non-classical.
  • hydrophilic amino acid is selected from a polar and positively charged hydrophilic amino acid, a polar and neutral of charge hydrophilic amino acid, and polar and negatively charged hydrophilic amino acid, and an aromatic, polar and positively charged hydrophilic amino acid.
  • the polar and positively charged hydrophilic amino acid is arginine (R) or lysine (K).
  • hydrophobic amino acid is selected from a hydrophobic, aliphatic amino acid and a hydrophobic, aromatic amino acid.
  • 36A The method of any one of the preceding paragraphs, wherein the hydrophobic, aliphatic amino acid is glycine (G), alanine (A), leucine (L), isoleucine (I), methionine (M), or valine (V).
  • 37A The method of any one of the preceding paragraphs, wherein the hydrophobic, aromatic amino acid is phenylalanine (F), tryptophan (W), or tyrosine (Y).
  • 38A The method of any one of the preceding paragraphs, wherein the hydrophobic, aromatic amino acid is phenylalanine (F), tryptophan (W), or tyrosine (Y).
  • non-classical amino acid is selected from selenocysteine, pyrrolysine, N-formylmethionine ⁇ -alanine, GABA, ⁇ - Aminolevulinic acid, 4-Aminobenzoic acid (PABA), D-isomers of the common amino acids, 2,4- diaminobutyric acid, ⁇ -amino isobutyric acid, 4-aminobutyric acid, Abu, 2-amino butyric acid, ⁇ -Abu, ⁇ - Ahx, 6-amino hexanoic acid, Aib, 2-amino isobutyric acid, 3-amino propionic acid, ornithine, norleucine, Attorney Docket No.: 33791/41005 norvaline, hydroxyproline, sarcosme, citrulline, homocitrulline, cysteic acid, t-butylglycine, t- butyla
  • the mutant ⁇ N-peptide is linked to at least 2, at least 3, or at least 4 deaminases, or fragments thereof.
  • 43A The method of any one of the preceding paragraphs, wherein the deaminase and the mutant ⁇ N-peptide comprise a nuclear localization signal.
  • 44A The method of any one of the preceding paragraphs, wherein the deaminase and the mutant ⁇ N-peptide comprise a nuclear localization signal and the RNA molecule comprising the target nucleotide is in the nucleus of the cell.
  • 45A The method of any one of the preceding paragraphs, wherein the mutant ⁇ N-peptide is linked to at least 2, at least 3, or at least 4 deaminases, or fragments thereof.
  • the nuclear localization signal is the SV40 Large T-antigen nuclear localization signal.
  • SV40 Large T-antigen nuclear localization signal comprises the amino acid sequence of SEQ ID NO: 21.
  • 47A The method of any one of the preceding paragraphs, wherein the antisense RNA nucleotide hybridizes with a wild-type target sequence in an endogenous RNA and comprises a target nucleotide to be edited.
  • 48A The method of any one of the preceding paragraphs, wherein the target nucleotide to be edited induces a beneficial mutation in the wild-type target sequence.
  • 49A The method of any one of the preceding paragraphs, wherein the antisense RNA nucleotide hybridizes with a mutant target sequence in an endogenous RNA and comprises a target nucleotide to be edited.
  • 50A The method of any one of the preceding paragraphs, wherein the target nucleotide to be edited eliminates a detrimental mutation in the mutant target sequence.
  • Attorney Docket No.: 33791/41005 [00241]
  • 51A The method of any one of the preceding paragraphs, wherein the target nucleotide is a genetic mutation associated with a genetic disease or disorder.
  • 52A The method of any one of the preceding paragraphs, wherein the target nucleotide is a genetic mutation associated with a genetic disease or disorder.
  • the antisense RNA oligonucleotide has perfect base-pairing complementarity with the RNA molecule comprising the target nucleotide.
  • 56A The method of any one of the preceding paragraphs, wherein the antisense RNA oligonucleotide comprises a one or more mismatches with the RNA molecule comprising the target nucleotide.
  • 57A The method of any one of the preceding paragraphs, wherein the antisense RNA oligonucleotide sequence comprises from 1 to 15 mismatches, e.g.
  • 58A The method of any one of the preceding paragraphs, wherein the antisense RNA oligonucleotide sequence is at least 80% complementary with the target sequence.
  • 59A The method of any one of the preceding paragraphs, wherein the 5' end of the antisense RNA oligonucleotide begins before the target nucleotide to be edited.
  • 60A The method of any one of the preceding paragraphs, wherein the 3' end of the oligonucleotide extends from 2-22 nucleotides 5' from the target nucleotide to be edited.
  • 61A The method of any one of the preceding paragraphs, wherein the antisense RNA oligonucleotide is linked to at least 2, 3, or 4 hairpin RNA oligonucleotides.
  • 62A The method of any one of the preceding paragraphs, wherein the hairpin RNA oligonucleotide comprises a nucleic acid sequence located from about 2-20 nucleotide residues 5' of the target mutation.
  • Attorney Docket No.: 33791/41005 [00253] 63A.
  • the hairpin RNA oligonucleotide comprises a nucleic acid sequence located from about 2-20 nucleotide residues 3' of the target mutation.
  • 64A The method of any one of the preceding paragraphs, wherein the hairpin RNA oligonucleotide is a BoxB hairpin RNA oligonucleotide.
  • 65A The method of any one of the preceding paragraphs, wherein the BoxB hairpin RNA oligonucleotide is the cognate hairpin oligonucleotide of the mutant ⁇ N-peptide.
  • 66A The method of any one of the preceding paragraphs, wherein the hairpin RNA oligonucleotide comprises a nucleic acid sequence located from about 2-20 nucleotide residues 3' of the target mutation.
  • BoxB hairpin RNA oligonucleotide comprises a nucleic acid sequence of SEQ ID NO: 10 or SEQ ID NO: 11, or mutants thereof.
  • 67A The method of any one of the preceding paragraphs, wherein the mutant ⁇ N peptide interacts with a ⁇ BoxB hairpin RNA oligonucleotide comprising a nucleic acid sequence of SEQ ID NO: 10 or SEQ ID NO: 11, or mutant thereof.
  • 68A The method of any one of the preceding paragraphs, wherein the BoxB hairpin RNA oligonucleotide comprises a nucleic acid sequence of SEQ ID NO: 10 or SEQ ID NO: 11, or mutant thereof.
  • the mutant ⁇ N peptide and ⁇ BoxB hairpin RNA oligonucleotide interaction adopts a 4-out GNRA-like pentaloop.
  • the nucleic acid sequence comprises at least one mutation selected from missense mutation, nonsense mutation, insertion, deletion, duplication, frameshift mutation, and repeat expansion.
  • 70A the nucleic acid sequence comprises at least one mutation selected from missense mutation, nonsense mutation, insertion, deletion, duplication, frameshift mutation, and repeat expansion.
  • ⁇ BoxB hairpin RNA oligonucleotide comprises a nucleic acid sequence having sequence identity to SEQ ID NO: 10 or SEQ ID NO: 11, and further comprises from 1 to 15 nucleotide mutations selected from one or more of nucleotide substitutions, nucleotide deletions, and nucleotide additions.
  • 71A The method of any one of the preceding paragraphs, wherein the one or more nucleotide mutations take(s) place at one or more of nucleotide residue positions 1 to 15, relative to the wild-type ⁇ BoxB hairpin RNA oligonucleotide.
  • 72A The method of any one of the preceding paragraphs, wherein the one or more nucleotide mutations take(s) place at one or more of nucleotide residue positions 1 to 15, relative to the wild-type ⁇ BoxB hairpin RNA oligonucleotide.
  • ⁇ BoxB hairpin RNA oligonucleotide comprises a nucleic acid sequence of one or more of SEQ ID NOs: 12-17.
  • 73A The method of any one of the preceding paragraphs, wherein components (i) and (ii) are within a plasmid, vector, mRNA, or lipid nanoparticle.
  • 74A The method of any one of the preceding paragraphs, wherein components (i) and (ii) are within a viral vector. Attorney Docket No.: 33791/41005 [00265] 75A.
  • the viral vector is an adeno- associated viruses (AAVs), adenoviruses, retroviruses, and lentiviruses vector.
  • AAVs adeno-associated viruses
  • retroviruses retroviruses
  • lentiviruses vector adeno-associated virus vector
  • 76A The method of any one of the preceding paragraphs, wherein the viral vector is an adeno- associated virus (AAV) vector.
  • AAV vector is selected from AAV1, or AAV2, or AAV3, or AAV4, or AAV5, or AAV6, or AAV7, or AAV8, or AAV9, or AAV10, or AAV11, and AAV12.
  • AAV vector is selected from AAV1, or AAV2, or AAV3, or AAV4, or AAV5, or AAV6, or AAV7, or AAV8, or AAV9, or AAV10, or AAV11, and AAV12.
  • Additional embodiments [00269] 1B.
  • a method of site-specific editing of a target nucleotide within an RNA molecule in a cell comprising: (a) contacting the cell with: (i) a deaminase linked to a lamboid P22 bacteriophage N-peptide, and (ii) an antisense RNA oligonucleotide linked to a hairpin RNA oligonucleotide, wherein: the antisense RNA oligonucleotide comprises a region complementary to an RNA molecule comprising the target nucleotide; the N-peptide and hairpin interact; and the deaminase domain causes editing of the target nucleotide to induce a base change. [00270] 2B.
  • a method of treating a disease or disorder by editing a target nucleotide within an RNA molecule in a cell comprising contacting the cell with: (i) a deaminase linked to a lamboid P22 bacteriophage N-peptide, and (ii) an antisense RNA oligonucleotide linked to a hairpin RNA oligonucleotide, wherein: the antisense RNA oligonucleotide comprises a region complementary to an RNA molecule comprising the target nucleotide; the N-peptide and hairpin interact; and the deaminase domain causes editing of the target nucleotide to induce a base change. [00271] 3B.
  • deaminase is cytidine deaminase or adenosine deaminase.
  • adenosine deaminase yields a uracil (U) nucleotide.
  • adenosine deaminase is selected from adenosine deaminase RNA specific 1 (ADAR1), adenosine deaminase RNA specific 2 Attorney Docket No.: 33791/41005 (ADAR2), adenosine deaminase RNA specific B1 (ADARB1), adenosine deaminase like (ADAL), adenosine deaminase 2 (ADA2), adenosine monophosphate deaminase 1 (AMPD1), adenosine monophosphate deaminase 2 (AMPD2), adenosine monophosphate deaminase 3 (AMPD3), adenosine deaminase domain containing 1 (ADAD1), adenosine deaminase domain containing 2 (ADAD2), adenosine deaminaminaminase RNA specific 2 Attorney Docket
  • the ADAR1 or ADAR2 comprises a fragment that comprises a catalytic domain.
  • the catalytic domain is the deaminase domain of human ADAR2, comprising an amino acid sequence having at least 90% sequence identity with SEQ ID NO: 18.
  • the ADAR2 comprises the amino acid sequence of SEQ ID NO: 18. [00280] 12B.
  • the ADAR induces a cytidine (C) to uridine (U) nucleotide mutation
  • the ADAR comprises one or more mutations that allow the ADAR to induce the C to U nucleotide mutation
  • the ADAR mutation(s) is selected from a substitution at one or more positions E396, C451, V351, R455, T375, K376, S486, Q488, R510, K594, R348, G593, S397, H443, L444, Y445, F442, E438, T448, A353, V355, T339, P539, V525 and I520, optionally relative to SEQ ID NO: 18 or SEQ ID NO: 19.
  • the P22 N-peptide is a variant that is the wild-type amino-terminal domain P22 N-peptide and comprises the amino acid sequence of SEQ ID NO: 53.
  • 19B The method of any one of the preceding paragraphs, wherein the amino-terminal domain P22 N-peptide comprises an arginine-rich motif.
  • 20B The method of any one of the preceding paragraphs, wherein the amino-terminal domain P22 N-peptide comprises an Ala at position 5 and an arginine at each of positions 8, 12, and 13 of SEQ ID NO: 53. [00289] 21B.
  • the amino-terminal domain P22 N-peptide variant comprises at least one mutation as compared to the wild type amino-terminal domain P22 N-peptide.
  • the mutation is selected from one or more of an amino acid substitution, deletion, and addition.
  • the amino-terminal domain P22 N-peptide variant comprises from 1 to 21 amino acid residue substitutions. [00292] 24B.
  • the substituted amino acid residue of the lambdoid bacteriophage N-peptide is any naturally-occurring amino acid.
  • 30B The method of any one of the preceding paragraphs, wherein the naturally-occurring amino acid is hydrophilic, hydrophobic, or non-classical.
  • 31B The method of any one of the preceding paragraphs, wherein the hydrophilic amino acid is selected from a polar and positively charged hydrophilic amino acid, a polar and neutral of charge hydrophilic amino acid, and polar and negatively charged hydrophilic amino acid, and an aromatic, polar and positively charged hydrophilic amino acid. [00300] 32B.
  • the polar and positively charged hydrophilic amino acid is arginine (R) or lysine (K).
  • 33B The method of any one of the preceding paragraphs, wherein the polar and neutral of charge hydrophilic amino acid is asparagine (N), glutamine (Q), serine (S), threonine (T), proline (P), or cysteine (C).
  • 34B The method of any one of the preceding paragraphs, wherein the polar and negatively charged hydrophilic amino acid is aspartate (D) or glutamate (E). [00303] 35B.
  • hydrophobic amino acid is selected from a hydrophobic, aliphatic amino acid and a hydrophobic, aromatic amino acid.
  • hydrophobic, aliphatic amino acid is glycine (G), alanine (A), leucine (L), isoleucine (I), methionine (M), or valine (V).
  • hydrophobic, aromatic amino acid is phenylalanine (F), tryptophan (W), or tyrosine (Y).
  • the non-classical amino acid is selected from selenocysteine, pyrrolysine, N-formylmethionine ⁇ -alanine, GABA, ⁇ - Attorney Docket No.: 33791/41005 Aminolevulinic acid, 4-Aminobenzoic acid (PABA), D-isomers of the common amino acids, 2,4- diaminobutyric acid, ⁇ -amino isobutyric acid, 4-aminobutyric acid, Abu, 2-amino butyric acid, ⁇ -Abu, ⁇ - Ahx, 6-amino hexanoic acid, Aib, 2-amino isobutyric acid, 3-amino propionic acid, or
  • the nuclear localization signal is the SV40 Large T-antigen nuclear localization signal.
  • SV40 Large T-antigen nuclear localization signal comprises the amino acid sequence of SEQ ID NO: 21i.
  • 48B The method of any one of the preceding paragraphs, wherein the antisense RNA nucleotide hybridizes with a wild-type target sequence in an endogenous RNA and comprises a target nucleotide to be edited.
  • 49B The method of any one of the preceding paragraphs, wherein the target nucleotide to be edited induces a beneficial mutation in the wild-type target sequence.
  • the antisense RNA oligonucleotide has perfect base-pairing complementarity with the RNA molecule comprising the target nucleotide.
  • the antisense RNA oligonucleotide comprises a one or more mismatches with the RNA molecule comprising the target nucleotide.
  • the antisense RNA oligonucleotide sequence comprises from 1 to 15 mismatches, e.g.
  • 59B The method of any one of the preceding paragraphs, wherein the antisense RNA oligonucleotide sequence is at least 80% complementary with the target sequence.
  • 60B The method of any one of the preceding paragraphs, wherein the 5' end of the antisense RNA oligonucleotide begins before the target nucleotide to be edited.
  • 61B The method of any one of the preceding paragraphs, wherein the 5' end of the antisense RNA oligonucleotide begins before the target nucleotide to be edited.
  • the hairpin RNA oligonucleotide is located from about 2-20 nucleotide residues 3' of the target mutation.
  • 65B The method of any one of the preceding paragraphs, wherein the hairpin RNA oligonucleotide is a BoxB hairpin RNA oligonucleotide.
  • 66B The method of any one of the preceding paragraphs, wherein the BoxB hairpin RNA oligonucleotide is the cognate hairpin oligonucleotide of the N-peptide.
  • 67B is the method of any one of the preceding paragraphs, wherein the hairpin RNA oligonucleotide is located from about 2-20 nucleotide residues 3' of the target mutation.
  • the BoxB hairpin RNA oligonucleotide comprises a nucleic acid sequence of any one of SEQ ID NOs: 79-80, or variants thereof.
  • the P22 N peptide interacts with a P22 BoxB hairpin RNA oligonucleotide comprising the nucleic acid sequence of SEQ ID NO: 79 or SEQ ID NO: 80, or variant thereof.
  • 69B The method of any one of the preceding paragraphs, wherein the P22 N peptide interacts with a P22 BoxB hairpin RNA oligonucleotide comprising the nucleic acid sequence of SEQ ID NO: 79 or SEQ ID NO: 80, or variant thereof.
  • the P22 BoxB hairpin RNA oligonucleotide comprises the nucleic acid sequence of SEQ ID NO: 79 or SEQ ID NO: 80, and further comprises from 1 to 17 nucleotide mutations selected from one or more of nucleotide substitutions, nucleotide deletions, and nucleotide additions.
  • 72B The method of any one of the preceding paragraphs, wherein the one or more nucleotide mutations take(s) place at one or more of nucleotide residue positions 1 to 17, relative to the wild type P22 BoxB hairpin RNA oligonucleotide.
  • 73B The method of any one of the preceding paragraphs, wherein the one or more nucleotide mutations take(s) place at one or more of nucleotide residue positions 1 to 17, relative to the wild type P22 BoxB hairpin RNA oligonucleotide.
  • components (i) and (ii) are within a plasmid, vector, mRNA, or lipid nanoparticle.
  • components (i) and (ii) are within a viral vector.
  • the viral vector is an adeno- associated viruses (AAVs), adenoviruses, retroviruses, and lentiviruses vector.
  • AAVs adeno-associated viruses
  • adenoviruses adenoviruses
  • retroviruses retroviruses
  • lentiviruses vector lentiviruses vector.
  • the viral vector is an adeno-associated virus (AAV) vector.
  • AAV vector is selected from AAV1, or AAV2, or AAV3, or AAV4, or AAV5, or AAV6, or AAV7, or AAV8, or AAV9, or AAV10, or AAV11, and AAV12.
  • AAV vector is selected from AAV1, or AAV2, or AAV3, or AAV4, or AAV5, or AAV6, or AAV7, or AAV8, or AAV9, or AAV10, or AAV11, and AAV12.
  • a method of site-specific editing of a target nucleotide within an RNA molecule in a cell comprising: (a) contacting the cell with: (i) a deaminase linked to a lamboid P21 bacteriophage N-peptide, and (ii) an antisense RNA oligonucleotide linked to a hairpin RNA oligonucleotide, wherein: the antisense RNA oligonucleotide comprises a region complementary to an RNA molecule comprising the target nucleotide; the N-peptide and hairpin interact; and the deaminase domain causes editing of the target nucleotide to induce a base change. [00348] 2C.
  • a method of treating a disease or disorder by editing a target nucleotide within an RNA molecule in a cell comprising contacting the cell with: (i) a deaminase linked to a lamboid P21 bacteriophage N-peptide, and (ii) an antisense RNA oligonucleotide linked to a hairpin RNA oligonucleotide, wherein: the antisense RNA oligonucleotide comprises a region complementary to an RNA molecule comprising the target nucleotide; the N-peptide and hairpin interact; and the deaminase domain causes editing of the target nucleotide to induce a base change. [00349] 3C.
  • deaminase is cytidine deaminase or adenosine deaminase.
  • deaminase is cytidine deaminase or adenosine deaminase.
  • adenosine deaminase yields a uracil (U) nucleotide.
  • U uracil
  • adenosine deaminase is selected from adenosine deaminase RNA specific 1 (ADAR1), adenosine deaminase RNA specific 2 (ADAR2), adenosine deaminase RNA specific B1 (ADARB1), adenosine deaminase like (ADAL), adenosine deaminase 2 (ADA2), adenosine monophosphate deaminase 1 (AMPD1), adenosine Attorney Docket No.: 33791/41005 monophosphate deaminase 2 (AMPD2), adenosine monophosphate deaminase 3 (AMPD3), adenosine deaminase domain containing 1 (ADAD1), adenosine deaminase domain containing 2 (ADAD2), adenosine deaminaminaminamina
  • the ADAR1 or ADAR2 comprises a fragment that comprises a catalytic domain.
  • the catalytic domain is the deaminase domain of human ADAR2, comprising an amino acid sequence having at least 90% sequence identity with SEQ ID NO: 18.
  • the ADAR2 comprises the amino acid sequence of SEQ ID NO: 19.
  • [00358] 12C is the amino acid sequence of SEQ ID NO: 19.
  • the ADAR induces a cytidine (C) to uridine (U) nucleotide mutation
  • the ADAR comprises one or more mutations that allow the ADAR to induce the C to U nucleotide mutation
  • the ADAR mutation(s) is selected from a substitution at one or more positions E396, C451, V351, R455, T375, K376, S486, Q488, R510, K594, R348, G593, S397, H443, L444, Y445, F442, E438, T448, A353, V355, T339, P539, V525 and I520, optionally relative to SEQ ID NO: 18 or SEQ ID NO: 19.
  • the P21 N-peptide is the wild-type amino-terminal domain P21 N-peptide and comprises the amino acid sequence of SEQ ID NO: 95.
  • 19C The method of any one of the preceding paragraphs, wherein the amino-terminal domain P21 N-peptide comprises an arginine-rich motif.
  • 20C The method of any one of the preceding paragraphs, wherein the amino-terminal domain P21 N-peptide comprises an Ala at position 5 and an arginine at each of positions 8, 12, and 13 of SEQ ID NO: 95. [00367] 21C.
  • the amino-terminal domain P21 N-peptide variant comprises at least one mutation as compared to the wild type amino-terminal domain P21 N-peptide.
  • the mutation is selected from one or more of an amino acid substitution, deletion, and addition.
  • 23C The method of any one of the preceding paragraphs, wherein the amino-terminal domain P21 N-peptide variant comprises from 1 to 21 amino acid residue substitutions. [00370] 24C.
  • hydrophilic amino acid is selected from a polar and positively charged hydrophilic amino acid, a polar and neutral of charge hydrophilic amino acid, and polar and negatively charged hydrophilic amino acid, and an aromatic, polar and positively charged hydrophilic amino acid.
  • the polar and positively charged hydrophilic amino acid is arginine (R) or lysine (K).
  • hydrophobic amino acid is selected from a hydrophobic, aliphatic amino acid and a hydrophobic, aromatic amino acid.
  • hydrophobic, aliphatic amino acid is glycine (G), alanine (A), leucine (L), isoleucine (I), methionine (M), or valine (V).
  • hydrophobic, aromatic amino acid is phenylalanine (F), tryptophan (W), or tyrosine (Y).
  • non-classical amino acid is selected from selenocysteine, pyrrolysine, N-formylmethionine ⁇ -alanine, GABA, ⁇ - Attorney Docket No.: 33791/41005 Aminolevulinic acid, 4-Aminobenzoic acid (PABA), D-isomers of the common amino acids, 2,4- diaminobutyric acid, ⁇ -amino isobutyric acid, 4-aminobutyric acid, Abu, 2-amino butyric acid, ⁇ -Abu, ⁇ - Ahx, 6-amino hexanoic acid, Aib, 2-amino isobutyric acid, 3-amino propionic acid, ornithine, norleucine, norvaline, hydroxyproline, sarcosme, citrulline, homocitrulline, cysteic acid, t-butylglycine, t-butyla
  • any one of the preceding paragraphs wherein the bacteriophage N- peptide is linked to at least 2, at least 3, or at least 4 deaminases.
  • 45C The method of any one of the preceding paragraphs, wherein the deaminase and the lambdoid bacteriophage N-peptide comprise a nuclear localization signal.
  • 46C The method of any one of the preceding paragraphs, wherein the deaminase and the lambdoid bacteriophage N-peptide comprise a nuclear localization signal and the RNA molecule comprising the target nucleotide is in the nucleus of the cell.
  • 47C The method of any one of the preceding paragraphs, wherein the bacteriophage N- peptide is linked to at least 2, at least 3, or at least 4 deaminases.
  • the nuclear localization signal is the SV40 Large T-antigen nuclear localization signal.
  • 48C The method of any one of the preceding paragraphs, wherein SV40 Large T-antigen nuclear localization signal comprises the amino acid sequence of SEQ ID NO: 21.
  • 49C The method of any one of the preceding paragraphs, wherein the antisense RNA nucleotide hybridizes with a wild-type target sequence in an endogenous RNA and comprises a target nucleotide to be edited.
  • the target nucleotide to be edited induces a beneficial mutation in the wild-type target sequence.
  • 51C The method of any one of the preceding paragraphs, wherein the antisense RNA nucleotide hybridizes with a mutant target sequence in an endogenous RNA and comprises a target nucleotide to be edited.
  • Attorney Docket No.: 33791/41005 [00398] 52C.
  • the method of any one of the preceding paragraphs, wherein the target nucleotide to be edited eliminates a detrimental mutation in the mutant target sequence.
  • 53C The method of any one of the preceding paragraphs, wherein the target nucleotide is a genetic mutation associated with a genetic disease or disorder.
  • 54C The method of any one of the preceding paragraphs, wherein the target nucleotide is a genetic mutation associated with a genetic disease or disorder.
  • the antisense RNA oligonucleotide has perfect base-pairing complementarity with the RNA molecule comprising the target nucleotide.
  • the antisense RNA oligonucleotide comprises a one or more mismatches with the RNA molecule comprising the target nucleotide.
  • the antisense RNA oligonucleotide sequence comprises from 1 to 15 mismatches, e.g.
  • the hairpin RNA oligonucleotide is located from about 2-20 nucleotide residues 3' of the target mutation.
  • 66C The method of any one of the preceding paragraphs, wherein the hairpin RNA oligonucleotide is a BoxB hairpin RNA oligonucleotide.
  • 67C The method of any one of the preceding paragraphs, wherein the BoxB hairpin RNA oligonucleotide is the cognate hairpin oligonucleotide of the N-peptide.
  • 68C The method of any one of the preceding paragraphs, wherein the hairpin RNA oligonucleotide is located from about 2-20 nucleotide residues 3' of the target mutation.
  • the BoxB hairpin RNA oligonucleotide comprises a nucleic acid sequence of any one of SEQ ID NOs: 96-97, or variants thereof.
  • the P21 N peptide interacts with a P21 BoxB hairpin RNA oligonucleotide comprising the nucleic acid sequence of SEQ ID NO: 96 or SEQ ID NO: 97, or variant thereof.
  • 70C the P21 BoxB hairpin RNA oligonucleotide
  • the P21 BoxB hairpin RNA oligonucleotide comprises the nucleic acid sequence of SEQ ID NO: 96 or SEQ ID NO: 97, and further comprises from 1 to 20 nucleotide mutations selected from one or more of nucleotide substitutions, nucleotide deletions, and nucleotide additions.
  • the one or more nucleotide mutations take(s) place at one or more of nucleotide residue positions 1 to 20, relative to the wild type P21 BoxB hairpin RNA oligonucleotide.
  • 74C The method of any one of the preceding paragraphs, wherein the one or more nucleotide mutations take(s) place at one or more of nucleotide residue positions 1 to 20, relative to the wild type P21 BoxB hairpin RNA oligonucleotide.
  • the viral vector is an adeno-associated virus (AAV) vector.
  • AAV vector is selected from AAV1, or AAV2, or AAV3, or AAV4, or AAV5, or AAV6, or AAV7, or AAV8, or AAV9, or AAV10, or AAV11, and AAV12.

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Abstract

The present disclosure provides, in part, compositions and methods comprising nucleic acid editing complexes and uses thereof, as well as methods of treatment for diseases and disorders originating from genetic mutations.

Description

Attorney Docket No.: 33791/41005 LAMBDA N-BASED COMPOSITIONS AND METHODS FOR NUCLEIC ACID EDITING FIELD OF THE DISCLOSURE [0001] The present disclosure relates to the field of nucleic acid editing. Specifically, the present disclosure provides, in part, compositions and methods comprising nucleic acid editing complexes and uses thereof, as well as methods of treatment for diseases, conditions and disorders originating from genetic mutations. INCORPORATION BY REFERENCE OF MATERIAL SUBMITTED ELECTRONICALLY [0002] This application contains, as a separate part of the disclosure, a Sequence Listing in computer- readable form which is incorporated by reference in its entirety and identified as follows: 41005_SeqListing.xml; Size: 135,417 bytes; Created: February 11, 2025. BACKGROUND [0003] The process of RNA editing alters the nucleotide sequences of RNA transcripts (e.g., messenger RNAs) once they are synthesized and thereby changes the coded message the mRNA transcript carries. In animals, two principal types of mRNA editing occur: the deamination of adenosine to produce inosine (A-to-I editing) and, less frequently, the deamination of cytosine to produce uracil (C-to-U editing). In the former, the resulting inosine is read as guanosine by translation machinery. If the edit occurs in a coding region, it can have a profound impact on downstream processes, such as changing the amino acids of the protein or producing a truncated protein by creating a premature stop codon, thereby affecting the protein’s structure and function. Edits that occur outside coding sequences can affect the pattern of pre-mRNA splicing, the transport of mRNA from the nucleus to the cytosol, the efficiency with which the RNA is translated, or the base-pairing between microRNAs (miRNAs) and their mRNA targets. [0004] The process of A-to-I editing is particularly prevalent in humans, where it occurs in approximately 1,000 genes. Enzymes called ADARs (adenosine deaminases acting on RNA) perform this type of editing. Endogenously, these enzymes recognize double-stranded RNA structures that are formed through base-pairing between the site to be edited and a complementary sequence located elsewhere on the same RNA molecule, typically in an intron. The structure of the double-stranded RNA specifies whether the mRNA is to be edited, and if so, where the edit should be made. C-to-U editing, which is carried out by a different set of enzymes is also crucial in mammals. Attorney Docket No.: 33791/41005 [0005] Advances in the field have led to the development of technologies that harness the power of nucleic acid-editing enzymes by way of editing or altering specific nucleobases in RNA and DNA of cells. However, there is still a need in the field for gene editing strategies for the purpose of therapeutically targeting and correcting genetic mutations that give rise to genetic diseases, conditions and disorders. Furthermore, there remains the need for nucleic acid-editing processes that yield lower off-target mutations, such as those resulting from technologies involving nuclease activities (e.g., CRISPR). [0006] Though site-specific RNA editing strategies have progressed in the field and look promising, challenges remain with regards to various RNA editing systems known in the art. See, Vogel and Stafforst, “Critical review on engineering deaminases for site-directed RNA editing,” Current Opinion in Biotech 55 (2019) at 75-76. Accordingly, there remains the need for enhanced RNA-editing systems. SUMMARY OF THE DISCLOSURE [0007] Accordingly, the present disclosure provides, in part, compositions and methods for site- specific editing of a target nucleotide (e.g., within an RNA molecule) in a cell. Such compositions and methods, in various embodiments, provide increased efficiency and/or specificity of nucleic acid editing than which is provided in present systems. Further, such compositions and methods, in various embodiments, provide for nucleotide changes which are reversible and tunable in nature. Without wishing to be bound by theory, this limited duration of effect reduces a likelihood of danger related to harmful off- site editings, and tunability allows continuous adjustment of the effect in a dose-dependent manner, to mitigate or eliminate adverse effects. Further still, the present disclosure allows for manipulation of cellular pathways and processes of which permanent manipulation would have serious health consequences. Importantly, in various embodiments, the present disclosure allows for genetic manipulation that is nuclease-free and spares the genetic information encoded in DNA. Stated another way, in embodiments, the present disclosure allows for genetic manipulation that is not DNA level and therefore less likely to cause a permanent effect (e.g. avoids an adverse outcome at the DNA level). [0008] In aspects, the present compositions and methods provide for targeted enzymatic functionality that supports editing of a target nucleotide combined with targeted nucleic acid specificity that locates the enzymatic functionality to the target nucleotide. [0009] In aspects, fusion proteins of a deaminase linked to a mutant λ (also referred to as “lambda” herein) N-peptide, a lamboid P22 bacteriophage N-peptide, or a lamboid P21 bacteriophage N-peptide are provided. In embodiments, these fusion proteins find use in efficient and/or specific base editing. In some Attorney Docket No.: 33791/41005 embodiments, the present disclosure relates to a fusion protein between a deaminase, such as an ADAR, or the catalytic domain thereof, linked to a mutant λ N-peptide, a lamboid P22 bacteriophage N-peptide, or a lamboid P21 bacteriophage N-peptide. In various embodiments, the fusion protein is capable of specifically interacting with a hairpin (e.g., a hairpin RNA) oligonucleotide. [0010] In aspects, methods described herein comprise contacting a cell with a deaminase linked to a mutant λ N-peptide, a lamboid P22 bacteriophage N-peptide, or a lamboid P21 bacteriophage N-peptide, and an antisense RNA oligonucleotide linked to a hairpin (e.g., a hairpin RNA) oligonucleotide. In some embodiments, the hairpin RNA oligonucleotide is the cognate hairpin oligonucleotide of the mutant λ N- peptide. For example, the cognate hairpin oligonucleotide can be a BoxB hairpin RNA oligonucleotide. In some embodiments, the antisense RNA oligonucleotide comprises a region complementary to an RNA molecule comprising the target nucleotide. In further embodiments, the mutant N-peptide and hairpin oligonucleotide interact, and the deaminase domain causes editing of the target nucleotide to induce a base change. [0011] The disclosure also provides methods for treating diseases, conditions and/or disorders that manifest from genetic mutation(s). Accordingly, methods of treating a disorder, condition or disease by editing a target nucleotide within an RNA molecule in a cell include contacting a cell with a deaminase linked to a mutant λ N-peptide, a lamboid P22 bacteriophage N-peptide, or a lamboid P21 bacteriophage N- peptide, and an antisense RNA oligonucleotide linked to a hairpin (e.g., a hairpin RNA) oligonucleotide. In some embodiments, the hairpin RNA oligonucleotide is the cognate hairpin of the mutant λ N-peptide. For example, the cognate hairpin can be a BoxB hairpin RNA oligonucleotide. In some embodiments, the antisense RNA oligonucleotide comprises a region complementary to an RNA molecule comprising the target nucleotide. In further embodiments, the mutant λ N-peptide, a lamboid P22 bacteriophage N- peptide, or a lamboid P21 bacteriophage N-peptide and hairpin interact, and the deaminase domain causes editing of the target nucleotide to induce a base change. [0012] Methods described herein further contemplate adenosine or cytidine deaminases, wherein a cytidine deaminase may yield a uridine nucleotide upon inducing a cytidine (C) to uridine (U) nucleotide change. In some embodiments, an adenosine deaminase induces a cytidine (C) to uridine (U) nucleotide change. In various embodiments, the adenosine or cytidine deaminase is a fragment comprising the catalytic domain of the adenosine or cytidine deaminase. In further embodiments, the fragment comprises Attorney Docket No.: 33791/41005 a catalytic domain and one or more mutations. In still further embodiments, the adenosine deaminase is selected from ADAR1 and ADAR2, or fragments or variants thereof. [0013] In various embodiments, the mutant λ N-peptide is derived from the λ lambdoid bacteriophage N protein. In some embodiments, the λ N-peptide is the wild-type amino-terminal domain λ N-peptide and comprises the amino acid sequence of SEQ ID NO: 1. In some embodiments, the λ N-peptide is a mutant of the wild-type amino-terminal domain λ N-peptide and comprises at least one mutation as compared to the wild-type amino-terminal domain λ N-peptide (SEQ ID NO: 1). For example, the mutant λ N-peptide can comprise from 1 to 21 amino acid residue substitutions, as compared to the wild-type λ N-peptide. In various embodiments, such mutations increase the binding affinity of the mutant λ N-peptide to its hairpin, as compared to the binding affinity of the wild-type λ N-peptide to its hairpin. [0014] For example, the mutant λ N-peptide can comprise from 1 to 21 amino acid residue substitutions, as compared to the wild-type λ N-peptide. In various embodiments, such mutations increase the binding affinity of the mutant λ N-peptide to its hairpin, as compared to the binding affinity of the wild- type λ N-peptide to its hairpin. [0015] In various embodiments, the deaminase and the mutant λ N-peptide are a fusion protein, optionally connected by a chemical linker. By way of non-limiting example, the deaminase can be linked to at least 2, at least 3, at least 4, at least 5, at least 6, or at least 7 mutant λ N-peptides. In some embodiments, the deaminase and the mutant λ N-peptide comprise a nuclear localization signal, optionally wherein the RNA molecule comprising the target nucleotide is in the nucleus of the cell. In further embodiments, the nuclear localization signal is the SV40 Large T-antigen nuclear localization signal. [0016] In various embodiments, the P22 N-peptide is a variant that is the wild-type amino-terminal domain P22 N-peptide and comprises the amino acid sequence of SEQ ID NO: 2. In various embodiments, the amino-terminal domain P22 N-peptide comprises an arginine-rich motif. In various embodiments, the amino-terminal domain P22 N-peptide comprises an Ala at position 5 and an arginine at each of positions 8, 12, and 13 of SEQ ID NO: 2. In various embodiments, the amino-terminal domain P22 N-peptide variant comprises at least one mutation as compared to the wild type amino-terminal domain P22 N-peptide. In various embodiments, the amino-terminal domain P22 N-peptide variant comprises from 1 to 21 amino acid residue substitutions. In various embodiments, the amino acid substitution takes place at one or more of amino acid residue positions 1 to 21, relative to the wild type amino-terminal domain P22 N-peptide sequence (SEQ ID NO: 2). In various embodiments, the amino-terminal domain P22 N-peptide variant Attorney Docket No.: 33791/41005 comprises the amino acid sequence of any one of SEQ ID NO: 10 to SEQ ID NO: 34. In various embodiments, such mutations increase the binding affinity of the P22 N-peptide variant for the BoxB hairpin RNA, as compared to the binding affinity of the wild type P22 N-peptide for the BoxB hairpin RNA. [0017] In various embodiments, the P12 N-peptide is the wild-type amino-terminal domain P21 N- peptide and comprises the amino acid sequence of SEQ ID NO: 3. In various embodiments, the amino- terminal domain P21 N-peptide comprises an arginine-rich motif. In various embodiments, the amino- terminal domain P21 N-peptide comprises an Ala at position 5 and an arginine at each of positions 8, 12, and 13 of SEQ ID NO: 3. In various embodiments, the amino-terminal domain P21 N-peptide variant comprises at least one mutation as compared to the wild type amino-terminal domain P21 N-peptide. In various embodiments, the amino-terminal domain P21 N-peptide variant comprises from 1 to 21 amino acid residue substitutions. In various embodiments, the amino acid substitution takes place at one or more of amino acid residue positions 1 to 21, relative to the wild type amino-terminal domain P21 N-peptide sequence (SEQ ID NO: 3). In various embodiments, the amino-terminal domain P21 N-peptide variant comprises one or more mutations at positions R13 and I17 of SEQ ID NO: 3. In various embodiments, such mutations increase the binding affinity of the P21 N-peptide variant for the BoxB hairpin RNA, as compared to the binding affinity of the wild type P21 N-peptide for the BoxB hairpin RNA. [0018] Methods described herein further contemplate an antisense RNA oligonucleotide that hybridizes with a wild-type or mutant target sequence in an endogenous RNA molecule that comprises a target nucleotide to be edited. In some embodiments of the present disclosure, the target nucleotide to be edited induces a beneficial mutation in the wild-type target sequence. In some embodiments, the target nucleotide to be edited eliminates a detrimental mutation in the mutant target sequence. For example, the target nucleotide can be a genetic mutation associated with a genetic disease, condition or disorder. [0019] In some embodiments, the mutant λ N-peptide interacts with a hairpin (e.g., a hairpin RNA, where there is hairpin recognition of the λ N-peptide) oligonucleotide. In some embodiments, the hairpin RNA oligonucleotide is the cognate hairpin of λ N-peptide. By way of non-limitation, the cognate hairpin can be a BoxB hairpin RNA oligonucleotide. In some embodiments, the BoxB hairpin RNA oligonucleotide is located from about 2-20 nucleotide residues 5’ of the target mutation. In some embodiments, the BoxB hairpin RNA oligonucleotide is located from about 2-20 nucleotide residues 3’ of the target mutation. [0020] In further embodiments, such components described herein are synthetically generated or generated from a plasmid. In still further embodiments, the components are contained within a plasmid or Attorney Docket No.: 33791/41005 vector, optionally wherein the vector is a viral vector. Such viral vectors can include, but are not limited to, adeno-associated viruses (AAVs), adenoviruses, retroviruses, and lentiviruses. In further embodiments, the present disclosure contemplates the use of mRNA and/or lipid nanoparticles for delivery of the components of the nucleic acid-editing system to a cell. DESCRIPTION OF THE DRAWINGS [0021] Figure 1 is a schematic that depicts an illustrative, non-limiting example of the embodiments of the present disclosure. The figure depicts editing of a target nucleotide within an RNA molecule, mediated by (i) a deaminase linked to a lambdoid bacteriophage N-peptide, and (ii) an antisense RNA oligonucleotide linked to a hairpin RNA oligonucleotide, wherein the lambdoid bacteriophage N-peptide interacts with the hairpin RNA oligonucleotide. [0022] Figure 2 is a schematic that depicts an illustrative, non-limiting example of the embodiments of the present disclosure. The figure depicts editing of a target nucleotide within a disease target, mediated by (i) a deaminase domain linked to a lambdoid bacteriophage N-peptide, and (ii) an antisense 2boxB guide RNA oligonucleotide linked to a hairpin RNA oligonucleotide, wherein the lambdoid bacteriophage N- peptide interacts with the hairpin RNA oligonucleotide. DETAILED DESCRIPTION OF THE DISCLOSURE [0023] The present disclosure provides, in part, compositions and methods for site-specific editing of a target nucleotide (e.g., within an endogenous RNA molecule) in a cell. Specifically, in embodiments, the fusion of a deaminase, such as (without limitation) an ADAR, or the catalytic domain thereof, with a mutant λ N-peptide, allows for nucleic acid editing that is specific and not substantially hindered by off-target effects, while also allowing for a transient and tunable effect. [0024] Accordingly, the compositions and methods of the present disclosure permit alteration of the genetic code in a therapeutically beneficial manner. [0025] In aspects, methods described herein comprise (a) contacting a cell with (i) a deaminase linked to a mutant λ N-peptide, and (ii) an antisense RNA oligonucleotide linked to a hairpin (e.g., a hairpin RNA) oligonucleotide. In some embodiments, the hairpin RNA oligonucleotide is the cognate hairpin of the λ N- peptide. For example, the cognate hairpin can be a BoxB hairpin RNA oligonucleotide. In other aspects, methods described herein comprise (a) contacting a cell with (i) a deaminase linked to a lambdoid bacteriophage N-peptide, and (ii) an antisense RNA oligonucleotide linked to a hairpin (e.g., a hairpin RNA) Attorney Docket No.: 33791/41005 oligonucleotide. In some embodiments, the hairpin RNA oligonucleotide is the cognate hairpin of the N- peptide. For example, the cognate hairpin can be a BoxB hairpin RNA oligonucleotide. In some embodiments, the lambdoid bacteriophage is P22 or P21. [0026] In some embodiments, the antisense RNA oligonucleotide comprises a region complementary to an RNA molecule comprising the target nucleotide. In further embodiments, the N-peptide and hairpin interact, and the deaminase domain causes editing of the target nucleotide. [0027] In some embodiments, the antisense RNA oligonucleotide comprises a region complementary to an RNA molecule comprising the target nucleotide. In further embodiments, the λ N-peptide and hairpin interact, and the deaminase domain causes editing of the target nucleotide. [0028] The disclosure further provides methods for treating diseases, conditions and/or disorders that manifest from genetic mutation(s). Accordingly, methods of treating a disorder, conditions or disease by editing a target nucleotide within an RNA molecule in a cell include contacting a cell with a deaminase linked to a mutant λ N-peptide, lamboid P21 N-peptide, or lamboid P22 N-peptide, and an antisense RNA oligonucleotide linked to a hairpin (e.g., hairpin RNA) oligonucleotide. In some embodiments, the hairpin RNA oligonucleotide is the cognate hairpin of the λ N-peptide, lamboid P21 N-peptide, or lamboid P22 N- peptide. For example, the cognate hairpin can be a BoxB hairpin RNA oligonucleotide sequence. In some embodiments, the antisense RNA oligonucleotide comprises a region complementary to an RNA molecule comprising the target nucleotide. In further embodiments, the λ N-peptide, lamboid P21 N-peptide, or lamboid P22 N-peptide and hairpin interact, and the deaminase domain causes editing of the target nucleotide to induce a base change. [0029] In certain embodiments, the disclosure provides a method of site-specific editing of a target nucleotide within an RNA molecule in a cell comprising: (a) contacting the cell with: (i) a deaminase linked to a mutant λ N-peptide, lamboid P21 N-peptide, or lamboid P22 N-peptide, and (ii) an antisense RNA oligonucleotide linked to a BoxB hairpin RNA oligonucleotide, the BoxB hairpin RNA oligonucleotide being the cognate hairpin oligonucleotide of the λ N-peptide, lamboid P21 N-peptide, or lamboid P22 N-peptide, and wherein: the antisense RNA oligonucleotide comprises a region complementary to an RNA molecule comprising the target nucleotide; the λ N-peptide, lamboid P21 N-peptide, or lamboid P22 N-peptide and BoxB hairpin RNA oligonucleotide interact; and the deaminase domain causes editing of the target nucleotide to induce a base change. Attorney Docket No.: 33791/41005 [0030] In certain embodiments, the present disclosure contemplates a method of treating a disease, condition or disorder by editing of a target nucleotide within an RNA molecule in a cell comprising: (a) contacting the cell with: (i) a deaminase linked to a mutant λ N-peptide, lamboid P21 N-peptide, or lamboid P22 N-peptide, and (ii) an antisense RNA oligonucleotide linked to a BoxB hairpin RNA oligonucleotide, the BoxB hairpin RNA oligonucleotide being the cognate hairpin of the λ N-peptide, lamboid P21 N-peptide, or lamboid P22 N-peptide, and wherein: the antisense RNA oligonucleotide comprises a region complementary to an RNA molecule comprising the target nucleotide; the λ N-peptide, lamboid P21 N- peptide, or lamboid P22 N-peptide and BoxB hairpin RNA oligonucleotide interact; and the deaminase domain causes editing of the target nucleotide to induce a base change. A. Nucleic Acid-Editing Enzymes and Deaminase Domains [0031] Some embodiments of this disclosure provide strategies, systems, reagents, and methods that are useful for the targeted editing of nucleic acids, including editing a single site within a subject's genome, e.g., the human genome. In some embodiments, nucleic acid editing enzymes or enzyme domains, e.g., deaminase domains, are provided. Methods of the present disclosure further contemplate the use of adenosine and/or cytidine deaminases, wherein a cytidine deaminase may yield a uridine nucleotide upon inducing a cytidine (C) to uridine (U) nucleotide change. In some embodiments, an adenosine deaminase induces a cytidine (C) to uridine (U) nucleotide change. [0032] In some embodiments, the nucleic acid-editing domain is an RNA-editing domain. In some embodiments, the nucleic acid-editing domain is a deaminase domain. In some embodiments, the deaminase is an adenosine deaminase. For example, the deaminase can be selected from adenosine deaminase, RNA specific (ADAR), adenosine deaminase, RNA specific 2 (ADAR2), adenosine deaminase, RNA specific B1 (ADARB1), adenosine deaminase like (ADAL), adenosine deaminase 2 (ADA2), adenosine monophosphate deaminase 1 (AMPD1), adenosine monophosphate deaminase 2 (AMPD2), adenosine monophosphate deaminase 3 (AMPD3), adenosine deaminase domain containing 1 (ADAD1), adenosine deaminase domain containing 2 (ADAD2), adenosine deaminase, tRNA specific 1 (ADAT1), adenosine deaminase, tRNA specific 2 (ADAT2), adenosine deaminase, tRNA specific 3 (ADAT3), TadA or fragments or variants thereof. In some embodiments, the deaminase is an AD AT family deaminase. In various embodiments, adenosine deaminase of the present disclosure is a fragment comprising the catalytic domain of the adenosine deaminase. In further embodiments, the fragment comprises a catalytic domain and one or more mutations. For example, the fragment or variant of the adenosine deaminase can Attorney Docket No.: 33791/41005 comprise an amino acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity with the adenosine deaminase amino acid sequences provided herein. In some embodiments, the fragment is the catalytic domain of the deaminase. In further embodiments, the deaminase comprises any isoform thereof, such as those known in the art (e.g., ADAR comprises two isoforms: ADAR1p150 and ADAR1p110). Non- limiting examples of adenosine deaminases can be found throughout Y. Savva et al., Genome Biology (2012) 13:252, which is hereby incorporated by reference in its entirety. [0033] In some embodiments, the adenosine deaminase comprises an amino acid sequence modified by one or more mutations at one or more positions selected from E396, C451, V351, R455, T375, K376, S486, Q488, R510, K594, R348, G593, S397, H443, L444, Y445, F442, E438, T448, A353, V355, T339, P539, V525 and I520. In some embodiments, the adenosine deaminase comprises an amino acid sequence modified by one or more mutations at one or more positions selected from E396X, C451X, V351X, R455X, T375X, K376X, S486X, Q488X, R510X, K594X, R348X, G593X, S397X, H443X, L444X, Y445X, F442X, E438X, T448X, A353X, V355X, T339X, P539X, V525X and I520X, wherein X is selected from arginine (R), lysine (K), asparagine (N), glutamine (Q), serine (S), threonine (T), proline (P), cysteine (C), aspartate (D), glutamate (E), histidine (H), glycine (G), alanine (A), leucine (L), isoleucine (I), methionine (M), valine (V), phenylalanine (F), tryptophan (W), and tyrosine (Y). According to embodiments of the present disclosure, a substituted amino acid residue is any naturally-occurring amino acid, such as a hydrophilic, hydrophobic, or non-classical amino acid. The hydrophilic amino acid can be selected from a polar and positively charged hydrophilic amino acid, a polar and neutral of charge hydrophilic amino acid, and polar and negatively charged hydrophilic amino acid, and an aromatic, polar and positively charged hydrophilic amino acid. A polar and positively charged hydrophilic amino acid can be selected from arginine (R) and lysine (K). A polar and neutral of charge hydrophilic amino acid can be selected from asparagine (N), glutamine (Q), serine (S), threonine (T), proline (P), and cysteine (C). A polar and negatively charged hydrophilic amino acid can be selected from aspartate (D) and glutamate (E). An aromatic, polar and positively charged hydrophilic amino acid can be histidine (H). A hydrophobic amino acid can be selected from a hydrophobic, aliphatic amino acid and a hydrophobic, aromatic amino acid. The hydrophobic, aliphatic amino acid can be glycine (G), alanine (A), leucine (L), isoleucine (I), methionine (M), or valine (V). A hydrophobic, aromatic amino acid can be phenylalanine (F), tryptophan (W), or tyrosine (Y). A non-classical amino acid can be selected from selenocysteine, pyrrolysine, N- formylmethionine β-alanine, GABA, δ-Aminolevulinic acid, 4-Aminobenzoic acid (PABA), D-isomers of the Attorney Docket No.: 33791/41005 common amino acids, 2,4-diaminobutyric acid, α-amino isobutyric acid, 4-aminobutyric acid, Abu, 2-amino butyric acid, γ-Abu, ε-Ahx, 6-amino hexanoic acid, Aib, 2-amino isobutyric acid, 3-amino propionic acid, ornithine, norleucine, norvaline, hydroxyproline, sarcosme, citrulline, homocitrulline, cysteic acid, t- butylglycine, t-butylalanine, phenylglycine, cyclohexylalanine, β-alanine, fluoroamino acids, designer amino acids such as β methyl amino acids, C α-methyl amino acids, N α -methyl amino acids, and amino acid analogs in general.In such embodiments, the adenosine deaminase is modified to convert activity to that of a cytidine deaminase. In some embodiments, an adenosine deaminase induces a cytidine (C) to uridine (U) nucleotide change. [0034] In various embodiments, the adenosine deaminase of the present disclosure is adenosine deaminase, RNA specific 2 (ADAR2). For example, the ADAR2 deaminase can comprise a fragment that comprises a catalytic domain, wherein the catalytic domain is the deaminase domain of human ADAR2 (SEQ ID NO: 18), shown below: LHLDQTPSRQPIPSEGLQLHLPQVLADAVSRLVLGKFGDLTDNFSSPHA RRKVLAGVVMTTGTDVKDAKVISVSTGTKCINGEYMSDRGLALNDCHAE IISRRSLLRFLYTQLELYLNNKDDQKRSIFQKSERGGFRLKENVQFHLY ISTSPCGDARIFSPHEPILEEPADRHPNRKARGQLRTKIESGEGTIPVR SNASIQTWDGVLQGERLLTMSCSDKIARWNVVGIQGSLLSIFVEPIYFS SIILGSLYHGDHLSRAMYQRISNIEDLPPLYTLNKPLLSGISNAEARQP GKAPNFSVNWTVGDSAIEVINATTGKDELGRASRLCKHALYCRWMRVHG KVPSHLLRSKITKPNVYHESKLAAKEYQAAKARLFTAFIKAGLGAWVEK PTEQDQFSLTP (SEQ ID NO: 18). [0035] In further embodiments, the ADAR2 fragment comprises a catalytic domain and one or more mutations. For example, the fragment or variant of ADAR2 can comprise an amino acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity with the amino acid sequence of SEQ ID NO: 18. In further embodiments, the catalytic domain is the deaminase domain of human ADAR2 comprising an amino acid sequence having at least 90% sequence identity with the amino acid sequence of SEQ ID NO: 18. In some embodiments, the ADAR2 comprises the amino acid sequence of SEQ ID NO: 18. [0036] In still further embodiments, the ADAR2 comprises an amino acid sequence comprising a mutation of V351G with respect to SEQ ID NO: 18. In such embodiments, the V351G mutation allows the ADAR2 to induce a cytidine (C) to uridine (U) nucleotide change. In some embodiments, the fragment or Attorney Docket No.: 33791/41005 variant of ADAR2 comprises an amino acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity with the amino acid sequence of SEQ ID NO: 19, as shown below: LHLDQTPSRQPIPSEGLQLHLPQVLADAVSRLVLGKFGDLTDNFSSPHA RRKGLAGVVMTTGTDVKDAKVISVSTGTKCINGEYMSDRGLALNDCHAE IISRRSLLRFLYTQLELYLNNKDDQKRSIFQKSERGGFRLKENVQFHLY ISTSPCGDARIFSPHEPILEEPADRHPNRKARGQLRTKIESGEGTIPVR SNASIQTWDGVLQGERLLTMSCSDKIARWNVVGIQGSLLSIFVEPIYFS SIILGSLYHGDHLSRAMYQRISNIEDLPPLYTLNKPLLSGISNAEARQP GKAPNFSVNWTVGDSAIEVINATTGKDELGRASRLCKHALYCRWMRVHG KVPSHLLRSKITKPNVYHESKLAAKEYQAAKARLFTAFIKAGLGAWVEK PTEQDQFSLTP (SEQ ID NO: 19, V351G emphasis added). [0037] In some embodiments, the catalytic domain is a variant deaminase domain of human ADAR2 comprising an amino acid sequence having at least 90% sequence identity with the amino acid sequence of SEQ ID NO: 19. In some embodiments, the ADAR2 comprises the amino acid sequence of SEQ ID NO: 19. In further embodiments, the ADAR2 comprising the amino acid sequence of SEQ ID NO: 19 induces a cytidine (C) to uridine (U) nucleotide change. [0038] In still further embodiments, the ADAR2 comprises an amino acid sequence comprising an addition of amino acid residues LV with respect to SEQ ID NO: 18. In some embodiments, the fragment or variant of ADAR2 comprises an amino acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity with the amino acid sequence of SEQ ID NO: 38, as shown below: LHLDQTPSRQPIPSEGLQLHLPQVLADAVSRLVLGKFGDLTDNFSSPHA RRKVLAGVVMTTGTDVKDAKVISVSTGTKCINGEYMSDRGLALNDCHAE IISRRSLLRFLYTQLELYLNNKDDQKRSIFQKSERGGFRLKENVQFHLY ISTSPCGDARIFSPHEPILEEPADRHPNRKARGQLRTKIESGEGTIPVR SNASIQTWDGVLQGERLLTMSCSDKIARWNVVGIQGSLLSIFVEPIYFS SIILGSLYHGDHLSRAMYQRISNIEDLPPLYTLNKPLLSGISNAEARQP GKAPNFSVNWTVGDSAIEVINATTGKDELGRASRLCKHALYCRWMRVHG KVPSHLLRSKITKPNVYHESKLAAKEYQAAKARLFTAFIKAGLGAWVEK Attorney Docket No.: 33791/41005 PTEQDQFSLTPLV (SEQ ID NO: 38, LV addition emphasis added). [0039] In some embodiments, the catalytic domain is a variant deaminase domain of human ADAR2 comprising an amino acid sequence having at least 90% sequence identity with the amino acid sequence of SEQ ID NO: 38. In some embodiments, the ADAR2 comprises the amino acid sequence of SEQ ID NO: 38. [0040] In some embodiments, the ADAR induces a cytidine (C) to uridine (U) nucleotide mutation. In some embodiments, the ADAR comprises one or more mutations that allow it to induce the C to U nucleotide mutation. In further embodiments, the ADAR mutation is selected from a substitution at one or more positions E396, C451, V351, R455, T375, K376, S486, Q488, R510, K594, R348, G593, S397, H443, L444, Y445, F442, E438, T448, A353, V355, T339, P539, V525 and I520 relative to SEQ ID NO: 18 or SEQ ID NO: 19. [0041] In some embodiments, the nucleic acid-editing domain is an RNA-editing domain. In some embodiments, the nucleic acid-editing domain is a deaminase domain. In some embodiments, the deaminase is a cytidine deaminase. In some embodiments, the deaminase is an apolipoprotein B niRNA- editing complex (APOBEC) family deaminase. For example, the cytidine deaminase can be selected from APOBEC1, activation-induced cytidine deaminase (AID), APOBEC2, APOBEC3A, APOBEC3B, APOBEC3C, APOBEC3D, APOBEC3E, APOBEC3F, APOBEC3G, and APOBEC3H, or fragments or variants thereof. In some embodiments, the deaminase is an APOBEC 1 family deaminase. In some embodiments, the deaminase is pmCDA1, or fragments or variants thereof. In some embodiments, the deaminase is an ACF1/ASE deaminase, or fragments or variants thereof. In some embodiments, the deaminase is an activation-induced cytidine deaminase (AID), or fragments or variants thereof. In various embodiments, cytidine deaminase of the present disclosure is a fragment comprising the catalytic domain of the cytidine deaminase. In further embodiments, the fragment comprises a catalytic domain and one or more mutations. For example, the fragment or variant of the cytidine deaminase can comprise an amino acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the cytidine deaminase amino acid sequences provided herein. In some embodiments, the fragment is the catalytic domain of the cytidine deaminase. In further embodiments, the cytidine deaminase comprises any isoform thereof, such as those known in the art. Non-limiting examples of cytidine deaminases can be found throughout Navaratnam et Attorney Docket No.: 33791/41005 al., Intl. J. of Hematology (2006) 83:3; and Salter et al., Trends Biochem Sci. (2016) 41(7): 578–594, all of which is hereby incorporated by reference in its entirety. [0042] In various embodiments, the adenosine or cytidine deaminase is a fragment comprising the catalytic domain of the adenosine or cytidine deaminase. In further embodiments, the fragment comprises a catalytic domain and one or more mutations. In some embodiments, deaminase enzyme or deaminase domain amino acid sequences of the present disclosure are variants having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the amino acid sequences provided herein. In still further embodiments, the adenosine deaminase is ADAR2, or fragments or variants thereof. Additional suitable deaminase enzymes or domains will be apparent to the skilled artisan based on this disclosure. [0043] In various embodiments, the present compositions comprise a nucleic acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the nucleic acid sequences SEQ ID NOs: 39, 41, 43, 45-52, provided in Table 4, or a codon-optimized version thereof. [0044] In some embodiments, the present compositions comprise a nucleic acid, or a codon- optimized version thereof, encoding a protein having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the amino acid sequences SEQ ID NOs: 40, 42, 44, provided in Table 4. [0045] In various embodiments, the present compositions comprise an amino acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the amino acid sequences SEQ ID NOs: 40, 42, 44, provided in Table 4. [0046] In various embodiments, the present compositions comprise a nucleic acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the nucleic acid sequences SEQ ID NOs: 98, 100, 102, 104, 106, or 108, provided in Table 8, or a codon-optimized version thereof. [0047] In some embodiments, the present compositions comprise a nucleic acid, or a codon- optimized version thereof, encoding a protein having at least 70%, at least 75%, at least 80%, at least 85%, Attorney Docket No.: 33791/41005 at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the amino acid sequences SEQ ID NOs: 99, 101, 103, 105, or 107 provided in Table 8. [0048] In various embodiments, the present compositions comprise an amino acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the amino acid sequences SEQ ID NOs: 99, 101, 103, 105, or 107 provided in Table 8. [0049] In various embodiments, the present compositions comprise a nucleic acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the nucleic acid sequences SEQ ID NOs: 98, 100, 102, 104, 106, or 108, provided in Table 8, or a codon-optimized version thereof. [0050] In some embodiments, the present compositions comprise a nucleic acid, or a codon- optimized version thereof, encoding a protein having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the amino acid sequences SEQ ID NOs: 99, 101, 103, 105, 107, or 109 provided in Table 8. [0051] In various embodiments, the present compositions comprise an amino acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the amino acid sequences SEQ ID NOs: 99, 101, 103, 105, 107, or 109 provided in Table 8. [0052] In various embodiments, the present compositions comprise a nucleic acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the nucleic acid sequences SEQ ID NOs: 81, 83, 85, 87, 89, 91, provided in Table 12, or a codon-optimized version thereof. [0053] In some embodiments, the present compositions comprise a nucleic acid, or a codon- optimized version thereof, encoding a protein having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% similarity to the amino acid sequences SEQ ID NOs: 82, 84, 86, 88, 90, or 92, provided in Table 12. [0054] In various embodiments, the present compositions comprise an amino acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least Attorney Docket No.: 33791/41005 97%, at least 98%, or at least 99% similarity to the amino acid sequences SEQ ID NOs: 82, 84, 86, 88, 90, or 92, provided in Table 12. B. λ Bacteriophage N-Peptide [0055] In various embodiments, the present disclosure contemplates a N-peptide linked to a deaminase domain, or variant thereof. In some embodiments, the N-peptide comprises a helical structure. In some embodiments, the helical peptide is a λ lambdoid bacteriophage N-peptide. In some embodiments, the present disclosure contemplates at least 2, at least 3, at least 4, at least 5, at least 6, or at least 7 N-peptides linked to a deaminase domain. [0056] In various embodiments, the mutant λ N-peptide of the present disclosure is derived from the λ lambdoid bacteriophage N protein. The lambdoid bacteriophage N proteins comprise arginine-rich motifs (ARMs) necessary for transcription antitermination that can bind to and/or interact with hairpin sequences. Without wishing to be bound by theory, various embodiments of the present disclosure contemplate that an arginine-rich motif (ARM) can bind to and/or interact with a RNA hairpin sequence (e.g., boxB RNA hairpin) with a characteristic induced α-induced helical structure. Indeed, the present disclosure contemplates that variants and/or mutant lambdoid bacteriophage N-peptides (e.g., mutant λ N-peptide) can exhibit enhanced binding affinity properties for their respective hairpin sequences compared to the wild-type phage N- peptides. [0057] In some embodiments, the λ N-peptide is the wild-type amino-terminal domain λ N-peptide and comprises the amino acid sequence of SEQ ID NO: 1: M DAQTRRRERR AEKQAQWK (SEQ ID NO: 1). [0058] In some embodiments, a λ N-peptide, and/or mutants thereof, comprises an arginine-rich motif (ARM). In further embodiments, an amino-terminal domain λ N-peptide of the present disclosure comprises an Alanine (Ala) at position 3 (respective of wild-type λ N-peptide of SEQ ID NO: 1) and an Arginine (Arg) at each of positions 6, 10, and 11 (respective of wild-type λ N-peptide of SEQ ID NO: 1). In some embodiments, the amino-terminal domain λ N-peptide is a mutant of the wild-type amino-terminal domain λ N-peptide and comprises at least one mutation as compared to the wild-type amino-terminal domain λ N- peptide. Such a mutation can be selected from one or more of an amino acid substitution, amino acid deletion, and amino acid addition. For example, a mutant amino-terminal domain λ N-peptide can comprise from 1 to 19 amino acid residue substitutions, as compared to the wild-type λ N-peptide (SEQ ID NO: 1). In Attorney Docket No.: 33791/41005 some embodiments, the mutant amino-terminal domain λ N-peptide comprises at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, or at least 19 amino acid residue substitutions, as compared to the wild-type amino-terminal domain λ N-peptide (SEQ ID NO: 1). In further embodiments, an amino acid substitution of the mutant amino-terminal domain λ N-peptide takes place at one or more of amino acid residue positions 1 to 19, relative to the wild-type amino-terminal domain λ N- peptide (SEQ ID NO: 1). In some embodiments, the mutant amino-terminal domain λ N-peptide comprises an amino acid substitution that takes place at one or more of amino acid residue positions 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or 19, as compared to the wild-type amino-terminal domain λ N- peptide (SEQ ID NO: 1). In some embodiments, a mutant amino-terminal domain λ N-peptide of the present disclosure comprises the amino acid sequence of any one of SEQ ID NO: 2 to SEQ ID NO: 9. The mutant amino-terminal domain λ N-peptide of the present disclosure can comprise the amino acid sequence of M NAQTRRRERR AEKQAQWK (SEQ ID NO: 2), M NAKTRRRERR AEKQAQWK (SEQ ID NO: 3), M NARTRRRERR AEKQAQWK (SEQ ID NO: 4), G NAKTRRRERR AEKQAQWK (SEQ ID NO: 5), G NARTRRRERR AEKQAQWK (SEQ ID NO: 6), M NAQTRRRLRR AEKQAQWK (SEQ ID NO: 7), M DAQTRARERR AEKQAQWK (SEQ ID NO: 8), or M DAQTRRRERK AEKQAQWK (SEQ ID NO: 9). [0059] In various embodiments, one or more amino acids of SEQ ID NO: 1 is substituted with a naturally occurring amino acid, such as a hydrophilic amino acid (e.g. a polar and positively charged hydrophilic amino acid, such as arginine (R) or lysine (K); a polar and neutral of charge hydrophilic amino acid, such as asparagine (N), glutamine (Q), serine (S), threonine (T), proline (P), and cysteine (C), a polar and negatively charged hydrophilic amino acid, such as aspartate (D) or glutamate (E), or an aromatic, polar and positively charged hydrophilic amino acid, such as histidine (H)) or a hydrophobic amino acid (e.g. a hydrophobic, aliphatic amino acid such as glycine (G), alanine (A), leucine (L), isoleucine (I), methionine (M), or valine (V), a hydrophobic, aromatic amino acid, such as phenylalanine (F), tryptophan (W), or tyrosine (Y) or a non-classical amino acid (e.g. selenocysteine, pyrrolysine, N-formylmethionine β- alanine, GABA and δ-Aminolevulinic acid.4-Aminobenzoic acid (PABA), D-isomers of the common amino acids, 2,4-diaminobutyric acid, α-amino isobutyric acid, 4-aminobutyric acid, Abu, 2-amino butyric acid, γ- Abu, ε-Ahx, 6-amino hexanoic acid, Aib, 2-amino isobutyric acid, 3-amino propionic acid, ornithine, norleucine, norvaline, hydroxyproline, sarcosme, citrulline, homocitrulline, cysteic acid, t-butylglycine, t- butylalanine, phenylglycine, cyclohexylalanine, β-alanine, fluoro-amino acids, designer amino acids such as Attorney Docket No.: 33791/41005 β methyl amino acids, C α -methyl amino acids, N α -methyl amino acids, and amino acid analogs in general). [0060] In some embodiments, the amino-terminal domain λ N-peptide is a mutant of the wild-type amino-terminal domain λ N-peptide and comprises at least one mutation as compared to the wild-type amino-terminal domain λ N-peptide (SEQ ID NO: 1). In further embodiments, the at least one mutation to SEQ ID NO: 1 comprises an amino acid substitution selected from any one of the following amino acid substitutions: Met1Ala; Met1Cys; Met1Asp; Met1Glu; Met1Phe; Met1Gly; Met1His; Met1Ile; Met1Lys; Met1Leu; ; Met1Asn; Met1Pro; Met1Gln; Met1Arg; Met1Ser; Met1Thr; Met1Val; Met1Trp; Met1Tyr; Asp2Ala; Asp2Cys; ; Asp2Glu; Asp2Phe; Asp2Gly; Asp2His; Asp2Ile; Asp2Lys; Asp2Leu; Asp2Met; Asp2Asn; Asp2Pro; Asp2Gln; Asp2Arg; Asp2Ser; Asp2Thr; Asp2Val; Asp2Trp; Asp2Tyr; ; Ala3Cys; Ala3Asp; Ala3Glu; Ala3Phe; Ala3Gly; Ala3His; Ala3Ile; Ala3Lys; Ala3Leu; Ala3Met; Ala3Asn; Ala3Pro; Ala3Gln; Ala3Arg; Ala3Ser; Ala3Thr; Ala3Val; Ala3Trp; Ala3Tyr; Gln4Ala; Gln4Cys; Gln4Asp; Gln4Glu; Gln4Phe; Gln4Gly; Gln4His; Gln4Ile; Gln4Lys; Gln4Leu; Gln4Met; Gln4Asn; Gln4Pro; ; Gln4Arg; Gln4Ser; Gln4Thr; Gln4Val; Gln4Trp; Gln4Tyr; Thr5Ala; Thr5Cys; Thr5Asp; Thr5Glu; Thr5Phe; Thr5Gly; Thr5His; Thr5Ile; Thr5Lys; Thr5Leu; Thr5Met; Thr5Asn; Thr5Pro; Thr5Gln; Thr5Arg; Thr5Ser; ; Thr5Val; Thr5Trp; Thr5Tyr; Arg6Ala; Arg6Cys; Arg6Asp; Arg6Glu; Arg6Phe; Arg6Gly; Arg6His; Arg6Ile; Arg6Lys; Arg6Leu; Arg6Met; Arg6Asn; Arg6Pro; Arg6Gln; ; Arg6Ser; Arg6Thr; Arg6Val; Arg6Trp; Arg6Tyr; Arg7Ala; Arg7Cys; Arg7Asp; Arg7Glu; Arg7Phe; Arg7Gly; Arg7His; Arg7Ile; Arg7Lys; Arg7Leu; Arg7Met; Arg7Asn; Arg7Pro; Arg7Gln; ; Arg7Ser; Arg7Thr; Arg7Val; Arg7Trp; Arg7Tyr; Arg8Ala; Arg8Cys; Arg8Asp; Arg8Glu; Arg8Phe; Arg8Gly; Arg8His; Arg8Ile; Arg8Lys; Arg8Leu; Arg8Met; Arg8Asn; Arg8Pro; Arg8Gln; ; Arg8Ser; Arg8Thr; Arg8Val; Arg8Trp; Arg8Tyr; Glu9Ala; Glu9Cys; Glu9Asp; ; Glu9Phe; Glu9Gly; Glu9His; Glu9Ile; Glu9Lys; Glu9Leu; Glu9Met; Glu9Asn; Glu9Pro; Glu9Gln; Glu9Arg; Glu9Ser; Glu9Thr; Glu9Val; Glu9Trp; Glu9Tyr; Arg10Ala; Arg10Cys; Arg10Asp; Arg10Glu; Arg10Phe; Arg10Gly; Arg10His; Arg10Ile; Arg10Lys; Arg10Leu; Arg10Met; Arg10Asn; Arg10Pro; Arg10Gln; ; Arg10Ser; Arg10Thr; Arg10Val; Arg10Trp; Arg10Tyr; Arg11Ala; Arg11Cys; Arg11Asp; Arg11Glu; Arg11Phe; Arg11Gly; Arg11His; Arg11Ile; Arg11Lys; Arg11Leu; Arg11Met; Arg11Asn; Arg11Pro; Arg11Gln; ; Arg11Ser; Arg11Thr; Arg11Val; Arg11Trp; Arg11Tyr; ; Ala12Cys; Ala12Asp; Ala12Glu; Ala12Phe; Ala12Gly; Ala12His; Ala12Ile; Ala12Lys; Ala12Leu; Ala12Met; Ala12Asn; Ala12Pro; Ala12Gln; Ala12Arg; Ala12Ser; Ala12Thr; Ala12Val; Ala12Trp; Ala12Tyr; Glu13Ala; Glu13Cys; Glu13Asp; ; Glu13Phe; Glu13Gly; Glu13His; Glu13Ile; Glu13Lys; Glu13Leu; Glu13Met; Glu13Asn; Glu13Pro; Glu13Gln; Glu13Arg; Glu13Ser; Glu13Thr; Glu13Val; Glu13Trp; Glu13Tyr; Lys14Ala; Lys14Cys; Lys14Asp; Lys14Glu; Lys14Phe; Lys14Gly; Lys14His; Lys14Ile; ; Lys14Leu; Lys14Met; Attorney Docket No.: 33791/41005 Lys14Asn; Lys14Pro; Lys14Gln; Lys14Arg; Lys14Ser; Lys14Thr; Lys14Val; Lys14Trp; Lys14Tyr; Gln15Ala; Gln15Cys; Gln15Asp; Gln15Glu; Gln15Phe; Gln15Gly; Gln15His; Gln15Ile; Gln15Lys; Gln15Leu; Gln15Met; Gln15Asn; Gln15Pro; ; Gln15Arg; Gln15Ser; Gln15Thr; Gln15Val; Gln15Trp; Gln15Tyr; Ala16Cys; Ala16Asp; Ala16Glu; Ala16Phe; Ala16Gly; Ala16His; Ala16Ile; Ala16Lys; Ala16Leu; Ala16Met; Ala16Asn; Ala16Pro; Ala16Gln; Ala16Arg; Ala16Ser; Ala16Thr; Ala16Val; Ala16Trp; Ala16Tyr; Gln17Ala; Gln17Cys; Gln17Asp; Gln17Glu; Gln17Phe; Gln17Gly; Gln17His; Gln17Ile; Gln17Lys; Gln17Leu; Gln17Met; Gln17Asn; Gln17Pro; ; Gln17Arg; Gln17Ser; Gln17Thr; Gln17Val; Gln17Trp; Gln17Tyr; Trp18Ala; Trp18Cys; Trp18Asp; Trp18Glu; Trp18Phe; Trp18Gly; Trp18His; Trp18Ile; Trp18Lys; Trp18Leu; Trp18Met; Trp18Asn; Trp18Pro; Trp18Gln; Trp18Arg; Trp18Ser; Trp18Thr; Trp18Val; ; Trp18Tyr; Lys19Ala; Lys19Cys; Lys19Asp; Lys19Glu; Lys19Phe; Lys19Gly; Lys19His; Lys19Ile; Lys19Leu; Lys19Met; Lys19Asn; Lys19Pro; Lys19Gln; Lys19Arg; Lys19Ser; Lys19Thr; Lys19Val; Lys19Trp; and Lys19Tyr. [0061] In some embodiments, the amino acid substitution is selected from any one of the amino acid substitutions listed in Table 1. [0062] In various embodiments, the mutant λ N-peptide sequence comprises an amino acid substitution selected from Table 1, with respect to SEQ ID NO: 1. In various embodiments, the mutant λ N- peptide sequence comprises 1, or 2, or 3, or 4, or 5, or 6, or 7, or 8, or 9, or 10, or 11, or 12, or 13, or 14, or 15, or 16, or 17, or 18, or 19 amino acid substitutions selected from Table 1, with respect to SEQ ID NO: 1. In various embodiments, the mutant λ N-peptide sequence comprises 1-9, or 1-8, or 1-7, or 1-6, or 1-5, or 1-4, or 1-3, or 1-2 amino acid substitutions selected from Table 1, with respect to SEQ ID NO: 1. Table 1. 1 2 3 4 5 6 7 8 9 a s p e y s Attorney Docket No.: 33791/41005 Met1Ile Asp2Lys Ala3Lys Gln4Ile Thr5Ile Arg6Ile Arg7Ile Arg8Ile Glu9Lys Mt1L A 2L Al3L Gln4L Thr5L Ar6L Ar7L Ar8L Gl9Lu t n o n g r r l p r Table 1 (continued). 10 11 12 13 14 15 16 17 s p e Attorney Docket No.: 33791/41005 Arg10Met Arg11Met Ala12Asn Glu13Asn Lys14Asn Gln15Met Ala16Asn Gln17Met Ar10An Ar11An Al12Pr Gl13Pr L 14Pr Gln15An Al16Pr Gln17An r Ta ble 1 (continued). 18 19 Attorney Docket No.: 33791/41005 Trp18Gln Lys19Arg Tr 18Ar L 19S r [0063] In various embodiments, such mutations increase the binding affinity of the mutant λ N-peptide to its respective hairpin RNA oligonucleotide, as compared to the binding affinity of the wild-type λ N- peptide to its respective hairpin RNA oligonucleotide. In some embodiments, the binding affinity of the inventive contemplated mutant λ N-peptide for its hairpin RNA oligonucleotide (e.g., λ BoxB hairpin RNA oligonucleotide) is greater than the affinity of the wild-type λ N-peptide for its hairpin RNA oligonucleotide (e.g., wild-type λ BoxB hairpin RNA oligonucleotide). The present disclosure contemplates mutant λ bacteriophage amino-terminal domain N-peptides having binding affinities for respective hairpin oligonucleotides that are greater than the wild-type λ bacteriophage N-peptide binding affinities for respective hairpin oligonucleotides by at least 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10- fold, 15-fold, 20-fold, 25-fold, 30-fold, 35-fold, 40-fold, 45-fold, 50-fold, or 100-fold. C. Lambdoid Bacteriophage N-Peptide [0064] In various embodiments, the present disclosure contemplates a N-peptide linked to a deaminase domain, or variant thereof. In some embodiments, the N-peptide comprises a helical structure. In some embodiments, the helical peptide is a lambdoid bacteriophage N-peptide. In some embodiments, the present disclosure contemplates at least 2, at least 3, at least 4, at least 5, at least 6, or at least 7 N- peptides linked to a deaminase domain. [0065] In various embodiments, the lambdoid bacteriophage N-peptide of the present disclosure is derived from the P22 or lambdoid bacteriophage. In various embodiments, the lambdoid bacteriophage N- peptide of the present disclosure is not the wild-type λ N-peptide (SEQ ID NO: 1). The lambdoid bacteriophages comprise arginine-rich motifs (ARMs) necessary for transcription antitermination that can bind to and/or interact with hairpin oligonucleotides. Without wishing to be bound by theory, various embodiments of the present disclosure contemplate that an arginine-rich motif (ARM) can bind to and/or Attorney Docket No.: 33791/41005 interact with a hairpin RNA oligonucleotide (e.g., BoxB hairpin RNA oligonucleotide) with a characteristic induced α-induced helical structure. Indeed, the present disclosure contemplates that variants and/or mutant lambdoid bacteriophage N-peptides can exhibit enhanced binding affinity properties for their respective hairpins compared to the wild-type phage N-peptides. 1. P22 [0066] In some embodiments, the lambdoid bacteriophage N-peptide is the wild-type amino-terminal domain P22 N-peptide and comprises the amino acid sequence of SEQ ID NO: 53: FAG NAKTRRHERR RKLAIERD (SEQ ID NO: 53). [0067] In some embodiments, a P22 N-peptide, and/or variants thereof, comprises an arginine-rich motif (ARM). In further embodiments, an amino-terminal domain P22 N-peptide of the present disclosure comprises an Alanine (Ala) at position 5 (respective of wild-type P22 N-peptide of SEQ ID NO: 53) and an Arginine (Arg) at each of positions 8,12, and 13 (respective of wild-type P22 N-peptide of SEQ ID NO: 53). In some embodiments, the amino-terminal domain P22 N-peptide is a variant of the wild-type amino- terminal domain P22 N-peptide and comprises at least one mutation as compared to the wild-type amino- terminal domain P22 N-peptide. Such a mutation can be selected from one or more of an amino acid substitution, amino acid deletion, and amino acid addition. For example, a variant amino-terminal domain P22 N-peptide can comprise from 1 to 21 amino acid residue substitutions, as compared to the wild-type P22 N-peptide (SEQ ID NO: 53). In some embodiments, the variant amino-terminal domain P22 N-peptide comprises at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 amino acid residue substitutions, as compared to the wild-type amino- terminal domain P22 N-peptide (SEQ ID NO: 53). In further embodiments, an amino acid substitution of the variant amino-terminal domain P22 N-peptide takes place at one or more of amino acid residue positions 1 to 21, relative to the wild-type amino-terminal domain P22 N-peptide (SEQ ID NO: 53). In some embodiments, the variant amino-terminal domain P22 N-peptide comprises an amino acid substitution that takes place at one or more of amino acid residue positions 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21, as compared to the wild-type amino-terminal domain P22 N-peptide (SEQ ID NO: 53). In some embodiments, an amino-terminal domain P22 N-peptide variant of the present disclosure comprises the amino acid sequence of any one of SEQ ID NO: 54 to SEQ ID NO: 78. The amino-terminal domain P22 N-peptide variant of the present disclosure can comprise the amino acid sequence of FAG Attorney Docket No.: 33791/41005 TAKTRRHERR RKLAIERD (SEQ ID NO: 54), FAG NARTRRHERR RKLAIERD (SEQ ID NO: 55), FAG NAKSRRHERR RKLAIERD (SEQ ID NO: 56), FAG NAKWRRHERR RKLAIERD (SEQ ID NO: 57), FAG NAKYRRHERR RKLAIERD (SEQ ID NO: 58), FAG NAKARRHERR RKLAIERD (SEQ ID NO: 59), FAG NAKRRRHERR RKLAIERD (SEQ ID NO: 60), FAG NAKTRRFERR RKLAIERD (SEQ ID NO: 61), FAG NAKTRRWERR RKLAIERD (SEQ ID NO: 62), FAG NAKTRRHLRR RKLAIERD (SEQ ID NO: 63), FAG NAKTRRHERR RQLAIERD (SEQ ID NO: 64), FAG NAKTRRHERR RRLAIERD (SEQ ID NO: 65), FAG NAKTRRHERR RSLAIERD (SEQ ID NO: 66), FAG NAKTRRHERR RKAAIERD (SEQ ID NO: 67), FAG NAKTRRHERR RKKAIERD (SEQ ID NO: 68), FAG NAKTRRHERR RKLSIERD (SEQ ID NO: 69), FAG NAKTRRHERR RKLALERD (SEQ ID NO: 70), FAG NAKTRRHERR RKLAMERD (SEQ ID NO: 71), FAG NAKTRRHERR RKLATERD (SEQ ID NO: 72), FAG NAKTRRHERR RKLAVERD (SEQ ID NO: 73), FAG NAKTRRHERR RKLAISRD (SEQ ID NO: 74), FAG NAKTRRHERR RKLAILRD (SEQ ID NO: 75), FAG NAKTRRHERR RKLAIEKD (SEQ ID NO: 76), FAG NAKTRRHERR RKLAIEFD (SEQ ID NO: 77), or FAG NAKTRRHERR RKLAIEWD (SEQ ID NO: 78). In further embodiments, one or more mutations of the wild- type amino-terminal domain P22 N-peptide do not yield the wild-type amino-terminal domain λ N-peptide (SEQ ID NO: 1). [0068] In various embodiments, one or more amino acids of SEQ ID NO: 53 is substituted with a naturally occurring amino acid, such as a hydrophilic amino acid (e.g. a polar and positively charged hydrophilic amino acid, such as arginine (R) or lysine (K); a polar and neutral of charge hydrophilic amino acid, such as asparagine (N), glutamine (Q), serine (S), threonine (T), proline (P), and cysteine (C), a polar and negatively charged hydrophilic amino acid, such as aspartate (D) or glutamate (E), or an aromatic, polar and positively charged hydrophilic amino acid, such as histidine (H)) or a hydrophobic amino acid (e.g. a hydrophobic, aliphatic amino acid such as glycine (G), alanine (A), leucine (L), isoleucine (I), methionine (M), or valine (V), a hydrophobic, aromatic amino acid, such as phenylalanine (F), tryptophan (W), or tyrosine (Y) or a non-classical amino acid (e.g. selenocysteine, pyrrolysine, N-formylmethionine β- alanine, GABA and δ-Aminolevulinic acid.4-Aminobenzoic acid (PABA), D-isomers of the common amino acids, 2,4-diaminobutyric acid, α-amino isobutyric acid, 4-aminobutyric acid, Abu, 2-amino butyric acid, γ- Abu, ε-Ahx, 6-amino hexanoic acid, Aib, 2-amino isobutyric acid, 3-amino propionic acid, ornithine, norleucine, norvaline, hydroxyproline, sarcosme, citrulline, homocitrulline, cysteic acid, t-butylglycine, t- butylalanine, phenylglycine, cyclohexylalanine, β-alanine, fluoro-amino acids, designer amino acids such as β methyl amino acids, C α -methyl amino acids, N α -methyl amino acids, and amino acid analogs in general). Attorney Docket No.: 33791/41005 [0069] In some embodiments, the amino-terminal domain P22 N-peptide is a variant of the wild-type amino-terminal domain P22 N-peptide and comprises at least one mutation as compared to the wild-type amino-terminal domain P22 N-peptide (SEQ ID NO: 53). In further embodiments, the at least one mutation to SEQ ID NO: 53 comprises an amino acid substitution selected from any one of the following amino acid substitutions: Phe1Ala; Phe1Cys; Phe1Asp; Phe1Glu; Phe1Phe; Phe1Gly; Phe1His; Phe1Ile; Phe1Lys; Phe1Leu; Phe1Met; Phe1Asn; Phe1Pro; Phe1Gln; Phe1Arg; Phe1Ser; Phe1Thr; Phe1Val; Phe1Trp; Phe1Tyr; Ala2Ala; Ala2Cys; Ala2Asp; Ala2Glu; Ala2Phe; Ala2Gly; Ala2His; Ala2Ile; Ala2Lys; Ala2Leu; Ala2Met; Ala2Asn; Ala2Pro; Ala2Gln; Ala2Arg; Ala2Ser; Ala2Thr; Ala2Val; Ala2Trp; Ala2Tyr; Gly3Ala; Gly3Cys; Gly3Asp; Gly3Glu; Gly3Phe; Gly3Gly; Gly3His; Gly3Ile; Gly3Lys; Gly3Leu; Gly3Met; Gly3Asn; Gly3Pro; Gly3Gln; Gly3Arg; Gly3Ser; Gly3Thr; Gly3Val; Gly3Trp; Gly3Tyr; Asn4Ala; Asn4Cys; Asn4Asp; Asn4Glu; Asn4Phe; Asn4Gly; Asn4His; Asn4Ile; Asn4Lys; Asn4Leu; Asn4Met; Asn4Asn; Asn4Pro; Asn4Gln; Asn4Arg; Asn4Ser; Asn4Thr; Asn4Val; Asn4Trp; Asn4Tyr; Ala5Ala; Ala5Cys; Ala5Asp; Ala5Glu; Ala5Phe; Ala5Gly; Ala5His; Ala5Ile; Ala5Lys; Ala5Leu; Ala5Met; Ala5Asn; Ala5Pro; Ala5Gln; Ala5Arg; Ala5Ser; Ala5Thr; Ala5Val; Ala5Trp; Ala5Tyr; Lys6Ala; Lys6Cys; Lys6Asp; Lys6Glu; Lys6Phe; Lys6Gly; Lys6His; Lys6Ile; Lys6Lys; Lys6Leu; Lys6Met; Lys6Asn; Lys6Pro; Lys6Gln; Lys6Arg; Lys6Ser; Lys6Thr; Lys6Val; Lys6Trp; Lys6Tyr; Thr7Ala; Thr7Cys; Thr7Asp; Thr7Glu; Thr7Phe; Thr7Gly; Thr7His; Thr7Ile; Thr7Lys; Thr7Leu; Thr7Met; Thr7Asn; Thr7Pro; Thr7Gln; Thr7Arg; Thr7Ser; Thr7Thr; Thr7Val; Thr7Trp; Thr7Tyr; Arg8Ala; Arg8Cys; Arg8Asp; Arg8Glu; Arg8Phe; Arg8Gly; Arg8His; Arg8Ile; Arg8Lys; Arg8Leu; Arg8Met; Arg8Asn; Arg8Pro; Arg8Gln; Arg8Arg; Arg8Ser; Arg8Thr; Arg8Val; Arg8Trp; Arg8Tyr; Arg9Ala; Arg9Cys; Arg9Asp; Arg9Glu; Arg9Phe; Arg9Gly; Arg9His; Arg9Ile; Arg9Lys; Arg9Leu; Arg9Met; Arg9Asn; Arg9Pro; Arg9Gln; Arg9Ser; Arg9Thr; Arg9Val; Arg9Trp; Arg9Tyr; His10Ala; His10Cys; His10Asp; His10Glu; His10Phe; His10Gly; His10His; His10Ile; His10Lys; His10Leu; His10Met; His10Asn; His10Pro; His10Gln; His10Arg; His10Ser; His10Thr; His10Val; His10Trp; His10Tyr; Glu11Ala; Glu11Cys; Glu11Asp; Glu11Glu; Glu11Phe; Glu11Gly; Glu11His; Glu11Ile; Glu11Lys; Glu11Leu; Glu11Met; Glu11Asn; Glu11Pro; Glu11Gln; Glu11Arg; Glu11Ser; Glu11Thr; Glu11Val; Glu11Trp; Glu11Tyr; Arg12Ala; Arg12Cys; Arg12Asp; Arg12Glu; Arg12Phe; Arg12Gly; Arg12His; Arg12Ile; Arg12Lys; Arg12Leu; Arg12Met; Arg12Asn; Arg12Pro; Arg12Gln; Arg12Arg; Arg12Ser; Arg12Thr; Arg12Val; Arg12Trp; Arg12Tyr; Arg13Ala; Arg13Cys; Arg13Asp; Arg13Glu; Arg13Phe; Arg13Gly; Arg13His; Arg13Ile; Arg13Lys; Arg13Leu; Arg13Met; Arg13Asn; Arg13Pro; Arg13Gln; Arg13Arg; Arg13Ser; Arg13Thr; Arg13Val; Arg13Trp; Arg13Tyr; Arg14Ala; Arg14Cys; Arg14Asp; Arg14Glu; Arg14Phe; Arg14Gly; Arg14His; Arg14Ile; Arg14Lys; Arg14Leu; Arg14Met; Arg14Asn; Arg14Pro; Arg14Gln; Arg14Arg; Arg14Ser; Arg14Thr; Arg14Val; Arg14Trp; Arg14Tyr; Lys15Ala; Lys15Cys; Lys15Asp; Attorney Docket No.: 33791/41005 Lys15Glu; Lys15Phe; Lys15Gly; Lys15His; Lys15Ile; Lys15Lys; Lys15Leu; Lys15Met; Lys15Asn; Lys15Pro; Lys15Gln; Lys15Arg; Lys15Ser; Lys15Thr; Lys15Val; Lys15Trp; Lys15Tyr; Leu16Ala; Leu16Cys; Leu16Asp; Leu16Glu; Leu16Phe; Leu16Gly; Leu16His; Leu16Ile; Leu16Lys; Leu16Leu; Leu16Met; Leu16Asn; Leu16Pro; Leu16Gln; Leu16Arg; Leu16Ser; Leu16Thr; Leu16Val; Leu16Trp; Leu16Tyr; Ala17Ala; Ala17Cys; Ala17Asp; Ala17Glu; Ala17Phe; Ala17Gly; Ala17His; Ala17Ile; Ala17Lys; Ala17Leu; Ala17Met; Ala17Asn; Ala17Pro; Ala17Gln; Ala17Arg; Ala17Ser; Ala17Thr; Ala17Val; Ala17Trp; Ala17Tyr; Ile18Ala; Ile18Cys; Ile18Asp; Ile18Glu; Ile18Phe; Ile18Gly; Ile18His; Ile18Ile; Ile18Lys; Ile18Leu; Ile18Met; Ile18Asn; Ile18Pro; Ile18Gln; Ile18Arg; Ile18Ser; Ile18Thr; Ile18Val; Ile18Trp; Ile18Tyr; Glu19Ala; Glu19Cys; Glu19Asp; Glu19Glu; Glu19Phe; Glu19Gly; Glu19His; Glu19Ile; Glu19Lys; Glu19Leu; Glu19Met; Glu19Asn; Glu19Pro; Glu19Gln; Glu19Arg; Glu19Ser; Glu19Thr; Glu19Val; Glu19Trp; Glu19Tyr; Arg20Ala; Arg20Cys; Arg20Asp; Arg20Glu; Arg20Phe; Arg20Gly; Arg20His; Arg20Ile; Arg20Lys; Arg20Leu; Arg20Met; Arg20Asn; Arg20Pro; Arg20Gln; Arg20Arg; Arg20Ser; Arg20Thr; Arg20Val; Arg20Trp; Arg20Tyr; Asp21Ala; Asp21Cys; Asp21Asp; Asp21Glu; Asp21Phe; Asp21Gly; Asp21His; Asp21Ile; Asp21Lys; Asp21Leu; Asp21Met; Asp21Asn; Asp21Pro; Asp21Gln; Asp21Arg; Asp21Ser; Asp21Thr; Asp21Val; Asp21Trp; and Asp21Tyr. In some embodiments, the amino acid substitution is selected from any one of the amino acid substitutions listed in Table 2. [0070] In various embodiments, the P22 N-peptide sequence comprises an amino acid substitution selected from Table 2, with respect to SEQ ID NO: 53. In various embodiments, the P22 N-peptide sequence comprises 1, or 2, or 3, or 4, or 5, or 6, or 7, or 8, or 9, or 10, or 11, or 12, or 13, or 14, or 15, or 16, or 17, or 18, or 19, or 20, or 21 amino acid substitutions selected from Table 2, with respect to SEQ ID NO: 53. In various embodiments, the P22 N-peptide sequence comprises 1-20, or 1-10, or 1-5, or 1-4, or 1-3, or 1-2 amino acid substitutions selected from Table 2, with respect to SEQ ID NO: 53. Table 2. 1 2 3 4 5 6 7 8 9 a ys sp lu Attorney Docket No.: 33791/41005 Phe1Gly Ala2Gly Gly3Phe Asn4Phe Ala5Gly Lys6Phe Thr7Phe Arg8Phe Arg9Phe ly s s u et sn o ln er r al p r Table 2 (continued) 10 11 12 13 14 15 16 17 ys p u e y s Attorney Docket No.: 33791/41005 His10Ile Glu11Ile Arg12His Arg13His Arg14His Lys15His Leu16His Ala17Ile s u et n o n g r r l p r Table 2 (continued) 18 19 20 21 s u e y s Attorney Docket No.: 33791/41005 Ile18Leu Glu19Leu Arg20Lys Asp21Leu t n o n g r r l r [0071] In various emb inities of the variant N-peptides to their respective hairpin R NA oligonucleotides, as compared to the binding affinities of the wild-type N- peptides to their respective hairpin RNA oligonucleotides. In some embodiments, the affinity of any one of the inventive contemplated P22 N-peptide variants for their hairpin RNA oligonucleotide (e.g., P22 BoxB hairpin RNA oligonucleotide) is greater than the affinity of the wild-type P22 N-peptide for its hairpin RNA oligonucleotide (e.g., wild-type P22 BoxB hairpin RNA oligonucleotide). The present disclosure contemplates variant bacteriophage amino-terminal domain N-peptides having binding affinities for respective hairpin oligonucleotides that are greater than the wild-type bacteriophage N-peptide binding affinities for respective hairpin oligonucleotides by at least 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 15-fold, 20-fold, 25-fold, 30-fold, 35-fold, 40-fold, 45-fold, 50-fold, or 100-fold. [0072] In various embodiments, the lambdoid bacteriophage N-peptide of the present disclosure is derived from the P21 (a.k.a. phi21 or φ21) lambdoid bacteriophage. In various embodiments, the lambdoid bacteriophage N-peptide of the present disclosure is not the wild-type λ N-peptide (SEQ ID NO: 1). The lambdoid bacteriophages comprise arginine-rich motifs (ARMs) necessary for transcription antitermination that can bind to and/or interact with hairpin oligonucleotides. Without wishing to be bound by theory, various embodiments of the present disclosure contemplate that an arginine-rich motif (ARM) can bind to Attorney Docket No.: 33791/41005 and/or interact with a hairpin RNA oligonucleotide (e.g., BoxB hairpin RNA oligonucleotide) with a characteristic induced α-induced helical structure. Indeed, the present disclosure contemplates that variants and/or mutant lambdoid bacteriophage N-peptides can exhibit enhanced binding affinity properties for their respective hairpins compared to the wild-type phage N-peptides. 2. P21 [0073] In some embodiments, the lambdoid bacteriophage N-peptide is the wild-type amino-terminal domain P21 N-peptide and comprises the amino acid sequence of SEQ ID NO: 95: SKG TAKSRYKARR AELIAERR (SEQ ID NO: 95). [0074] In some embodiments, a P21 N-peptide, and/or variants thereof, comprises an arginine-rich motif (ARM). In further embodiments, an amino-terminal domain P21 N-peptide of the present disclosure comprises an Alanine (Ala) at position 5 (respective of wild-type P21 N-peptide of SEQ ID NO: 95) and an Arginine (Arg) at each of positions 8,12, and 13 (respective of wild-type P21 N-peptide of SEQ ID NO: 95). In some embodiments, the amino-terminal domain P21 N-peptide is a variant of the wild-type amino- terminal domain P21 N-peptide and comprises at least one mutation as compared to the wild-type amino- terminal domain P21 N-peptide. Such a mutation can be selected from one or more of an amino acid substitution, amino acid deletion, and amino acid addition. For example, a variant amino-terminal domain P21 N-peptide can comprise from 1 to 21 amino acid residue substitutions, as compared to the wild-type P21 N-peptide (SEQ ID NO: 95). In some embodiments, the variant amino-terminal domain P21 N-peptide comprises at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 amino acid residue substitutions, as compared to the wild-type amino- terminal domain P21 N-peptide (SEQ ID NO: 95). In further embodiments, an amino acid substitution of the variant amino-terminal domain P21 N-peptide takes place at one or more of amino acid residue positions 1 to 21, relative to the wild-type amino-terminal domain P21 N-peptide (SEQ ID NO: 95). In some embodiments, the variant amino-terminal domain P21 N-peptide comprises an amino acid substitution that takes place at one or more of amino acid residue positions 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21, as compared to the wild-type amino-terminal domain P21 N-peptide (SEQ ID NO: 95). In further embodiments, the variant amino-terminal domain P21 N-peptide comprises one or more mutations at position R13 and/or I17, with respect to SEQ ID NO: 95. In further embodiments, the variant amino-terminal domain P21 N-peptide is not mutated at position R13 and/or I17, with respect to SEQ ID Attorney Docket No.: 33791/41005 NO: 95. In further embodiments, one or more mutations of the wild-type amino-terminal domain P21 N- peptide do not yield the wild-type amino-terminal domain λ N-peptide (SEQ ID NO: 1). [0075] In various embodiments, one or more amino acids of SEQ ID NO: 95 is substituted with a naturally occurring amino acid, such as a hydrophilic amino acid (e.g. a polar and positively charged hydrophilic amino acid, such as arginine (R) or lysine (K); a polar and neutral of charge hydrophilic amino acid, such as asparagine (N), glutamine (Q), serine (S), threonine (T), proline (P), and cysteine (C), a polar and negatively charged hydrophilic amino acid, such as aspartate (D) or glutamate (E), or an aromatic, polar and positively charged hydrophilic amino acid, such as histidine (H)) or a hydrophobic amino acid (e.g. a hydrophobic, aliphatic amino acid such as glycine (G), alanine (A), leucine (L), isoleucine (I), methionine (M), or valine (V), a hydrophobic, aromatic amino acid, such as phenylalanine (F), tryptophan (W), or tyrosine (Y) or a non-classical amino acid (e.g. selenocysteine, pyrrolysine, N-formylmethionine β- alanine, GABA and δ-Aminolevulinic acid.4-Aminobenzoic acid (PABA), D-isomers of the common amino acids, 2,4-diaminobutyric acid, α-amino isobutyric acid, 4-aminobutyric acid, Abu, 2-amino butyric acid, γ- Abu, ε-Ahx, 6-amino hexanoic acid, Aib, 2-amino isobutyric acid, 3-amino propionic acid, ornithine, norleucine, norvaline, hydroxyproline, sarcosme, citrulline, homocitrulline, cysteic acid, t-butylglycine, t- butylalanine, phenylglycine, cyclohexylalanine, β-alanine, fluoro-amino acids, designer amino acids such as β methyl amino acids, C α -methyl amino acids, N α -methyl amino acids, and amino acid analogs in general). [0076] In some embodiments, the amino-terminal domain P21 N-peptide is a variant of the wild-type amino-terminal domain P21 N-peptide and comprises at least one mutation as compared to the wild-type amino-terminal domain P21 N-peptide (SEQ ID NO: 95). In further embodiments, the at least one mutation to SEQ ID NO: 95 comprises an amino acid substitution selected from any one of the following amino acid substitutions: Ser1Ala; Ser1Cys; Ser1Asp; Ser1Glu; Ser1Phe; Ser1Gly; Ser1His; Ser1Ile; Ser1Lys; Ser1Leu; Ser1Met; Ser1Asn; Ser1Pro; Ser1Gln; Ser1Arg; Ser1Thr; Ser1Val; Ser1Trp; Ser1Tyr; Lys2Ala; Lys2Cys; Lys2Asp; Lys2Glu; Lys2Phe; Lys2Gly; Lys2His; Lys2Ile; Lys2Leu; Lys2Met; Lys2Asn; Lys2Pro; Lys2Gln; Lys2Arg; Lys2Ser; Lys2Thr; Lys2Val; Lys2Trp; Lys2Tyr; Gly3Ala; Gly3Cys; Gly3Asp; Gly3Glu; Gly3Phe; Gly3His; Gly3Ile; Gly3Lys; Gly3Leu; Gly3Met; Gly3Asn; Gly3Pro; Gly3Gln; Gly3Arg; Gly3Ser; Gly3Thr; Gly3Val; Gly3Trp; Gly3Tyr; Thr4Ala; Thr4Cys; Thr4Asp; Thr4Glu; Thr4Phe; Thr4Gly; Thr4His; Thr4Ile; Thr4Lys; Thr4Leu; Thr4Met; Thr4Asn; Thr4Pro; Thr4Gln; Thr4Arg; Thr4Ser; Thr4Val; Thr4Trp; Thr4Tyr; Ala5Cys; Ala5Asp; Ala5Glu; Ala5Phe; Ala5Gly; Ala5His; Ala5Ile; Ala5Lys; Ala5Leu; Ala5Met; Ala5Asn; Ala5Pro; Ala5Gln; Ala5Arg; Ala5Ser; Ala5Thr; Ala5Val; Ala5Trp; Ala5Tyr; Lys6Ala; Lys6Cys; Attorney Docket No.: 33791/41005 Lys6Asp; Lys6Glu; Lys6Phe; Lys6Gly; Lys6His; Lys6Ile; Lys6Leu; Lys6Met; Lys6Asn; Lys6Pro; Lys6Gln; Lys6Arg; Lys6Ser; Lys6Thr; Lys6Val; Lys6Trp; Lys6Tyr; Ser7Ala; Ser7Cys; Ser7Asp; Ser7Glu; Ser7Phe; Ser7Gly; Ser7His; Ser7Ile; Ser7Lys; Ser7Leu; Ser7Met; Ser7Asn; Ser7Pro; Ser7Gln; Ser7Arg; Ser7Thr; Ser7Val; Ser7Trp; Ser7Tyr; Arg8Ala; Arg8Cys; Arg8Asp; Arg8Glu; Arg8Phe; Arg8Gly; Arg8His; Arg8Ile; Arg8Lys; Arg8Leu; Arg8Met; Arg8Asn; Arg8Pro; Arg8Gln; Arg8Arg; Arg8Ser; Arg8Thr; Arg8Val; Arg8Trp; Arg8Tyr; Tyr9Ala; Tyr9Cys; Tyr9Asp; Tyr9Glu; Tyr9Phe; Tyr9Gly; Tyr9His; Tyr9Ile; Tyr9Lys; Tyr9Leu; Tyr9Met; Tyr9Asn; Tyr9Pro; Tyr9Gln; Tyr9Arg; Tyr9Ser; Tyr9Thr; Tyr9Val; Tyr9Trp; Lys10Ala; Lys10Cys; Lys10Asp; Lys10Glu; Lys10Phe; Lys10Gly; Lys10His; Lys10Ile; Lys10Leu; Lys10Met; Lys10Asn; Lys10Pro; Lys10Gln; Lys10Arg; Lys10Ser; Lys10Thr; Lys10Val; Lys10Trp; Lys10Tyr; Ala11Cys; Ala11Asp; Ala11Glu; Ala11Phe; Ala11Gly; Ala11His; Ala11Ile; Ala11Lys; Ala11Leu; Ala11Met; Ala11Asn; Ala11Pro; Ala11Gln; Ala11Arg; Ala11Ser; Ala11Thr; Ala11Val; Ala11Trp; Ala11Tyr; Arg12Ala; Arg12Cys; Arg12Asp; Arg12Glu; Arg12Phe; Arg12Gly; Arg12His; Arg12Ile; Arg12Lys; Arg12Leu; Arg12Met; Arg12Asn; Arg12Pro; Arg 12Gln; Arg12Ser; Arg12Thr; Arg12Val; Arg12Trp; Arg12Tyr; Arg13Ala; Arg13Cys; Arg13Asp; Arg13Glu; Arg13Phe; Arg13Gly; Arg13His; Arg13Ile; Arg13Lys; Arg13Leu; Arg13Met; Arg13Asn; Arg13Pro; Arg13Gln; Arg13Ser; Arg13Thr; Arg13Val; Arg13Trp; Arg13Tyr; Ala14Cys; Ala14Asp; Ala14Glu; Ala14Phe; Ala14Gly; Ala14His; Ala14Ile; Ala14Lys; Ala14Leu; Ala14Met; Ala14Asn; Ala14Pro; Ala14Gln; Ala14Arg; Ala14Ser; Ala14Thr; Ala14Val; Ala14Trp; Ala14Tyr; Glu15Ala; Glu15Cys; Glu15Asp; Glu15Phe; Glu15Gly; Glu15His; Glu15Ile; Glu15Lys; Glu15Leu; Glu15Met; Glu15Asn; Glu15Pro; Glu15Gln; Glu15Arg; Glu15Ser; Glu15Thr; Glu15Val; Glu15Trp; Glu15Tyr; Leu16Ala; Leu16Cys; Leu16Asp; Leu16Glu; Leu16Phe; Leu16Gly; Leu16His; Leu16Ile; Leu16Lys; Leu16Met; Leu16Asn; Leu16Pro; Leu16Gln; Leu16Arg; Leu16Ser; Leu16Thr; Leu16Val; Leu16Trp; Leu16Tyr; Ile17Ala; Ile17Cys; Ile17Asp; Ile17Glu; Ile17Phe; Ile17Gly; Ile17His; Ile17Lys; Ile17Leu; Ile17Met; Ile17Asn; Ile17Pro; Ile17Gln; Ile17Arg; Ile17Ser; Ile17Thr; Ile17Val; Ile17Trp; Ile17Tyr; Ala18Cys; Ala18Asp; Ala18Glu; Ala18Phe; Ala18Gly; Ala18His; Ala18Ile; Ala18Lys; Ala18Leu; Ala18Met; Ala18Asn; Ala18Pro; Ala18Gln; Ala18Arg; Ala18Ser; Ala18Thr; Ala18Val; Ala18Trp; Ala18Tyr; Glu19Ala; Glu19Cys; Glu19Asp; Glu19Phe; Glu19Gly; Glu19His; Glu19Ile; Glu19Lys; Glu19Leu; Glu19Met; Glu19Asn; Glu19Pro; Glu19Gln; Glu19Arg; Glu19Ser; Glu19Thr; Glu19Val; Glu19Trp; Glu19Tyr; Arg20Ala; Arg20Cys; Arg20Asp; Arg20Glu; Arg20Phe; Arg20Gly; Arg20His; Arg20Ile; Arg20Lys; Arg20Leu; Arg20Met; Arg20Asn; Arg20Pro; Arg20Gln; Arg20Ser; Arg20Thr; Arg20Val; Arg20Trp; Arg20Tyr; Arg21Ala; Arg21Cys; Arg21Asp; Arg21Glu; Arg21Phe; Arg21Gly; Arg21His; Arg21Ile; Arg21Lys; Arg21Leu; Arg21Met; Arg21Asn; Arg21Pro; Arg21Gln; Arg21Ser; Arg21Thr; Arg21Val; Attorney Docket No.: 33791/41005 Arg21Trp; and Arg21Tyr. In some embodiments, the amino acid substitution is selected from any one of the amino acid substitutions listed in Table 3. [0077] In various embodiments, the P21 N-peptide sequence comprises an amino acid substitution selected from Table 3, with respect to SEQ ID NO: 95. In various embodiments, the P21 N-peptide sequence comprises 1, or 2, or 3, or 4, or 5, or 6, or 7, or 8, or 9, or 10, or 11, or 12, or 13, or 14, or 15, or 16, or 17, or 18, or 19, or 20, or 21 amino acid substitutions selected from Table 3, with respect to SEQ ID NO: 95. In various embodiments, the P21 N-peptide sequence comprises 1-20, or 1-10, or 1-5, or 1-4, or 1-3, or 1-2 amino acid substitutions selected from Table 3, with respect to SEQ ID NO: 95. Table 3. 1 2 3 4 5 6 7 8 s p e u t n r Attorney Docket No.: 33791/41005 Ser1Thr Lys2Thr Gly3Thr Thr4Ser Ala5Thr Lys6Thr Ser7Thr Arg8Thr l Ta e co ue 9 10 11 12 13 14 15 16 a ys p u e y s s et n o n g r r l Attorney Docket No.: 33791/41005 Tyr9Val Lys10Trp Ala11Trp Arg12Trp Arg13Trp Ala14Trp Glu15Trp Leu16Trp r Ta 17 18 19 20 21 a s p u e y s s u t n o n r r l p r Attorney Docket No.: 33791/41005 [0078] In various embodiments, such mutations increase the binding affinities of the variant N- peptides to their respective hairpin RNA oligonucleotides, as compared to the binding affinities of the wild- type N-peptides to their respective hairpin RNA oligonucleotides. In some embodiments, the affinity of any one of the inventive contemplated P21 N-peptide variants for their hairpin RNA oligonucleotides (e.g., P21 BoxB hairpin RNA oligonucleotide) is greater than the affinity of the wild-type P21 N-peptide for its hairpin RNA oligonucleotide (e.g., wild-type P21 BoxB hairpin RNA oligonucleotide). The present disclosure provides v ariant bacteriophage amino-terminal domain N-peptides having binding affinities for respective hairpin oligonucleotides that are greater than the wild-type bacteriophage N-peptide binding affinities for respective hairpin oligonucleotides by at least 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10- fold, 15-fold, 20-fold, 25-fold, 30-fold, 35-fold, 40-fold, 45-fold, 50-fold, or 100-fold. [0079] Consequentially, in various embodiments, a high affinity interaction between the variant N- peptides described herein and the respective hairpin oligonucleotide allows for low dose uses of the present agents. Further, without wishing to be bound by theory, such high affinity interaction allows for reduced frequency of dosing and reduced off-target effects. Stated another way the tight interaction between the present mutant λ N-peptides and respective hairpin oligonucleotides favors the occurrence of the beneficial interaction which drives editing and disfavors interactions that do not support, or even hinder, a therapeutic effect. [0080] Methods of assaying binding affinity are known in the art. Non-limiting examples include optical assays, such as monitoring the change in fluorescence of a 2-aminopurine (2AP) base analogue substituted at different adenine positions within the target hairpin in order to measure kinetics; chemical assays, such as gel electrophoresis, ELISA, and immunoblots; and other methods studying RNA-protein interactions, such as electrophoretic mobility shift assay (EMSA), systematic evolution of ligands by exponential enrichment (SELEX), RNA pull-down assay, RNA footprinting, RNA immunoprecipitation (RIP), UV-induced crosslinking immunoprecipitation (CLIP). Pollard, Mol Biol Cell. (2010) 21(23): 4061-4067 and Popova et al. Mol. Biol. (2015) 49(3): 418-426, are hereby incorporated by reference in their entireties. D. Antisense RNA Oligonucleotide [0081] In some aspects, the target RNA sequence comprises a sequence associated with a disease, condition or disorder, and wherein the deamination of the nucleotide base results in an RNA sequence that is not associated with a disease, condition or disorder. In some aspects, the target RNA sequence Attorney Docket No.: 33791/41005 comprises a wild-type sequence, wherein the deamination of a particular nucleotide base therein results in a mutation that induces a beneficial and/or therapeutic effect. [0082] Accordingly, methods of the present disclosure further contemplate an antisense RNA oligonucleotide that hybridizes with a wild-type or mutant target sequence in an endogenous RNA molecule that comprises a target nucleotide to be edited. In some embodiments, the target nucleotide to be edited eliminates a detrimental mutation in the mutant target sequence. For example, the target nucleotide can be a genetic mutation associated with a genetic disease, condition or disorder. By way of non-limiting example, a genetic mutation of the target nucleotide may cause a premature termination codon (PTC) or an in-frame stop codon. In some embodiments, the genetic disorder or condition is caused by a substitution of C from U nucleotides so that C-to-U editing would correct the mutation. The present disclosure contemplates a nucleic acid-editing system that can edit any target nucleotide and/or genetic mutation (e.g., by facilitating splice modulation). In certain embodiments, the target RNA sequence relates to a target gene of interest. For example, the target gene of interest can include, but is not limited to, Human SerpinA1 E342K gene (NM_000295.4) and human IDUA gene (NM_000203.5) that contains the W402X mutation. [0083] In some embodiments, the antisense RNA oligonucleotide hybridizes with an RNA molecule comprising the target nucleotide in endogenous RNA of the cell. In some embodiments, the antisense RNA oligonucleotide has perfect base-pairing complementarity with the RNA molecule comprising the target nucleotide. In various embodiments, the antisense RNA oligonucleotide comprises one or more mismatches with the RNA molecule comprising the target nucleotide. For example, the antisense RNA oligonucleotide sequence can comprise from 1 to 15 mismatches, e.g., about 1, or about 2, or about 3, or about 4, or about 5, or about 6, or about 7, or about 8, or about 9, or about 10, or about 11, or about 12, or about 13, or about 14, or about 15 mismatches. In embodiments of the present disclosure, a mismatch is a non-complementary match hybridization between the antisense RNA oligonucleotide and the RNA molecule comprising the target nucleotide. In various embodiments, the antisense RNA oligonucleotide sequence is at least 80%, at least 85%, at least 90%, at least 93%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% complementary with the target sequence. In some embodiments, the 5' end of the antisense RNA oligonucleotide begins before the target nucleotide to be edited. In some embodiments, the 3' end of the oligonucleotide extends from 2-22, from 2-20, from 5-20, from 5-15, or from 5-10 nucleotides 5' from the target nucleotide to be edited. Attorney Docket No.: 33791/41005 [0084] The present disclosure further contemplates an antisense RNA oligonucleotide that hybridizes with a wild-type target sequence in an endogenous RNA molecule that comprises a target nucleotide to be edited. In such embodiments of the present disclosure, the target nucleotide to be edited induces a beneficial mutation in the wild-type target sequence. In some embodiments, an antisense RNA oligonucleotide hybridizes with a target sequence comprising a target nucleotide to be edited under stringent conditions. [0085] In certain embodiments, the present disclosure contemplates methods of editing RNA in any cell type of a subject. For example, the cell containing RNA to be edited can be a cell of the central nervous system (e.g., neurons) or a liver cell. In some embodiments, the cells to be edited are in a subject so that the methods of the present disclosure are in vivo methods of editing. In some embodiments, cells may be edited in vitro and subsequently delivered to a subject as ex vivo treatment. E. Hairpin Interaction [0086] According to the present disclosure, the term “hairpin” refers to a particular oligonucleotide and/or nucleic acid structure (e.g., RNA oligonucleotide and/or RNA structure) that is recognized by and interacts with a lambdoid bacteriophage N-peptide (e.g., amino-terminal domain N-peptide derived from λ N protein; amino-terminal domain N-peptide derived from P21; or amino-terminal domain N-peptide derived from P22) or other helical peptide. A particular example of such a hairpin is a BoxB hairpin RNA oligonucleotide that is the cognate hairpin of the lamboid bacteriophage N-peptide, or mutant thereof. [0087] In some embodiments of the present disclosure the lamboid bacteriophage N-peptide, or mutant thereof, interacts with a hairpin RNA (e.g., there is hairpin recognition of the lamboid bacteriophage N-peptide) oligonucleotide. In some embodiments, the hairpin RNA oligonucleotide is the cognate hairpin of the lamboid bacteriophage N-peptide. For example, by way of non-limiting example, the cognate hairpin can be a boxB hairpin RNA oligonucleotide. In some embodiments, the boxB hairpin RNA oligonucleotide is located from about 2-20 nucleotide residues 5’ of the target mutation. In some embodiments, the boxB hairpin RNA oligonucleotide is located from about 2-20 nucleotide residues 3’ of the target mutation. [0088] In various embodiments, the antisense RNA oligonucleotide of the present disclosure (described herein) is linked to one or more hairpin RNA oligonucleotides. In some embodiments, the antisense RNA oligonucleotide is linked to 1, 2, 3, or 4 hairpin RNA oligonucleotides. In some embodiments, the antisense RNA oligonucleotide is linked to at least 2, at least 3, or at least 4 hairpin RNA oligonucleotides. Attorney Docket No.: 33791/41005 [0089] In certain embodiments, a BoxB hairpin RNA oligonucleotide of the present disclosure comprises a nucleic acid sequence of SEQ ID NO: 10 or SEQ ID NO: 11, or mutants thereof. Specifically, a BoxB hairpin RNA oligonucleotide can comprise a nucleic acid sequence selected from the wild-type λ BoxB hairpin RNA oligonucleotide (e.g., nutRλ BoxB hairpin RNA oligonucleotide), right: GCCCUGAAAAAGGGC (SEQ ID NO: 10), and the wild-type λ BoxB hairpin RNA oligonucleotide (e.g., nutLλ BoxB hairpin RNA oligonucleotide), left:GCCCUGAAGAAGGGC (SEQ ID NO: 11). [0090] In some embodiments, the λ N-peptide, or mutant thereof, interacts with a λ BoxB hairpin RNA oligonucleotide comprising the nucleotide sequence of SEQ ID NO: 10 or SEQ ID NO: 11, or mutant thereof. In some embodiments the λ N-peptide, or mutant thereof, interacts with a mutant λ BoxB hairpin RNA oligonucleotide comprising a nucleotide sequence of any one of SEQ ID NOs: 12-17. In various embodiments, the λ N-peptide, or mutant thereof, and λ BoxB hairpin RNA oligonucleotide, or mutant thereof, interaction adopts a 4-out GNRA-like pentaloop. A tetraloop is a type of four-base hairpin loop motif in RNA secondary structures that cap many double helices. In ribosomal RNA, the N could be either uracil, adenine, cytosine, or guanine, and the R is either guanine or adenine. The GNRA tetraloop, specifically, has a guanine-adenine base pair, where the guanine is 5’ to the helix and the adenine is 3’ to the helix. [0091] In various embodiments, a hairpin oligonucleotide of the present disclosure comprises at least one mutation selected from missense mutation, nonsense mutation, insertion, deletion, duplication, frameshift mutation, and repeat expansion. By way of non-limiting example, such mutations can be made with respect to a hairpin oligonucleotide comprising one or more of SEQ ID NO: 10 or SEQ ID NO: 11. For example, in some embodiments, the λ BoxB hairpin RNA oligonucleotide comprises a nucleic acid sequence having sequence identity to SEQ ID NO: 10 or SEQ ID NO: 11, and further comprises from 1 to 15 nucleotide mutations selected from one or more of nucleotide substitutions, nucleotide deletions, and nucleotide additions. In further embodiments, the one or more nucleotide mutations take(s) place at one or more of nucleotide residue positions 1 to 15, relative to wild-type λ BoxB hairpin RNA oligonucleotide. In some embodiments, a mutant λ BoxB hairpin RNA oligonucleotide comprises a nucleotide sequence of any one of SEQ ID NOs: 12-17: SEQ ID NO: 12:GCCCUAAAAAAGGGC (λboxBR:G6A); SEQ ID NO: 13:GCCCUGAUAAAGGGC (λboxBR:A8U); SEQ ID NO: 14:GCCCGGAAAACGGGC (λboxBR:U5G,A11C); Attorney Docket No.: 33791/41005 SEQ ID NO: 15:GCCCUGAACAAGGGC (λboxBR:A9C); SEQ ID NO: 16:GCCCUGAAACAGGGC (λboxBR:A10C); and SEQ ID NO: 17:GCCCUGAAAAGGGGC (λboxBR:A11G). [0092] In certain embodiments, a BoxB hairpin RNA oligonucleotide of the present disclosure comprises a nucleic acid sequence of any one of SEQ ID NOs: 79-80, or variants thereof. Specifically, a BoxB hairpin RNA oligonucleotide comprises a nucleic acid sequence selected from the wild-type P22 BoxB RNA hairpin, right:ACCGCCGACAACGCGGU (SEQ ID NO: 79); the wild-type P22 BoxB RNA hairpin, left:UGCGCUGACAAAGCGCG (SEQ ID NO: 80). [0093] In some embodiments, the P22 N-peptide, or variant thereof, interacts with a P22 BoxB hairpin RNA oligonucleotide comprising the nucleic acid sequence of SEQ ID NO: 79 or SEQ ID NO: 80, or variant thereof. In various embodiments, the P22 N-peptide and P22 BoxB hairpin RNA oligonucleotide interaction adopts a 3-out GNRA-like pentaloop. A tetraloop is a type of four-base hairpin loop motif in RNA secondary structures that cap many double helices. In ribosomal RNA, the N could be either uracil, adenine, cytosine, or guanine, and the R is either guanine or adenine. The GNRA tetraloop, specifically, has a guanine-adenine base pair, where the guanine is 5’ to the helix and the adenine is 3’ to the helix. [0094] In various embodiments, a hairpin oligonucleotide of the present disclosure comprises at least one mutation selected from missense mutation, nonsense mutation, insertion, deletion, duplication, frameshift mutation, and repeat expansion. By way of non-limitation, such mutations can be made with respect to a hairpin oligonucleotide comprising one or more of nucleic acid sequences selected from SEQ ID NOs: 70-80. For example, in some embodiments, the P22 BoxB hairpin RNA oligonucleotide comprises the nucleic acid sequence of SEQ ID NO: 70 or SEQ ID NO: 80, and further comprises from 1 to 17 nucleotide mutations selected from one or more of nucleotide substitutions, nucleotide deletions, and nucleotide additions. In further embodiments, the one or more nucleotide mutations take(s) place at one or more of nucleotide residue positions 1 to 17, relative to wild-type P22 BoxB hairpin RNA oligonucleotide. [0095] In certain embodiments, a BoxB hairpin RNA oligonucleotide of the present disclosure comprises a nucleic acid sequence of any one of SEQ ID NOs: 96-97, or variants thereof. Specifically, a BoxB hairpin RNA oligonucleotide comprises a nucleic acid sequence selected from the wild-type P21 BoxB RNA hairpin, right:UUCACCUCUAACCGGGUGAG (SEQ ID NO: 96); and the wild-type P21 BoxB RNA hairpin, left:UCUCAACCUAACCGUUGAGA (SEQ ID NO: 97). Attorney Docket No.: 33791/41005 [0096] In some embodiments, the P21 N-peptide, or variant thereof, interacts with a P21 BoxB hairpin RNA oligonucleotide comprising the nucleic acid sequence of SEQ ID NO: 96 or SEQ ID NO: 97, or variant thereof. In various embodiments, the P21 N-peptide and P21 BoxB hairpin RNA oligonucleotide interaction adopts a non-GNRA U-turn with respect to the apical four nucleotides of the P21 BoxB hairpin RNA oligonucleotide. A tetraloop is a type of four-base hairpin loop motif in RNA secondary structures that cap many double helices. In ribosomal RNA, the N could be either uracil, adenine, cytosine, or guanine, and the R is either guanine or adenine. The GNRA tetraloop, specifically, has a guanine-adenine base pair, where the guanine is 5’ to the helix and the adenine is 3’ to the helix. [0097] In various embodiments, a hairpin oligonucleotide of the present invention comprises at least one mutation selected from missense mutation, nonsense mutation, insertion, deletion, duplication, frameshift mutation, and repeat expansion. By way of non-limitation, such mutations can be made with respect to a hairpin oligonucleotide comprising one or more of nucleic acid sequences selected from SEQ ID NOs: 96-97. For example, in some embodiments, the P21 BoxB hairpin RNA oligonucleotide comprises the nucleic acid sequence of SEQ ID NO: 96 or SEQ ID NO: 97, and further comprises from 1 to 20 nucleotide mutations selected from one or more of nucleotide substitutions, nucleotide deletions, and nucleotide additions. In further embodiments, the one or more nucleotide mutations take(s) place at one or more of nucleotide residue positions 1 to 20, relative to wild-type P21 BoxB hairpin RNA oligonucleotide. F. Fusion Proteins [0098] In various embodiments contemplated by the present disclosure, fusion proteins are provided comprising a deaminase, or fragment thereof, and a bacteriophage N-peptide, optionally connected by a chemical linker. By way of non-limiting example, the deaminase, or fragment thereof can be linked to at least 2, at least 3, or at least 4 N-peptides. Alternatively, the N-peptide can be linked to at least 2, at least 3, or at least 4 deaminases, or fragments thereof. Some aspects of the disclosure provide fusion proteins that comprise one or more deaminase domains (e.g., adenosine deaminase and/or cytidine deaminase). For example, in some embodiments, the fusion protein comprises at least two deaminase domains. Without wishing to be bound by any particular theory, dimerization of deaminases (e.g., in cis or in trans) may improve the ability (e.g., efficiency) of the fusion protein to edit a nucleic acid base and/or nucleotide, for example to deaminate adenosine and/or cytidine. In some embodiments, any of the fusion proteins may comprise at least 2, at least 3, at least 4 or at least 5 adenosine deaminase domains. In some embodiments, any of the fusion proteins provided herein comprise two deaminases. In some Attorney Docket No.: 33791/41005 embodiments, any of the fusion proteins provided herein contain only two deaminases. In some embodiments, the deaminases are the same. In some embodiments, the deaminases are any of the deaminases provided herein. In some embodiments, the deaminases are different. In some embodiments, the first deaminase is any of the adenosine or cytidine deaminases provided herein, and the second deaminase is any of the adenosine or cytidine deaminases provided herein, but is not identical to the first deaminase. [0099] In some embodiments, the deaminase and bacteriophage N-peptide fusion protein comprises one or more nuclear localization signals (NLS), optionally wherein the RNA molecule comprising the target nucleotide to be edited is located in the nucleus of the cell. In some embodiments, the fusion protein of the present disclosure comprises 1, 2, 3, 4, or 5 nuclear localization signals (e.g., nuclear localization sequences). In further embodiments, the nuclear localization signal is the SV40 Large T-antigen nuclear localization signal (SEQ ID NO: 21). [00100] The term "nuclear localization signal" or "NLS" refers to an amino acid sequence that promotes import of a protein into the cell nucleus, for example, by nuclear transport. Nuclear localization sequences are known in the art and would be apparent to the skilled artisan. For example, NLS sequences are described in Plank et al., International PCT application, PCT/EP2000/011690, filed November 23, 2000, published as WO/2001/038547 on May 31, 2001; and in Kosugi et al., J. Biol. Chem. (2009) 284: 478-485, the contents of which are incorporated herein by reference for their disclosure of exemplary nuclear localization sequences. Nuclear localization sequences can include the nuclear localization sequence of the SV40 virus large T-antigen the minimal functional unit of which is the seven amino acid sequence PKKKRKV (SEQ ID NO: 22). Other examples of nuclear localization sequences include the nucleoplasmin bipartite NLS with the sequence NLSKRPAAIKKAGQAKKKK (SEQ ID NO: 23); the c-myct nuclear localization sequence having the amino acid sequence PAAKRVKLD (SEQ ID NO: 24) or RQRRNELKRSF (SEQ ID NO: 25); and the hRNPAI M9 NLS having the sequence NQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGY (SEQ ID NO: 26). Further examples of nuclear localization sequences are: the sequence RMRKFKNKGKDTAELRRRRVEVSVELRKAKKDEQILKRRNV (SEQ ID NO: 27) of the IBB domain from importin-alpha; the sequences VSRKRPRP (SEQ ID NO: 28) and PPKKARED (SEQ ID NO: 29) of the myoma T protein; the sequence PQPKKKPL (SEQ ID NO: 30) of human p53; the sequence SALIKKKKKMAP (SEQ ID NO: 31) of mouse c-abl IV; the sequences DRLRR (SEQ ID NO: 32) and PKQKKRK (SEQ ID NO: 33) of the influenza virus NS1; the sequence RKLKKKIKKL (SEQ ID NO: 34) of Attorney Docket No.: 33791/41005 the Hepatitis virus delta antigen; and the sequence REKKKFLKRR (SEQ ID NO: 35) of the mouse Mx1 protein. It is also possible to use bipartite nuclear localization sequences such as the sequence KRKGDEVDGVDEVAKKKSKK (SEQ ID NO: 36) of the human poly(ADP-ribose) polymerase or the sequence RKCLQAGMNLEARKTKK (SEQ ID NO: 37) of the steroid hormone receptors (human) glucocorticoid. In some embodiments, a NLS of the present disclosure comprises the amino acid sequence SV40 Large T-antigen NLS comprising the amino acid sequence: DPKKKRKVDPKKKRKVDPKKKRKV (SEQ ID NO: 21). [00101] In some embodiments, the NLS contemplated by the present disclosure comprises one or more mutations (e.g., amino acid substitutions, deletions, and/or insertions) with respect to any one of SEQ ID NOs: 21-37. [00102] In some embodiments, the fusion proteins provided herein further comprise one or more nuclear targeting sequences, for example, a nuclear localization signal/sequence (NLS). In some embodiments, a NLS comprises an amino acid sequence that facilitates the importation of a protein, that comprises an NLS, into the cell nucleus. In some embodiments, the NLS is fused to the N-terminus of the fusion protein. In some embodiments, the NLS is fused to the C-terminus of the fusion protein. In some embodiments, the NLS is fused to the N-terminus of the deaminase. In some embodiments, the NLS is fused to the C-terminus of the deaminase. In some embodiments, the NLS is fused to the N-terminus of the λ N-peptide. In some embodiments, the NLS is fused to the C-terminus of the λ N-peptide. In some embodiments, the NLS is fused to the fusion protein via one or more linkers. In some embodiments, the NLS is fused to the fusion protein without a linker. In some embodiments, the NLS comprises an amino acid sequence of any one of the NLS sequences provided or referenced herein. In some embodiments, the NLS comprises an amino acid sequence as set forth in SEQ ID NO: 21-37, or variants thereof. Additional nuclear localization sequences are known in the art and would be apparent to the skilled artisan. For example, NLS sequences are described in Plank et al., PCT/EP2000/011690, the contents of which are incorporated herein by reference for their disclosure of illustrative nuclear localization sequences. G. Vector Delivery [00103] In some embodiments, components (i) a deaminase linked to a mutant λ N-peptide, and (ii) an antisense RNA oligonucleotide linked to a hairpin (e.g., a BoxB hairpin RNA) oligonucleotide, of the present disclosure are contained within various delivery vehicles. Attorney Docket No.: 33791/41005 [00104] For example, in some embodiments, the components of the present disclosure are contained within a plasmid or vector. In further embodiments, components (i) and (ii) of the present disclosure are contained within a viral vector. In further embodiments, such components of the present disclosure as previously described are synthetically generated or generated from a plasmid. In still further embodiments, the components are contained within a plasmid or vector, optionally wherein the vector is a viral vector. Such viral vectors can include, but are not limited to, adeno-associated viruses (AAVs), adenoviruses, retroviruses, and lentiviruses. In specific embodiments, the viral vector is an adeno-associated virus (AAV) vector. The AAV can be selected from AAV1, or AAV2, or AAV3, or AAV4, or AAV5, or AAV6, or AAV7, or AAV8, or AAV9, or AAV10, or AAV11, and AAV12. [00105] In some embodiments, components of the present disclosure are contained within mRNA for delivery. For example, in some embodiments, a synthetic oligonucleotide encoding the present compositions is provided. The synthetic oligonucleotide can have non-canonical nucleotides that, without wishing to be bound by theory, reduce innate immune responses. In various embodiments, the synthetic oligonucleotide is an mRNA comprising one or more non-canonical nucleotides. In some embodiments, the mRNA comprises one or more non-canonical nucleotides found in U.S. Patent No.8,278,036, the entire contents of which are hereby incorporated by reference. In some embodiments, the mRNA comprises one or more of m5C, m5U, m6A, s2U, Ψ, and 2′-O-methyl-U. [00106] In further embodiments, the components of the present disclosure are contained in lipid nanoparticles for gene delivery. In particular, an excipient may be used that aids in enhancing the stability, solubility, absorption, bioavailability, activity, pharmacokinetics, pharmacodynamics and/or delivery of the components of the present disclosure to a cell and into a cell. In embodiments, particular excipients capable of forming complexes, vesicles, nanoparticles, microparticles, nanotubes, nanogels, hydrogels, poloxamers or pluronics, polymersomes, colloids, microbubbles, vesicles, micelles, lipoplexes and/or liposomes, that deliver components complexed or trapped in the vesicles or liposomes through a cell membrane find use. Examples of nanoparticles that are useful in various emobodiments include gold nanoparticles, magnetic nanoparticles, silica nanoparticles, lipid nanoparticles, sugar particles, protein nanoparticles and peptide nanoparticles. Another group of nanoparticles that are useful in various emobodiments are polymeric nanoparticles. Many of these polymeric substances are known in the art. Suitable substances that are useful in various emobodiments comprise e.g. polyethylenimine (PEI), ExGen 500, polypropyleneimine (PPI), poly(2-hydroxypropylenimine (pHP)), dextran derivatives (e.g. polycations such like diethyl amino ethyl amino ethyl (DEAE)-dextran, which are well known as DNA transfection Attorney Docket No.: 33791/41005 reagent can be combined with butylcyanoacrylate (PBCA) and hexylcyanoacrylate (PHCA) to formulate cationic nanoparticles that can deliver said compound across cell membranes into cells), butylcyanoacrylate (PBCA), hexylcyanoacrylate (PHCA), poly(lactic-co-gly colic acid) (PLGA), polyamines (e.g. spermine, spermidine, putrescine, cadaverine), chitosan, poly(amido amines) (PAMAM), poly(ester amine), polyvinyl ether, polyvinyl pyrrolidone (PVP), polyethylene glycol (PEG) cyclodextrins, hyaluronic acid, colominic acid, and derivatives thereof), dendrimers (e.g. poly(amidoamine), lipids (e.g.1,2-dioleoyl-3- dimethylammonium propane (DODAP), dioleoyldimethylammonium chloride (DODAC), phosphatidylcholine derivatives (e.g 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC)), lyso-phosphatidylcholine derivatives (e.g.1-stearoyl-2-lyso-sn-glycero-3-phosphocholine (S-LysoPC)), sphingomyeline, 2-{3-[bis-(3-amino- propyl)-amino]-propylamino}-N-ditetracedyl carbamoyl methylacetamide (RPR209120), phosphoglycerol derivatives (e.g.1,2-dipalmitoyl-sn-glycero-3-phosphoglycerol, sodium salt (DPPG-Na), phosphaticid acid derivatives (1,2-distearoyl-sn-glycero-3-phosphaticid acid, sodium salt (DSPA), phosphatidylethanolamine derivatives (e.g. dioleoyl-J-R-phosphatidylethanolamine (DOPE), 1,2-distearoyl-sn-glycero-3- phosphoethanolamine (DSPE), 2-diphytanoyl-sn-glycero-3-phosphoethanolamine (DPhyPE)), JV-[1-(2,3- dioleoyloxy)propyl]-N,N,N-trimethyl ammonium (DOTAP), 1,3-di-oleoyloxy-2-(6-carboxy-spermyl)- propylamid (DOSPER), (1,2-dimyristyolxypropyl-3-dimethylhydroxy ethyl ammonium (DMRIE), (N1- cholesteryloxycarbonyl-3,7-diazanonane-1,9-diamine (CD AN), dimethyldioctadecylammonium bromide (DDAB), 1-palmitoyl-2-oleoyl-sn-glycerol-3-phosphocholine (POPC), (b-L-Arginyl-2,3-L-diaminopropionic acid-N-palmityl-N-olelyl-amide trihydrochloride (AtuFECTOl), N,N-dimethyl-3-aminopropane derivatives (e.g.1,2-distearoyloxy-N,N-dimethyl-3-aminopropane (DSDMA), 1,2-dioleyloxy-N,N-dimethyl-3- aminopropane (DoDMA), 1,2-dilinoleyloxy-N,N-3-dimethylaminopropane (DLinDMA), 2,2-dilinoleyl-4- dimethylaminomethyl[1,3]-dioxolane (DLin-K-DMA), phosphatidylserine derivatives [1,2-dioleyl-sn-glycero- 3-phospho-L-serine, sodium salt (DOPS)], cholesterol), synthetic amphiphils (SAINT-18), lipofectin, proteins (e.g. albumin, gelatins, atellocollagen), peptides (e.g. PepFects, NickFects, polyarginine, polylysine, CADY, MPG) combinations thereof and/or viral capsid proteins that are capable of self assembly into particles that can deliver said components of the disclosure to a cell. [00107] Lipofectin is an illutrative liposomal transfection agent that finds use in various embodiments. It consists of at least two lipid components, a cationic lipid N-[1-(2,3-dioleoyloxy)propyl]-N,N,N- trimethylammonium chloride (DOTMA) (cp. DOTAP which is the methylsulfate salt) and a neutral lipid dioleoylphosphatidylethanolamine (DOPE). The neutral component mediates the intracellular release. Attorney Docket No.: 33791/41005 [00108] In addition to these nanoparticle materials, the cationic peptide protamine offers an alternative approach to formulate components of the present disclosure as colloids. This colloidal nanoparticle system can form so called proticles, which can be prepared by a simple self-assembly process to package and mediate intracellular release of a component as defined herein. The skilled person may select and adapt any of the above or other commercially available or not commercially available alternative excipients and delivery systems. [00109] In certain embodiments of the disclosure, the components of the present disclosure are contained within the same or separate vectors, plasmids, mRNAs, and/or lipid nanoparticles, thus allowing for consecutive (e.g., before or after) or concurrent (e.g., at the same time) delivery to the target cells in the same composition or in separate compositions. [00110] In some embodiments, the deaminase and lambdoid bacteriophage N-peptide are not linked and/or fused. In such embodiments, the present disclosure contemplates the use of an endogenous deaminase. For example, the deaminase may be recruited by the nucleic acid-editing system that includes some or all of the previously mentioned components. H. Pharmaceutically Acceptable Carriers [00111] In some embodiments, compositions of the present disclosure (e.g., compositions comprising plasmids and/or viral vectors) further comprise a pharmaceutically acceptable carrier. In some embodiments, the composition is formulated in appropriate pharmaceutical vehicles for administration to human or animal subjects. [00112] Some examples of materials which can serve as pharmaceutically-acceptable carriers include: (1) sugars, such as lactose, glucose and sucrose; (2) starches, such as corn starch and potato starch; (3) cellulose, and its derivatives, such as sodium carboxymethyl cellulose, methylcellulose, ethyl cellulose, microcrystalline cellulose and cellulose acetate; (4) powdered tragacanth; (5) malt; (6) gelatin; (7) lubricating agents, such as magnesium stearate, sodium lauryl sulfate and talc; (8) excipients, such as cocoa butter and suppository waxes; (9) oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; (10) glycols, such as propylene glycol; (11) polyols, such as glycerin, sorbitol, mannitol and polyethylene glycol (PEG); (12) esters, such as ethyl oleate and ethyl laurate; (13) agar; (14) buffering agents, such as magnesium hydroxide and aluminum hydroxide; (15) alginic acid; (16) pyrogen-free water; (17) isotonic saline; (18) Ringer’s solution; (19) ethyl alcohol; (20) pH buffered solutions; (21) polyesters, polycarbonates and/or polyanhydrides; (22) bulking agents, such as polypeptides Attorney Docket No.: 33791/41005 and amino acids (23) serum component, such as serum albumin, HDL and LDL; (22) C2-C12 alcohols, such as ethanol; and (23) other non-toxic compatible substances employed in pharmaceutical formulations. Wetting agents, coloring agents, release agents, coating agents, sweetening agents, flavoring agents, perfuming agents, preservative and antioxidants can also be present in the formulation. The terms such as "excipient", "carrier", "pharmaceutically acceptable carrier" or the like are used interchangeably herein. I. Methods of Use [00113] The present compositions and methods find use in various embodiments in altering nucleotides within an RNA molecule to provide a medically-beneficial effect. By way of example, the present compositions and methods are useful in reducing the prevalence of, or ablating, a mutation. By way of further example, the present compositions and methods are useful in introducing a mutation that beneficially affects a subject’s health. The compositions and methods described herein for the purpose of site-specific editing of a target nucleotide (e.g., within an RNA molecule) in a cell may be administered to a subject in need thereof in a therapeutically effective amount to treat and/or prevent a disease, condition or disorder the subject is suffering from. Alternatively, the subject may not be suffering from a disease, condition or disorder, and the site-specific editing of a target nucleotide (e.g., within an RNA molecule) in a cell may induce a beneficial mutation in the wild-type target sequence. [00114] In some embodiments, the present disclosure contemplates a method of site-specific base editing of a target nucleotide within a SerpinA1 gene in a cell using the compositions and methods described herein (including, without limitation, a wild-type λ N-peptide). In some embodiments, the present disclosure contemplates a method of site-specific base editing of a target nucleotide within a SerpinA1 gene in a cell comprising: (a) contacting the cell with: (i) a deaminase linked to a mutant or wild-type λ N- peptide, and (ii) an antisense RNA oligonucleotide linked to a BoxB hairpin RNA oligonucleotide, the BoxB hairpin RNA oligonucleotide being the cognate hairpin oligonucleotide of the λ N-peptide, and wherein: the antisense RNA oligonucleotide comprises a region complementary to an RNA molecule comprising the target nucleotide; the λ N-peptide and BoxB hairpin RNA oligonucleotide interact; and the deaminase domain causes editing of the target nucleotide to induce a base change. [00115] In some embodiments, the present disclosure contemplates a method of site-specific base editing of a target nucleotide within an IDUA gene in a cell using the compositions and methods described herein (including, without limitation, a wild-type lamboid bacteriophage N-peptide). In some embodiments, the present disclosure contemplates a method of site-specific base editing of a target nucleotide within an Attorney Docket No.: 33791/41005 IDUA gene in a cell comprising: (a) contacting the cell with: (i) a deaminase linked to a mutant or wild-type lamboid bacteriophage N-peptide, and (ii) an antisense RNA oligonucleotide linked to a BoxB hairpin RNA oligonucleotide, the BoxB hairpin RNA oligonucleotide being the cognate hairpin oligonucleotide of the λ N- peptide, and wherein: the antisense RNA oligonucleotide comprises a region complementary to an RNA molecule comprising the target nucleotide; the lamboid bacteriophage N-peptide and BoxB hairpin RNA oligonucleotide interact; and the deaminase domain causes editing of the target nucleotide to induce a base change. [00116] The compositions of this disclosure may be administered or packaged as a unit dose, for example. The term "unit dose" when used in reference to a pharmaceutical composition of the present disclosure refers to physically discrete units suitable as unitary dosage for the subject, each unit containing a predetermined quantity of active material calculated to produce the desired therapeutic effect in association with the required diluent, i.e., a carrier or vehicle. [00117] Treatment of a disease, condition or disorder includes delaying the development or progression of the disease, or reducing disease severity. Treating the disease or condition does not necessarily require curative results. [00118] As used therein, "delaying" the development of a disease means to defer, hinder, slow, retard, stabilize, and/or postpone progression of the disease. This delay can be of varying lengths of time, depending on the history of the disease and/or individuals being treated. A method that "delays" or alleviates the development of a disease, or delays the onset of the disease, is a method that reduces probability of developing one or more symptoms of the disease in a given time frame and/or reduces extent of the symptoms in a given time frame, when compared to not using the method. Such comparisons are typically based on clinical studies, using a number of subjects sufficient to give a statistically significant result. [00119] "Development" or "progression" of a disease means initial manifestations and/or ensuing progression of the disease. Development of the disease can be detectable and assessed using standard clinical techniques as well known in the art. However, development also refers to progression that may be undetectable. For purpose of this disclosure, development or progression refers to the biological course of the symptoms. "Development" includes occurrence, recurrence, and onset. [00120] As used herein "onset" or "occurrence" of a disease includes initial onset and/or recurrence. Conventional methods, known to those of ordinary skill in the art of medicine, can be used to administer the Attorney Docket No.: 33791/41005 isolated polypeptide or pharmaceutical composition to the subject, depending upon the type of disease to be treated or the site of the disease. J. Host Cells [00121] Cells that may contain any of the compositions described herein include prokaryotic cells and eukaryotic cells. The methods described herein are used to deliver a deaminase and other components contemplated herein into a eukaryotic cell (e.g., a mammalian cell, such as a human cell). In some embodiments, the cell is in vitro (e.g., cultured cell). In some embodiments, the cell is in vivo (e.g., in a subject such as a human subject). In some embodiments, the cell is ex vivo (e.g., isolated from a subject and may be administered back to the same or a different subject). [00122] Mammalian cells of the present disclosure include human cells, primate cells (e.g., vero cells), rat cells (e.g., GH3 cells, OC23 cells) or mouse cells (e.g., MC3T3 cells). There are a variety of human cell lines, including, without limitation, human embryonic kidney (HEK) cells, HeLa cells, cancer cells from the National Cancer Institute's 60 cancer cell lines (NCI60), DU145 (prostate cancer) cells, Lncap (prostate cancer) cells, MCF-7 (breast cancer) cells, MDA-MB-438 (breast cancer) cells, PC3 (prostate cancer) cells, T47D (breast cancer) cells, THP-1 (acute myeloid leukemia) cells, U87 (glioblastoma) cells, SHSY5Y human neuroblastoma cells (cloned from a myeloma) and Saos-2 (bone cancer) cells. In some embodiments, plasmids or viral vectors (e.g., adeno-associated virus (AAV) vectors) are delivered into human embryonic kidney (HEK) cells (e.g., HEK 293 or HEK 293T cells). In some embodiments, AAV vectors are delivered into stem cells (e.g., human stem cells) such as, for example, pluripotent stem cells (e.g., human pluripotent stem cells including human induced pluripotent stem cells (hiPSCs)). A stem cell refers to a cell with the ability to divide for indefinite periods in culture and to give rise to specialized cells. A pluripotent stem cell refers to a type of stem cell that is capable of differentiating into all tissues of an organism, but not alone capable of sustaining full organismal development. A human induced pluripotent stem cell refers to a somatic (e.g., mature or adult) cell that has been reprogrammed to an embryonic stem cell-like state by being forced to express genes and factors important for maintaining the defining properties of embryonic stem cells (see, e.g., Takahashi and Yamanaka, Cell 126 (4): 663-76, 2006, incorporated by reference herein). Human induced pluripotent stem cell cells express stem cell markers and are capable of generating cells characteristic of all three germ layers (ectoderm, endoderm, mesoderm). [00123] Additional non-limiting examples of cell lines that may be used in accordance with the present disclosure include 293-T, 293-T, 3T3, 4T1, 721, 9L, A-549, A172, A20, A253, A2780, A2780ADR, Attorney Docket No.: 33791/41005 A2780cis, A431, ALC, B 16, B35, BCP-1, BEAS-2B, bEnd.3, BHK-21, BR 293, BxPC3, C2C12, C3H- 10T1/2, C6, C6/36, Cal-27, CGR8, CHO, CML Tl, CMT, COR-L23, COR-L23/5010, COR-L23/CPR, COR- L23/R23, COS-7, COV-434, CT26, D17, DH82, DU145, DuCaP, E14Tg2a, EL4, EM2, EM3, EMT6/AR1, EMT6/AR10.0, FM3, H1299, H69, HB54, HB55, HCA2, Hepalclc7, High Five cells, HL-60, HMEC, HT-29, HUVEC, J558L cells, Jurkat, JY cells, K562 cells, KCL22, KG1, Ku812, KYOl, LNCap, Ma-Mel 1, 2, 3....48, MC-38, MCF-IOA, MCF-7, MDA-MB-231, MDA-MB-435, MDA-MB-468, MDCK II, MG63, MONO-MAC 6, MOR/0.2R, MRC5, MTD-1A, MyEnd, NALM-1, NCI-H69/CPR, NCI-H69/LX10, NCI-H69/LX20, NCI- H69/LX4, NIH-3T3, NW-145, OPCN/OPCT Peer, PNT-1A/PNT 2, PTK2, Raji, RBL cells, RenCa, RIN-5F, RMA/RMAS, S2, Saos-2 cells, Sf21, Sf9, SiHa, SKBR3, SKOV-3, T-47D, T2, T84, THP1, U373, U87, U937, VCaP, WM39, WT-49, X63, YAC-1 and YAR cells. K. Kits [00124] The compositions of the present disclosure may be assembled into kits. In some embodiments, the kit comprises nucleic acid vectors for the expression of the components of the nucleic acid-editing systems described herein. [00125] The kit described herein may include one or more containers housing components for performing the methods described herein and optionally instructions for use. Any of the kit described herein may further comprise components needed for performing the assay methods. Each component of the kits, where applicable, may be provided in liquid form (e.g., in solution) or in solid form, (e.g., a dry powder). In certain cases, some of the components may be reconstitutable or otherwise processible (e.g., to an active form), for example, by the addition of a suitable solvent or other species (for example, water), which may or may not be provided with the kit. [00126] In some embodiments, the kits may optionally include instructions and/or promotion for use of the components provided. As used herein, "instructions" can define a component of instruction and/or promotion, and typically involve written instructions on or associated with packaging of the disclosure. Instructions also can include any oral or electronic instructions provided in any manner such that a user will clearly recognize that the instructions are to be associated with the kit, for example, audiovisual (e.g., videotape, DVD, etc.), Internet, and/or web-based communications, etc. The written instructions may be in a form prescribed by a governmental agency regulating the manufacture, use, or sale of pharmaceuticals or biological products, which can also reflect approval by the agency of manufacture, use or sale for animal administration. As used herein, "promoted" includes all methods of doing business including methods of Attorney Docket No.: 33791/41005 education, hospital and other clinical instruction, scientific inquiry, drug discovery or development, academic research, pharmaceutical industry activity including pharmaceutical sales, and any advertising or other promotional activity including written, oral and electronic communication of any form, associated with the disclosure. Additionally, the kits may include other components depending on the specific application, as described herein. [00127] The kits may contain any one or more of the components described herein in one or more containers. The components may be prepared sterilely, packaged in a syringe and shipped refrigerated. Alternatively, it may be housed in a vial or other container for storage. A second container may have other components prepared sterilely. Alternatively, the kits may include the active agents premixed and shipped in a vial, tube, or other container. [00128] The kits may have a variety of forms, such as a blister pouch, a shrink wrapped pouch, a vacuum sealable pouch, a sealable thermoformed tray, or a similar pouch or tray form, with the accessories loosely packed within the pouch, one or more tubes, containers, a box or a bag. The kits may be sterilized after the accessories are added, thereby allowing the individual accessories in the container to be otherwise unwrapped. The kits can be sterilized using any appropriate sterilization techniques, such as radiation sterilization, heat sterilization, or other sterilization methods known in the art. The kits may also include other components, depending on the specific application, for example, containers, cell media, salts, buffers, reagents, syringes, needles, a fabric, such as gauze, for applying or removing a disinfecting agent, disposable gloves, a support for the agents prior to administration, etc. [00129] Without further elaboration, it is believed that one skilled in the art can, based on the above description, utilize the present disclosure to its fullest extent. The following specific embodiments are, therefore, to be construed as merely illustrative, and not limiting of the remainder of the disclosure in any way whatsoever. EXAMPLES Example 1: Construction of nucleic acid-editing system [00130] A nucleic acid-editing system of the present disclosure was constructed. A nucleic acid construct, e.g., a plasmid, was created composed of a nucleic acid sequence encoding a mutant λ N- peptide, a P21 N-peptide, or a P22 N-peptide linked to a deaminase domain, described herein, according to methods known to those skilled in the art. Attorney Docket No.: 33791/41005 C to U nucleic acid-editing system using bacteriophage lambda To build the C to U λN-deaminase nucleic acid-editing system, a mutation was introduced in the deaminase domain of human ADAR2 sequence of 4λN_DD wild type, corresponding to amino acid position 222, changing a valine to glycine. This plasmid henceforth will be denoted as “4λN_DD V222G” and its nucleic acid sequence is SEQ ID NO: 41. Additionally, a hyper-editing mutation was introduced in 4λN_DD V222G enzyme at amino acid position 349, changing a glutamic acid to glutamate. This plasmid henceforth will be denoted as “4λN_DD E359Q_V222G,” and its nucleic acid sequence is SEQ ID NO: 43. This construct is sequenced verified. [00131] A further nucleic acid construct, e.g., the same plasmid or a different plasmid, composed of a nucleic acid sequence encoding an antisense RNA oligonucleotide, which is complementary to a targeted nucleic acid allele sequence, linked to a hairpin RNA oligonucleotide, as described herein. Specifically, the deaminase domain is the human ADAR2 catalytic domain, optionally mutated (e.g., without limitation, with one or more mutations at one or more positions selected from E396, C451, V351, R455, T375, K376, S486, Q488, R510, K594, R348, G593, S397, H443, L444, Y445, F442, E438, T448, A353, V355, T339, P539, V525 and I520). The construct can be modified to include a NLS sequence (e.g. SV40). [00132] The antisense oligonucleotide linked to a hairpin RNA oligonucleotide was made by obtaining a DNA oligonucleotide encoding a U6 (RNA Polymerase III) promoter at the 5′ end followed by a sequence comprising the antisense oligonucleotide linked to the hairpin RNA oligonucleotide. A U6 RNA polymerase promoter from the pENTR plasmid was used for plasmids that encode the antisense RNA oligonucleotide used for substrate specificity and selectivity because a U6 promoter gives a very defined 5’-end transcription start site that confers the editing specificity and selectivity. The antisense oligonucleotide sequence corresponds to a variable length of antisense sequence, complementary to the RNA molecule that was targeted. A hairpin RNA oligonucleotide of the present disclosure was used. An antisense version of the same DNA oligonucleotide was also synthesized. The two were then hybridized together and used as a template to make RNA with an RNA polymerase (e.g. U6). [00133] Human SerpinA1 E342K gene (NM_000295.4) was synthesized and cloned into pcDNA3.1 plasmid under the control of the CMV promoter using BamHI and XbaI restriction sites (Quintara Bio, Berkeley, CA) and the correct insert was sequence verified. This plasmid henceforth will be denoted as “SerpinA1/E342K/pcDNA3.1” and is nucleic acid sequence is SEQ ID NO: 45. Attorney Docket No.: 33791/41005 [00134] The heterologous IDUA genetic fusion was designed to express Td Tomato gene fused a 2A peptide that was fused in frame to a small region of the human IDUA gene (NM_000203.5) that contains the W402X mutation. This was then fused in frame to eGFP. This entire genetic sequence was synthesized and cloned into pcDNA3.1 plasmid under the control of the CMV promoter using BamHI and XbaI restriction sites (Life Technologies). This plasmid henceforth will be denoted as “Td_IDUA W402X_eGFP/pcDNA3.1” and the correct insert was sequence verified as SEQ ID NO: 46. [00135] The sequence for bacteriophage lambda 2boxBLambda guide RNA designed for the SerpinA1 E342K allele is SEQ ID NO: 47 and was cloned into pENTR/U6 plasmid. The correct insert was sequence verified. This plasmid is denoted as “2boxBLambda SerpinA1 E342K.” The sequence for bacteriophage lambda 2boxBLambda guide RNA designed for the Td_IDUA W402X_eGFP mRNA is SEQ ID NO: 48 and was cloned into pENTR/U6 plasmid. The correct insert was sequence verified. This plasmid is denoted as “2boxBLambda IDUA W402X.” [00136] If desired, AAV vectors containing the plasmids and/or synthetic oligonucleotides are then prepared according to knowledge of those skilled in the art. [00137] The proper construction of the nucleic acid-editing system is verified via sequence analysis. [00138] The following tables provides the above-mentioned nucleic acid and/or amino acid sequences: Table 4. Sequence of Editase (i.e., nucleic acid-editing system) SEQ ID Name Sequence (5’ to 3’) NO: A AA A C G G C C T T G T A G G C C Attorney Docket No.: 33791/41005 GGCTGCTCACCATGTCCTGCAGTGACAAGATTGCACGCTGGAACGTGGTGGGCATCCAGG GATCCCTGCTCAGCATTTTCGTGGAGCCCATTTACTTCTCGAGCATCATCCTGGGCAGCCT TTACCACGGGGACCACCTTTCCAGGGCCATGTACCAGCGGATCTCCAACATAGAGGACCT A C T G G N R R V RL T NI A Q A AA A C G G C C T T G T A G G C C G T T A C T G G N R R V RL T NI Attorney Docket No.: 33791/41005 EDLPPLYTLNKPLLSGISNAEARQPGKAPNFSVNWTVGDSAIEVINATTGKDELGRASRLCKHA LYCRWMRVHGKVPSHLLRSKITKPNVYHESKLAAKEYQAAKARLFTAFIKAGLGAWVEKPTEQ DQFSLTPLV A AA A C G G C C T T G T A G G C C G T T A C T G G N R R V RL T NI A Q Table 5. Sequence of Target Substrate SEQ ID Name Sequence (5’ to 3’) NO: C C G C C A Attorney Docket No.: 33791/41005 GATCCATGAAGGCTTCCAGGAACTCCTCCGTACCCTCAACCAGCCAGACAGCCAGCT CCAGCTGACCACCGGCAATGGCCTGTTCCTCAGCGAGGGCCTGAAGCTAGTGGATAA GTTTTTGGAGGATGTTAAAAAGTTGTACCACTCAGAAGCCTTCACTGTCAACTTCGGG G T A G C G T T T T C A G C A T G T C A A A C C G C C G G C C C G G G G A A ct C G A A G G G CA C C C Attorney Docket No.: 33791/41005 CGCCCTGTCCAAGGACCCTAACGAGAAGAGGGACCACATGGTCCTCCTGGAGTTCGT GACCGCCGCTGGCATCACCCTGGGAATGGACGAGCTCTACAAATGA abe 6. ambda box sequence and annotaton SEQ ID Name Sequence (5’ to 3’) NO: C A Table 7. Primer sequences SEQ ID Name Sequence (5’ to 3’) NO: C to U nucleic acid-editing system using bacteriophage P21 [00139] To build the C to U P21N-deaminase nucleic acid-editing system a mutation was introduced at amino acid position 123 of 1P21N_DD wild type and amino acid position 258 of 4P21N_DD wild type, in both cases changing a valine to glycine. Henceforth, these two plasmids are denoted as 1P21N_DD V123G and 4P21N_DD V258G, respectively. These plasmids were sequence verified. Additionally, a hyper-editing mutation at amino acid position of 260 and amino acid position 295 was introduced in 1P21N_DD V123G and 4P21N_DD V258G, respectively, changing in both cases glutamic acid to glutamate. Henceforth, these plasmids will be denoted as 1P21N_DD E260Q_V123G and 4P21N_DD E295Q_V258G. These plasmids were sequence verified and are provided in Table 8 below. [00140] A further nucleic acid construct, e.g., the same plasmid or a different plasmid, composed of a nucleic acid sequence encoding an antisense RNA oligonucleotide, which is complementary to a targeted nucleic acid allele sequence, linked to a hairpin RNA oligonucleotide, as described herein. Specifically, the deaminase domain is the human ADAR2 catalytic domain, optionally mutated (e.g., without limitation, with one or more mutations at one or more positions selected from E396, C451, V351, R455, T375, K376, Attorney Docket No.: 33791/41005 S486, Q488, R510, K594, R348, G593, S397, H443, L444, Y445, F442, E438, T448, A353, V355, T339, P539, V525 and I520). The construct can be modified to include a NLS sequence (e.g. SV40). [00141] The antisense oligonucleotide linked to a hairpin RNA oligonucleotide was made by obtaining a DNA oligonucleotide encoding a U6 (RNA Polymerase III) promoter at the 5′ end followed by a sequence comprising the antisense oligonucleotide linked to the hairpin RNA oligonucleotide. A U6 RNA polymerase promoter from the pENTR plasmid was used for plasmids that encode the antisense RNA oligonucleotide used for substrate specificity and selectivity because a U6 promoter gives a very defined 5’-end transcription start site that confers the editing specificity and selectivity. The antisense oligonucleotide sequence corresponds to a variable length of antisense sequence, complementary to the RNA molecule that was targeted. A hairpin RNA oligonucleotide of the present invention was used. An antisense version of the same DNA oligonucleotide was also synthesized. The two were then hybridized together and used as a template to make RNA with an RNA polymerase (e.g. U6). [00142] Human SerpinA1 E342K gene (NM_000295.4) was synthesized and cloned into pcDNA3.1 plasmid under the control of the CMV promoter using BamHI and XbaI restriction sites (Quintara Bio, Berkeley, CA) and the correct insert was sequence verified. This plasmid henceforth will be denoted as “SerpinA1/E342K/pcDNA3.1” and is nucleic acid sequence is SEQ ID NO: 45. [00143] The heterologous IDUA genetic fusion was designed to express Td Tomato gene fused a 2A peptide that was fused in frame to a small region of the human IDUA gene (NM_000203.5) that contains the W402X mutation. This was then fused in frame to eGFP. This entire genetic sequence was synthesized and cloned into pcDNA3.1 plasmid under the control of the CMV promoter using BamHI and XbaI restriction sites (Life Technologies). This plasmid henceforth will be denoted as “Td_IDUA W402X_eGFP/pcDNA3.1” and the correct insert was sequence verified as SEQ ID NO: 46. [00144] The sequence for bacteriophage P212boxB guide RNA designed for the SerpinA1 E342K allele is SEQ ID NO: 110 and was cloned into pENTR/U6 plasmid. The correct insert was sequence verified. This plasmid is denoted as “2boxBP21 SerpinA1 E342K.” The sequence for bacteriophage P212boxB guide RNA designed for the Td_IDUA W402X_eGFP mRNA was cloned into pENTR/U6 plasmid. The correct insert was sequence verified. This plasmid is denoted as “2boxBP21 IDUA W402X.” [00145] If desired, AAV vectors containing the plasmids and/or synthetic oligonucleotides are then prepared according to knowledge of those skilled in the art. Attorney Docket No.: 33791/41005 [00146] The proper construction of the nucleic acid-editing system is verified via sequence analysis. [00147] The following tables provides the above-mentioned nucleic acid and/or amino acid sequences: Table 8. Sequence of Editase (i.e., nucleic acid-editing system) SEQ ID Name Sequence (5’ to 3’) NO: A AT C C G G TA T C A G C C C C A C A C T TT G C IA G D KI L T A A AT C C G G T T A G T T T Attorney Docket No.: 33791/41005 GCTCACCATGTCCTGCAGTGACAAGATTGCACGCTGGAACGTGGTGGGCATCCAGGGATC CCTGCTCAGCATTTTCGTGGAGCCCATTTACTTCTCGAGCATCATCCTGGGCAGCCTTTAC CACGGGGACCACCTTTCCAGGGCCATGTACCAGCGGATCTCCAACATAGAGGACCTGCCA C C C C IA G D KI L T A A AT C C G G T T A G T T T C C A C C C C IA G D KI L T A A AT C T A A Attorney Docket No.: 33791/41005 GTGGAGGCGGAGGATCCGGGGGCGGGGGCTCCATTGTGTGGAAGGAATCAAAGGGGAC GGCGAAGAGCAGGTATAAGGCGCGAAGAGCCGAACTGATCGCTGAAAGGCGGTCCAACG AAGCAGGGGGGGGCGGTAGTGGAGGTGGTGGGTCCGGTGGGGGAGGGAGTATCGTATG C C C T T G T TT A A C T A A C C G G C T G IA G T N R R LS N A A AT C T A A C G G C C C C C T T TT C A T G Attorney Docket No.: 33791/41005 TCCTGCAGTGACAAGATTGCACGCTGGAACGTGGTGGGCATCCAGGGATCCCTGCTCAGC ATTTTCGTGGAGCCCATTTACTTCTCGAGCATCATCCTGGGCAGCCTTTACCACGGGGACC ACCTTTCCAGGGCCATGTACCAGCGGATCTCCAACATAGAGGACCTGCCACCTCTCTACAC C C C C C G IA G T N R R LS N A A AT C T A A C G G C C C C C T T TT C A T G C C C C C C C C G IA G T N R Attorney Docket No.: 33791/41005 FLYTQLELYLNNKDDQKRSIFQKSERGGFRLKENVQFHLYISTSPCGDARIFSPHEPILEEPADR HPNRKARGQLRTKIESGQGTIPVRSNASIQTWDGVLQGERLLTMSCSDKIARWNVVGIQGSLL SIFVEPIYFSSIILGSLYHGDHLSRAMYQRISNIEDLPPLYTLNKPLLSGISNAEARQPGKAPNFSV L Table 9. Sequence of Target Substrate SEQ ID Name Sequence (5’ to 3’) NO: C C G C C A T A G G T A G C G T T T T C A G C A T G T C A A A C C G C C G G C C C Attorney Docket No.: 33791/41005 TGTACCCCCGCGACGGCGTGCTGAAGGGCGAGATCCACCAGGCCCTGAAGCTGAAG GACGGCGGCCACTACCTGGTGGAGTTCAAGACCATCTACATGGCCAAGAAGCCCGTG CAACTGCCCGGCTACTACTACGTGGACACCAAGCTGGACATCACCTCCCACAACGAG G A A G C A C C G T C C C G C A A Table 10. P222boxB sequence and annotation SEQ ID Name Sequence (5’ to 3’) NO: Table 11. Primer sequences SEQ ID Name Sequence (5’ to 3’) NO: C to U nucleic acid-editing system using bacteriophage P22 [00148] To build the C to U P22N-deaminase nucleic acid-editing system a mutation was introduced at amino acid position 116 of 1P22N_DD wild type and amino acid position 230 of 4P22N_DD wild type, in both cases changing a valine to glycine. Henceforth, these two plasmids are denoted as 1P22N_DD V116G and 4P22N_DD V230G, respectively. These plasmids were sequence verified. Additionally, a Attorney Docket No.: 33791/41005 hyper-editing mutation at amino acid position of 253 and amino acid position 267 was introduced in 1P22N_DD V116G and 4P22N_DD V230G, respectively, changing in both cases glutamic acid to glutamate. Henceforth, these plasmids will be denoted as 1P22N_DD E253Q_V116G and 4P22N_DD E267Q_V230G. These plasmids were sequence verified and are provided in Table 12 below. [00149] A further nucleic acid construct, e.g., the same plasmid or a different plasmid, composed of a nucleic acid sequence encoding an antisense RNA oligonucleotide, which is complementary to a targeted nucleic acid allele sequence, linked to a hairpin RNA oligonucleotide, as described herein. Specifically, the deaminase domain is the human ADAR2 catalytic domain, optionally mutated (e.g., without limitation, with one or more mutations at one or more positions selected from E396, C451, V351, R455, T375, K376, S486, Q488, R510, K594, R348, G593, S397, H443, L444, Y445, F442, E438, T448, A353, V355, T339, P539, V525 and I520). The construct can be modified to include a NLS sequence (e.g. SV40). [00150] The antisense oligonucleotide linked to a hairpin RNA oligonucleotide was made by obtaining a DNA oligonucleotide encoding a U6 (RNA Polymerase III) promoter at the 5′ end followed by a sequence comprising the antisense oligonucleotide linked to the hairpin RNA oligonucleotide. A U6 RNA polymerase promoter from the pENTR plasmid was used for plasmids that encode the antisense RNA oligonucleotide used for substrate specificity and selectivity because a U6 promoter gives a very defined 5’-end transcription start site that confers the editing specificity and selectivity. The antisense oligonucleotide sequence corresponds to a variable length of antisense sequence, complementary to the RNA molecule that was targeted. A hairpin RNA oligonucleotide of the present invention was used. An antisense version of the same DNA oligonucleotide was also synthesized. The two were then hybridized together and used as a template to make RNA with an RNA polymerase (e.g. U6). [00151] Human SerpinA1 E342K gene (NM_000295.4) was synthesized and cloned into pcDNA3.1 plasmid under the control of the CMV promoter using BamHI and XbaI restriction sites (Quintara Bio, Berkeley, CA) and the correct insert was sequence verified. This plasmid henceforth will be denoted as “SerpinA1/E342K/pcDNA3.1” and is nucleic acid sequence is SEQ ID NO: 45. [00152] The heterologous IDUA genetic fusion was designed to express Td Tomato gene fused a 2A peptide that was fused in frame to a small region of the human IDUA gene (NM_000203.5) that contains the W402X mutation. This was then fused in frame to eGFP. This entire genetic sequence was synthesized and cloned into pcDNA3.1 plasmid under the control of the CMV promoter using BamHI and Attorney Docket No.: 33791/41005 XbaI restriction sites (Life Technologies). This plasmid henceforth will be denoted as “Td_IDUA W402X_eGFP/pcDNA3.1” and the correct insert was sequence verified as SEQ ID NO: 46. [00153] The sequence for bacteriophage lambda 2boxBP22 guide RNA designed for the SerpinA1 E342K allele is SEQ ID NO: 93 and was cloned into pENTR/U6 plasmid. The correct insert was sequence verified. This plasmid is denoted as “2boxBP22 SerpinA1 E342K.” The sequence for bacteriophage lambda 2boxBP22 guide RNA designed for the Td_IDUA W402X_eGFP mRNA is SEQ ID NO: 94 and was cloned into pENTR/U6 plasmid. The correct insert was sequence verified. This plasmid is denoted as “2boxBP22 IDUA W402X.” [00154] If desired, AAV vectors containing the plasmids and/or synthetic oligonucleotides are then prepared according to knowledge of those skilled in the art. [00155] The proper construction of the nucleic acid-editing system is verified via sequence analysis. [00156] The following tables provides the above-mentioned nucleic acid and/or amino acid sequences: Table 12. Sequence of Editase (i.e., nucleic acid-editing system) SEQ ID Name Sequence (5’ to 3’) NO: A G A A T C T TA A A A G C A C C T G G G G A C Attorney Docket No.: 33791/41005 1P22N_DD MYPYDVPDYAAPKKKRKVDPKKKRKVDPKKKRKVGSTSGVGNAKTRRHERRRKLAIERDTIGY wild type LHLDQTPSRQPIPSEGLQLHLPQVLADAVSRLVLGKFGDLTDNFSSPHARRKVLAGVVMTTGT (amino acid) DVKDAKVISVSTGTKCINGEYMSDRGLALNDCHAEIISRRSLLRFLYTQLELYLNNKDDQKRSIF TI LS G A A G A A T C T TA A A A G C A C C T G G G G A C Y T F TI LS G A A G A A T C T TA A A A G C A C C Attorney Docket No.: 33791/41005 ATGTACCAGCGGATCTCCAACATAGAGGACCTGCCACCTCTCTACACCCTCAACAAGCCTT TGCTCAGTGGCATCAGCAATGCAGAAGCACGGCAGCCAGGGAAGGCCCCCAACTTCAGTG TCAACTGGACGGTAGGCGACTCCGCTATTGAGGTCATCAACGCCACGACTGGGAAGGATG G G A C Y T F TI LS G A A G A A G C C A C C A G G G A TT A A G C T C G C C C G T Y PS IS F I I K T Attorney Docket No.: 33791/41005 4P22N_DD ATGTACCCATACGACGTCCCAGACTACGCTGCTCCAAAAAAGAAGAGAAAGGTAGATCCAA V230G AAAAGAAGAGAAAGGTAGATCCAAAAAAGAAGAGAAAGGTAGGATCCACCTCCGGAGTAG GAAACGCCAAGACCAGACGGCATGAAAGGAGACGCAAGCTGGCAATTGAAAGAGACACCA A G C C A C C A G G G A TT A A G C T C G C C C G T Y PS IS F I I K T A G A A G C C A C C A G G G A TT Attorney Docket No.: 33791/41005 CATCTGTACATCAGCACCTCTCCCTGTGGAGATGCCAGAATCTTCTCACCACATGAGCCAA TCCTGGAAGAACCAGCAGATAGACACCCAAATCGTAAAGCAAGAGGACAGCTACGGACCA AAATAGAGTCTGGTCAGGGGACGATTCCAGTGCGCTCCAATGCGAGCATCCAAACGTGGG C T C G C C C G T Y PS IS F I I K T Table 13. Sequence of Target Substrate SEQ ID Name Sequence (5’ to 3’) NO: C C G C C A T A G G T A G C G T T T T C A Attorney Docket No.: 33791/41005 46 Td_IDUA GCCACCATGGTGAGCAAGGGCGAGGAGGTCATCAAAGAGTTCATGCGCTTCAAGGTG W402X_eGFP/pcD CGCATGGAGGGCTCCATGAACGGCCACGAGTTCGAGATCGAGGGCGAGGGCGAGG NA3.1 GCCGCCCCTACGAGGGCACCCAGACCGCCAAGCTGAAGGTGACCAAGGGCGGCCC A T G T C A A A C C G C C G G C C C G G G G A A G C A C C G T C C C G C A A Table 14. P222boxB sequence and annotation SEQ ID Name Sequence (5’ to 3’) NO: C A Attorney Docket No.: 33791/41005 Table 15. Primer sequences SEQ ID Name Sequence (5’ to 3’) NO: Example 2: In vitro RNA editing in a model cell to test activity of the nucleic acid-editing system [00157] The nucleic acid-editing system is tested for its ability to specifically edit RNA. The test gene contains a specific nucleotide(s) that is to be targeted for editing. In typical editing experiments 3.64 ng of nucleic acid-editing system plasmid, 50 ng of BoxB guide RNA expressing plasmid and 0.91 ng of target plasmid are transfected into 2x105 HEK293T cells (ATCC) using Lipofectamine 3000 (0.2 µL/per well) in a 96-well format. All transfections using Lipofectamine 3000 are performed according to manufacturer’s instructions. 24 to 120 hours later, the cells are washed once with ice cold PBS and total mRNA isolation is performed using Dyna Beads mRNA Direct Kit (Life Technologies) adapted for KingFisher Flex Purification (Life Technologies). This is done according to manufacturer’s instructions. The samples are treated with TURBO DNase (Life Technologies) prior to elution. The resultant isolated mRNA is used for cDNA synthesis using SuperScript IV Vilo according the manufacturer’s instructions (Life Technologies). Two to six µl of the cDNA is used for as template for PCR (Platinum II Hot-Start PCR Master Mix; Life Technologies) using gene specific primers to generate an amplicon for Sanger sequencing (SEQ ID NOs: 49-52 are used for primers in RT PCR). Sanger sequencing is performed by QuintaraBio (USA) or Psomagen (USA). Deamination of base and subsequent editing yields are quantified by measuring the peak height of U and dividing the edited nucleotide peak height by the total peak height measurements of non-edited and edited nucleotide combined. [00158] In another experiment, the antisense RNA oligonucleotide linked to a hairpin RNA oligonucleotide complex is developed according to the method of Example 1. The antisense portion of the RNA oligonucleotide is complementary to specific nucleotides of the test gene mRNA. The hairpin RNA oligonucleotide is inserted in the antisense oligonucleotide as desired. In these experiments, the position and number (1 to 2) of the hairpin RNA oligonucleotide is varied and still has a functional interaction. This antisense RNA oligonucleotide linked to a hairpin RNA oligonucleotide is combined with a test gene mRNA Attorney Docket No.: 33791/41005 in vitro and a bacteriophage N-peptide linked to a deaminase domain protein, where they are expressed via the same or a separate plasmid promotor system, and brought in contact with the cell. After incubation, the test gene mRNA is converted into cDNA. Direct sequencing of RT-PCR products is undertaken to reveal editing at the specific nucleotide positions previously mentioned, directed by the antisense oligonucleotide and adjacent hairpin RNA oligonucleotide. Control experiments that lack either the antisense oligonucleotide linked to the hairpin RNA oligonucleotide or the λ N-peptide linked to a deaminase domain protein are expected to show no editing. A further control is to incorporate scrambled RNA sequence in place of the antisense sequence, which would be expected to show no editing and further demonstrates specificity. Taken together, these data are expected to show the hairpin RNA oligonucleotide-λ N-peptide interaction is required to target the catalytic domain of the deaminase to the nucleotide positions to be edited. [00159] Based on the above results, the system is further tested to correct a genetic mutation or sequence expressed endogenously in vitro (the type of genetic mutation described herein is illustrative of any of the various genetic mutations or wild type nucleotide that can be edited). A specific nucleotide of an mRNA is targeted in a human disease model (e.g. cell line). For example, a mutation can cause codons to change so that instead of an mRNA encoding and translating to an amino acid, a premature termination codon (PTC) is read, which can lead to these humans developing a disease or condition. Using the aforementioned nucleic acid-editing system and method of editing, a specific cytidine is converted to uracil by the acting deamination domain, thereby converting the PTC to a codon encoding tryptophan. The λ N- peptide linked to a deaminase domain protein will edit at a specific position based on being guided by the antisense RNA oligonucleotide linked to an inserted hairpin RNA oligonucleotide. Accordingly, construction of the antisense oligonucleotide linked to a hairpin RNA oligonucleotide will include selecting a sequence complementary to site to be edited with various lengths of nucleotides 5’ of the position. [00160] When this antisense oligonucleotide linked to the hairpin RNA oligonucleotide is combined with the λ N-peptide linked to a deaminase domain protein and the mutated mRNA in vitro, a percentage of the mutant mRNA is corrected, with the cytidine nucleotide being changed to uracil and thus correcting the codon. Editing is expected to be specific to the cytidine. Example 3: In vivo RNA editing in various genetic disorder models corrects mutation and recovers wild-type Attorney Docket No.: 33791/41005 [00161] The system and methods of Examples 1 and 2 can be tested in living cells or cell lysates. Any suitable model for the desired editing may be used. For instance, if genetically altered mice (e.g. wild type mice in which the target mutation is knocked in) are available, cells or tissues from such mice can be used to study the editing (either in vivo or ex vivo, e.g. by harvesting cells from the mice). Secondly, primary diseased human cell models in which the cells are procured from a human patient afflicted with the disease can be used to study the editing. Additionally, in vivo model can be employed to examine editing using wild type mice when targeting a wild type mRNA. [00162] Other suitable methods that may be employed in these Examples are described in PNAS November 5, 2013110 (45) 18285-18290; PNAS October 31, 2017114 (44) E9395-E9402; and Nature Methods February 8, 201916:239-242, the entire contents of which are incorporated by reference in their entireties. DEFINITIONS [00163] The following definitions are used in connection with the disclosure disclosed herein. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood to one of skill in the art to which this disclosure belongs. [00164] As used herein, “a,” “an,” or “the” can mean one or more than one. [00165] Further, the term “about” when used in connection with a referenced numeric indication means the referenced numeric indication plus or minus up to 10% of that referenced numeric indication. For example, the language “about 50” covers the range of 45 to 55. [00166] The term "deaminase" refers to an enzyme that catalyzes a deamination reaction. In some embodiments, the deaminase is a cytidine deaminase, catalyzing the hydrolytic deamination of cytidine or deoxycytidine to uracil or deoxyuracil, respectively. [00167] An “effective amount,” when used in connection with medical uses is an amount that is effective for providing a measurable treatment, prevention, or reduction in the rate of pathogenesis of a disease of interest, or optionally “effective amount” refers to an amount of a biologically active agent that is sufficient to elicit a desired biological response. For example, in some embodiments, an effective amount of a nuclease may refer to the amount of the nuclease that is sufficient to induce cleavage of a target site specifically bound and cleaved by the nuclease. In some embodiments, an effective amount of a fusion protein provided herein, e.g., of a fusion protein comprising a deaminase (e.g., a nucleic acid-editing Attorney Docket No.: 33791/41005 domain) and a lambdoid bacteriophage N-peptide may refer to the amount of the fusion protein that is sufficient to induce editing of a target site specifically bound and edited by the fusion protein. As will be appreciated by the skilled artisan, the effective amount of an agent, e.g., a fusion protein, a deaminase, a recombinase, a hybrid protein, a protein dimer, a complex of a protein (or protein dimer) and a polynucleotide, or a polynucleotide, may vary depending on various factors as, for example, on the desired biological response, e.g., on the specific allele, genome, or target site to be edited, on the cell or tissue being targeted, and on the agent being used. [00168] As referred to herein, all compositional percentages are by weight of the total composition, unless otherwise specified. As used herein, the word “include,” and its variants, is intended to be non- limiting, such that recitation of items in a list is not to the exclusion of other like items that may also be useful in the compositions and methods of this technology. Similarly, the terms “can” and “may” and their variants are intended to be non-limiting, such that recitation that an embodiment can or may comprise certain elements or features does not exclude other embodiments of the present technology that do not contain those elements or features. [00169] Although the open-ended term “comprising,” as a synonym of terms such as including, containing, or having, is used herein to describe and claim the disclosure, the present disclosure, or embodiments thereof, may alternatively be described using alternative terms such as “consisting of” or “consisting essentially of.” [00170] According to the present disclosure, the term “hairpin” refers to a particular RNA oligonucleotide and/or RNA structure that is recognized by and interacts with a bacteriophage N-peptide as disclosed herein (e.g., amino-terminal domain λ N-peptide derived from the λ N protein). A particular example of such a hairpin is a BoxB hairpin RNA oligonucleotide that is the cognate hairpin of the N- peptide. [00171] “Homology” or “identity” or “similarity” refers to sequence similarity between two peptides or between two nucleic acid molecules. Homology can be determined by comparing a position in each sequence that may be aligned for purposes of comparison. When a position in the compared sequence is occupied by the same base or amino acid, then the molecules are homologous at that position. A degree of homology between sequences is a function of the number of matching or homologous positions shared by the sequences. An “unrelated” or “non-homologous” sequence shares less than 40% identity, or alternatively less than 25% identity, with one of the sequences of the present disclosure. Attorney Docket No.: 33791/41005 [00172] “Homology” or “identity” or “similarity” can also refer to two nucleic acid molecules that hybridize under stringent conditions. [00173] “Hybridization” refers to a reaction in which one or more polynucleotides react to form a complex that is stabilized via hydrogen bonding between the bases of the nucleotide residues. The hydrogen bonding may occur by Watson-Crick base pairing, Hoogstein binding, or in any other sequence- specific manner. The complex may comprise two strands forming a duplex structure, three or more strands forming a multi-stranded complex, a single self-hybridizing strand, or any combination of these. A hybridization reaction may constitute a step in a more extensive process, such as the initiation of a PCR reaction, or the enzymatic cleavage of a polynucleotide by a ribozyme. [00174] Examples of stringent hybridization conditions include: incubation temperatures of about 25° C. to about 37° C.; hybridization buffer concentrations of about 6×SSC to about 10×SSC; formamide concentrations of about 0% to about 25%; and wash solutions from about 4×SSC to about 8×SSC. Examples of moderate hybridization conditions include: incubation temperatures of about 40° C. to about 50° C.; buffer concentrations of about 9×SSC to about 2×SSC; formamide concentrations of about 30% to about 50%; and wash solutions of about 5×SSC to about 2×SSC. Examples of high stringency conditions include: incubation temperatures of about 55° C. to about 68° C.; buffer concentrations of about 1×SSC to about 0.1×SSC; formamide concentrations of about 55% to about 75%; and wash solutions of about 1×SSC, 0.1×SSC, or deionized water. In general, hybridization incubation times are from 5 minutes to 24 hours, with 1, 2, or more washing steps, and wash incubation times are about 1, 2, or 15 minutes. SSC is 0.15 M NaCl and 15 mM citrate buffer. It is understood that equivalents of SSC using other buffer systems can be employed. [00175] As used herein, the term “specifically binds” refers to the binding specificity of a specific binding pair. Hybridization by a target-specific nucleic acid sequence of a particular target polynucleotide sequence in the presence of other potential targets is one characteristic of such binding. Specific binding involves two different nucleic acid molecules wherein one of the nucleic acid molecules specifically hybridizes with the second nucleic acid molecule through chemical or physical means. The two nucleic acid molecules are related in the sense that their binding with each other is such that they are capable of distinguishing their binding partner from other assay constituents having similar characteristics. The members of the binding component pair are referred to as ligand and receptor (anti-ligand), specific binding pair (SBP) member and SBP partner, and the like. Attorney Docket No.: 33791/41005 [00176] The term “linker,” as used herein, refers to a chemical group or a molecule linking two molecules or moieties, e.g., two domains of a fusion protein, such as, for example, a deaminase domain (e.g., a nucleic acid-editing domain) and lambdoid bacteriophage N-peptide. In some embodiments, a linker joins an antisense RNA oligonucleotide and a hairpin RNA oligonucleotide. Typically, the linker is positioned between, or flanked by, two groups, molecules, or other moieties and connected to each one via a covalent bond, thus connecting the two. In some embodiments, the linker is an amino acid or a plurality of amino acids (e.g., a peptide or protein). In some embodiments, the linker is an organic molecule, group, polymer, or chemical moiety. In some embodiments, the linker is 5-100 amino acids in length, for example, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 30-35, 35-40, 40-45, 45-50, 50-60, 60-70, 70-80, 80-90, 90-100, 100-150, or 150-200 amino acids in length. Longer or shorter linkers are also contemplated. [00177] According to the present disclosure a "mismatch" is found at any position where no direct Watson-Crick base pair (A/T, G/C, C/G, T/A) correspondence exists between the oligonucleotide and the target in the region of complementarity between the two strands. An artificial mismatch is typically provided at one or more single nucleotide positions in an oligonucleotide, but can include more extensive changes. A true mismatch in a duplex formed between an oligonucleotide and a variant target can include a substitution, an insertion, a deletion, and a rearrangement of oligonucleotide nucleic acid relative to the target. Substitution can be at one or more positions in the oligonucleotide. [00178] The term "mutation," as used herein, refers to a substitution of a residue within a sequence, e.g., a nucleic acid or amino acid sequence, with another residue, or a deletion or insertion of one or more residues within a sequence. Mutations are typically described herein by identifying the original residue followed by the position of the residue within the sequence and by the identity of the newly substituted residue. Various methods for making the amino acid substitutions (mutations) provided herein are well known in the art, and are provided by, for example, Green and Sambrook, Molecular Cloning: A Laboratory Manual (4th ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (2012)). According to embodiments of the present disclosure, a substituted amino acid residue is any naturally-occurring amino acid, such as a hydrophilic, hydrophobic, or non-classical amino acid. The hydrophilic amino acid can be selected from a polar and positively charged hydrophilic amino acid, a polar and neutral of charge hydrophilic amino acid, and polar and negatively charged hydrophilic amino acid, and an aromatic, polar and positively charged hydrophilic amino acid. A polar and positively charged hydrophilic amino acid can be selected from arginine (R) and lysine (K). A polar and neutral of charge hydrophilic amino acid can be Attorney Docket No.: 33791/41005 selected from asparagine (N), glutamine (Q), serine (S), threonine (T), proline (P), and cysteine (C). A polar and negatively charged hydrophilic amino acid can be selected from aspartate (D) and glutamate (E). An aromatic, polar and positively charged hydrophilic amino acid can be histidine (H). A hydrophobic amino acid can be selected from a hydrophobic, aliphatic amino acid and a hydrophobic, aromatic amino acid. The hydrophobic, aliphatic amino acid can be glycine (G), alanine (A), leucine (L), isoleucine (I), methionine (M), or valine (V). A hydrophobic, aromatic amino acid can be phenylalanine (F), tryptophan (W), or tyrosine (Y). A non-classical amino acid can be selected from selenocysteine, pyrrolysine, N- formylmethionine β-alanine, GABA, δ-Aminolevulinic acid, 4-Aminobenzoic acid (PABA), D-isomers of the common amino acids, 2,4-diaminobutyric acid, α-amino isobutyric acid, 4-aminobutyric acid, Abu, 2-amino butyric acid, γ-Abu, ε-Ahx, 6-amino hexanoic acid, Aib, 2-amino isobutyric acid, 3-amino propionic acid, ornithine, norleucine, norvaline, hydroxyproline, sarcosme, citrulline, homocitrulline, cysteic acid, t- butylglycine, t-butylalanine, phenylglycine, cyclohexylalanine, β-alanine, fluoroamino acids, designer amino acids such as β methyl amino acids, C α-methyl amino acids, N α -methyl amino acids, and amino acid analogs in general. [00179] The term "nuclear localization signal" or "NLS" refers to an amino acid sequence that promotes import of a protein into the cell nucleus, for example, by nuclear transport. Nuclear localization sequences are known in the art and would be apparent to the skilled artisan. For example, NLS sequences are described in Plank et al., international PCT application, PCT/EP2000/011690, filed November 23, 2000, published as WO/2001/038547 on May 31, 2001, the contents of which are incorporated herein by reference for their disclosure of exemplary nuclear localization sequences. [00180] The terms “nucleic acid” and “nucleic acid molecule,” as used herein, refer to a compound comprising a nucleobase and an acidic moiety, e.g., a nucleoside, a nucleotide, or a polymer of nucleotides. Typically, polymeric nucleic acids, e.g., nucleic acid molecules comprising three or more nucleotides are linear molecules, in which adjacent nucleotides are linked to each other via a phosphodiester linkage. In some embodiments, “nucleic acid” refers to individual nucleic acid residues (e.g. nucleotides and/or nucleosides). In some embodiments, “nucleic acid” refers to an oligonucleotide chain comprising three or more individual nucleotide residues. As used herein, the terms "oligonucleotide" and "polynucleotide" can be used interchangeably to refer to a polymer of nucleotides (e.g., a string of at least three nucleotides). In some embodiments, “nucleic acid” encompasses RNA as well as single- and/or double-stranded DNA. Nucleic acids may be naturally occurring, for example, in the context of a genome, a transcript, an mRNA, tRNA, rRNA, siRNA, snRNA, a plasmid, cosmid, chromosome, chromatid, or other Attorney Docket No.: 33791/41005 naturally occurring nucleic acid molecule. On the other hand, a nucleic acid molecule may be a non- naturally occurring molecule, e.g., a recombinant DNA or RNA, an artificial chromosome, an engineered genome, or fragment thereof, or a synthetic DNA, RNA, DNA/RNA hybrid, or including non-naturally occurring nucleotides or nucleosides. Furthermore, the terms “nucleic acid,” “DNA,” “RNA,” and/or similar terms include nucleic acid analogs, e.g., analogs having other than a phosphodiester backbone. Nucleic acids can be purified from natural sources, produced using recombinant expression systems and optionally purified, chemically synthesized, etc. Where appropriate, e.g., in the case of chemically synthesized molecules, nucleic acids can comprise nucleoside analogs such as analogs having chemically modified bases or sugars, and backbone modifications. A nucleic acid sequence is presented in the 5' to 3' direction unless otherwise indicated. In some embodiments, a nucleic acid is or comprises natural nucleosides (e.g. adenosine, thymidine, guanosine, cytidine, uridine, deoxyadenosine, deoxythymidine, deoxyguanosine, and deoxycytidine); nucleoside analogs (e.g., 2-aminoadenosine, 2-thiothymidine, inosine, pyrrolo-pyrimidine, 3-methyl adenosine, 5-methylcytidine, 2-aminoadenosine, C5-bromouridine, C5-fluorouridine, C5- iodouridine, C5-propynyl-uridine, C5-propynyl-cytidine, C5-methylcytidine, 2-aminoadenosine, 7- deazaadenosine, 7-deazaguanosine, 8-oxoadenosine, 8-oxoguanosine, 0(6)-methylguanine, and 2- thiocytidine); chemically modified bases; biologically modified bases (e.g. , methylated bases); intercalated bases; modified sugars (e.g., 2'-fluororibose, ribose, 2'-deoxyribose, arabinose, and hexose); and/or modified phosphate groups (e.g., phosphorothioates and 5'-N-phosphoramidite linkages). [00181] The term "pharmaceutically-acceptable carrier" means a pharmaceutically-acceptable material, composition or vehicle, such as a liquid or solid filler, diluent, excipient, manufacturing aid (e.g., lubricant, talc magnesium, calcium or zinc stearate, or steric acid), or solvent encapsulating material, involved in carrying or transporting the compound from one site (e.g., the delivery site) of the body, to another site (e.g., organ, tissue or portion of the body). A pharmaceutically acceptable carrier is "acceptable" in the sense of being compatible with the other ingredients of the formulation and not injurious to the tissue of the subject (e.g., physiologically compatible, sterile, physiologic pH, etc.). [00182] As used herein, the words “preferred” and “preferably” refer to embodiments of the technology that afford certain benefits, under certain circumstances. However, other embodiments may also be preferred, under the same or other circumstances. Furthermore, the recitation of one or more preferred embodiments does not imply that other embodiments are not useful, and is not intended to exclude other embodiments from the scope of the technology. Attorney Docket No.: 33791/41005 [00183] The term “subject,” as used herein, refers to an individual organism, for example, an individual mammal. In some embodiments, the subject is a human. In some embodiments, the subject is a non- human mammal. In some embodiments, the subject is a non-human primate. In some embodiments, the subject is a rodent. In some embodiments, the subject is a sheep, a goat, cattle, a cat, or a dog. In some embodiments, the subject is a vertebrate, an amphibian, a reptile, a fish, an insect, a fly, or a nematode. In some embodiments, the subject is a research animal. In some embodiments, the subject is genetically engineered, e.g., a genetically engineered non-human subject. The subject may be of either sex and at any stage of development. [00184] In certain embodiments, the effect will result in a quantifiable change of at least about 10%, at least about 20%, at least about 30%, at least about 50%, at least about 70%, or at least about 90%. In some embodiments, the effect will result in a quantifiable change of about 10%, about 20%, about 30%, about 50%, about 70%, or even about 90% or more. In certain embodiments, the effect will result in a quantifiable change of two-fold, or three-fold, or four-fold, or five-fold, or ten-fold. Therapeutic benefit also includes halting or slowing the progression of the underlying disease or disorder or reduction in toxicity, regardless of whether improvement is realized. EQUIVALENTS [00185] While the disclosure has been described in connection with specific embodiments thereof, it will be understood that it is capable of further modifications and this application is intended to cover any variations, uses, or adaptations of the disclosure following, in general, the principles of the disclosure and including such departures from the present disclosure as come within known or customary practice within the art to which the disclosure pertains and as may be applied to the essential features hereinbefore set forth and as follows in the scope of the appended claims. [00186] Those skilled in the art will recognize, or be able to ascertain, using no more than routine experimentation, numerous equivalents to the specific embodiments described specifically herein. Such equivalents are intended to be encompassed in the scope of the following claims. INCORPORATION BY REFERENCE [00187] All patents and publications referenced herein are hereby incorporated by reference in their entireties. Attorney Docket No.: 33791/41005 [00188] The publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the present disclosure is not entitled to antedate such publication by virtue of prior disclosure. [00189] As used herein, all headings are simply for organization and are not intended to limit the disclosure in any manner. The content of any individual section may be equally applicable to all sections. [00190] Exemplary embodiments: [00191] 1A. A method of site-specific editing of a target nucleotide within an RNA molecule in a cell comprising: (a) contacting the cell with: (i) a deaminase linked to a mutant λ bacteriophage N-peptide, a lamboid P22 bacteriophage N-peptide, and (ii) an antisense RNA oligonucleotide linked to a hairpin RNA oligonucleotide, wherein: the antisense RNA oligonucleotide comprises a region complementary to an RNA molecule comprising the target nucleotide; the N-peptide and hairpin interact; and the deaminase domain causes editing of the target nucleotide to induce a base change. [00192] 2A. A method of treating a disease or disorder by editing a target nucleotide within an RNA molecule in a cell, the method comprising contacting the cell with: (i) a deaminase linked to a mutant λ bacteriophage N-peptide, a lamboid P22 bacteriophage N-peptide, and (ii) an antisense RNA oligonucleotide linked to a hairpin RNA oligonucleotide, wherein: the antisense RNA oligonucleotide comprises a region complementary to an RNA molecule comprising the target nucleotide; the N-peptide and hairpin interact; and the deaminase domain causes editing of the target nucleotide to induce a base change. [00193] 3A. The method of any one of the preceding paragraphs, wherein the deaminase is cytidine deaminase or adenosine deaminase. [00194] 4A. The method of any one of the preceding paragraphs, wherein the adenosine deaminase yields an uracil (U) nucleotide. Attorney Docket No.: 33791/41005 [00195] 5A. The method of any one of the preceding paragraphs, wherein the adenosine deaminase is selected from adenosine deaminase RNA specific 1 (ADAR1), adenosine deaminase RNA specific 2 (ADAR2), adenosine deaminase RNA specific B1 (ADARB1), adenosine deaminase like (ADAL), adenosine deaminase 2 (ADA2), adenosine monophosphate deaminase 1 (AMPD1), adenosine monophosphate deaminase 2 (AMPD2), adenosine monophosphate deaminase 3 (AMPD3), adenosine deaminase domain containing 1 (ADAD1), adenosine deaminase domain containing 2 (ADAD2), adenosine deaminase tRNA specific 1 (ADAT1), adenosine deaminase tRNA specific 2 (ADAT2), adenosine deaminase tRNA specific 3 (ADAT3), TadA or fragments or variants thereof. [00196] 6A. The method of any one of the preceding paragraphs, wherein the adenosine deaminase is ADAR1 or ADAR2. [00197] 7A. The method of any one of the preceding paragraphs, wherein the adenosine deaminase is a fragment, the fragment comprising the catalytic domain of the adenosine deaminase. [00198] 8A. The method of any one of the preceding paragraphs, wherein the adenosine deaminase is a fragment, the fragment comprising a catalytic domain and one or more mutations. [00199] 9A. The method of any one of the preceding paragraphs, wherein the ADAR1 or ADAR2 comprises a fragment that comprises a catalytic domain. [00200] 10A. The method of any one of the preceding paragraphs, wherein the catalytic domain is the deaminase domain of human ADAR2, comprising an amino acid sequence having at least 90% amino acid sequence identity with SEQ ID NO: 18. [00201] 11A. The method of any one of the preceding paragraphs, wherein the ADAR2 comprises the amino acid sequence of SEQ ID NO: 19. [00202] 12A. The method of any one of the preceding paragraphs, wherein the ADAR induces a cytidine (C) to uridine (U) nucleotide mutation, optionally wherein the ADAR comprises one or more mutations that allow the ADAR to induce the C to U nucleotide mutation, optionally wherein the ADAR mutation(s) is selected from a substitution at one or more positions E396, C451, V351, R455, T375, K376, S486, Q488, R510, K594, R348, G593, S397, H443, L444, Y445, F442, E438, T448, A353, V355, T339, P539, V525 and I520, optionally relative to SEQ ID NO: 18 or SEQ ID NO: 19. [00203] 13A. The method of any one of the preceding paragraphs, wherein the cytidine deaminase yields a uridine (U) nucleotide. [00204] 14A. The method of any one of the preceding paragraphs, wherein the cytidine deaminase is selected from APOBEC1, activation-induced cytidine deaminase (AID), APOBEC2, APOBEC3A, Attorney Docket No.: 33791/41005 APOBEC3B, APOBEC3C, APOBEC3D, APOBEC3E, APOBEC3F, APOBEC3G, APOBEC3H, pmCDA1, and ACF1/ASE, or fragments or variants thereof. [00205] 15A. The method of any one of the preceding paragraphs, wherein the cytidine deaminase is a fragment, the fragment comprising the catalytic domain of the cytidine deaminase. [00206] 16A. The method of any one of the preceding paragraphs, wherein the cytidine deaminase is a fragment, the fragment comprising a catalytic domain and one or more mutations. [00207] 17A. The method of any one of the preceding paragraphs, wherein the mutant amino-terminal domain λ N-peptide is not the wild-type amino-terminal domain λ N-peptide (SEQ ID NO: 1). [00208] 18A. The method of any one of the preceding paragraphs, wherein the mutant amino-terminal domain λ N-peptide comprises an arginine-rich motif. [00209] 19A. The method of any one of the preceding paragraphs, wherein the mutant amino-terminal domain λ N-peptide comprises an Ala at position 3 and an arginine at each of positions 6, 10, and 11 of SEQ ID NO: 1. [00210] 20A. The method of any one of the preceding paragraphs, wherein the mutant amino-terminal domain λ N-peptide variant comprises at least one mutation as compared to the wild-type amino- terminal domain λ N-peptide (SEQ ID NO: 1). [00211] 21A. The method of any one of the preceding paragraphs, wherein the mutant mutant amino- terminal domain λ N-peptide comprises a mutation selected from one or more of an amino acid substitution, deletion, and addition. [00212] 22A. The method of any one of the preceding paragraphs, wherein the mutant amino-terminal domain λ N-peptide comprises from 1 to 19 amino acid residue substitutions. [00213] 23A. The method of any one of the preceding paragraphs, wherein the amino acid substitution takes place at one or more of amino acid residue positions 1 to 19, relative to the wild-type amino- terminal domain λ N-peptide sequence (SEQ ID NO: 1). [00214] 24A. The method of any one of the preceding paragraphs, wherein the amino acid substitution is selected from any one of the amino acid substitutions listed in Table 1. [00215] 25A. The method of any one of the preceding paragraphs, wherein the mutant amino-terminal domain λ N-peptide comprises the amino acid sequence of any one of SEQ ID NO: 2 to SEQ ID NO: 9. [00216] 26A. The method of any one of the preceding paragraphs, wherein the affinity of the mutant λ N-peptide for the BoxB hairpin RNA oligonucleotide is greater than the affinity of the wild-type λ N- peptide for the BoxB hairpin RNA oligonucleotide. Attorney Docket No.: 33791/41005 [00217] 27A. The method of any one of the preceding paragraphs, wherein the affinity is greater by at least 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 15-fold, 20-fold, 25-fold, 30-fold, 35-fold, 40-fold, 45-fold, 50-fold, or 100-fold. [00218] 28A. The method of any one of the preceding paragraphs, wherein the mutant λ N-peptide comprises a substituted amino acid residue that is any naturally-occurring amino acid. [00219] 29A. The method of any one of the preceding paragraphs, wherein the naturally-occurring amino acid is hydrophilic, hydrophobic, or non-classical. [00220] 30A. The method of any one of the preceding paragraphs, wherein the hydrophilic amino acid is selected from a polar and positively charged hydrophilic amino acid, a polar and neutral of charge hydrophilic amino acid, and polar and negatively charged hydrophilic amino acid, and an aromatic, polar and positively charged hydrophilic amino acid. [00221] 31A. The method of any one of the preceding paragraphs, wherein the polar and positively charged hydrophilic amino acid is arginine (R) or lysine (K). [00222] 32A. The method of any one of the preceding paragraphs, wherein the polar and neutral of charge hydrophilic amino acid is asparagine (N), glutamine (Q), serine (S), threonine (T), proline (P), or cysteine (C). [00223] 33A. The method of any one of the preceding paragraphs, wherein the polar and negatively charged hydrophilic amino acid is aspartate (D) or glutamate (E). [00224] 34A. The method of any one of the preceding paragraphs, wherein the aromatic, polar and positively charged hydrophilic amino acid is histidine. [00225] 35A. The method of any one of the preceding paragraphs, wherein the hydrophobic amino acid is selected from a hydrophobic, aliphatic amino acid and a hydrophobic, aromatic amino acid. [00226] 36A. The method of any one of the preceding paragraphs, wherein the hydrophobic, aliphatic amino acid is glycine (G), alanine (A), leucine (L), isoleucine (I), methionine (M), or valine (V). [00227] 37A. The method of any one of the preceding paragraphs, wherein the hydrophobic, aromatic amino acid is phenylalanine (F), tryptophan (W), or tyrosine (Y). [00228] 38A. The method of any one of the preceding paragraphs, wherein the non-classical amino acid is selected from selenocysteine, pyrrolysine, N-formylmethionine β-alanine, GABA, δ- Aminolevulinic acid, 4-Aminobenzoic acid (PABA), D-isomers of the common amino acids, 2,4- diaminobutyric acid, α-amino isobutyric acid, 4-aminobutyric acid, Abu, 2-amino butyric acid, γ-Abu, ε- Ahx, 6-amino hexanoic acid, Aib, 2-amino isobutyric acid, 3-amino propionic acid, ornithine, norleucine, Attorney Docket No.: 33791/41005 norvaline, hydroxyproline, sarcosme, citrulline, homocitrulline, cysteic acid, t-butylglycine, t- butylalanine, phenylglycine, cyclohexylalanine, β-alanine, fluoroamino acids, designer amino acids such as β methyl amino acids, C α-methyl amino acids, N α -methyl amino acids, and amino acid analogs in general. [00229] 39A. The method of any one of the preceding paragraphs, wherein the deaminase and the mutant λ N-peptide are a fusion protein. [00230] 40A. The method of any one of the preceding paragraphs, wherein the deaminase and the mutant λ N-peptide are a connected by a chemical linker. [00231] 41A. The method of any one of the preceding paragraphs, wherein the deaminase is linked to at least 2, at least 3, or at least 4 λ N-peptides. [00232] 42A. The method of any one of the preceding paragraphs, wherein the mutant λ N-peptide is linked to at least 2, at least 3, or at least 4 deaminases, or fragments thereof. [00233] 43A. The method of any one of the preceding paragraphs, wherein the deaminase and the mutant λ N-peptide comprise a nuclear localization signal. [00234] 44A. The method of any one of the preceding paragraphs, wherein the deaminase and the mutant λ N-peptide comprise a nuclear localization signal and the RNA molecule comprising the target nucleotide is in the nucleus of the cell. [00235] 45A. The method of any one of the preceding paragraphs, wherein the nuclear localization signal is the SV40 Large T-antigen nuclear localization signal. [00236] 46A. The method of any one of the preceding paragraphs, wherein SV40 Large T-antigen nuclear localization signal comprises the amino acid sequence of SEQ ID NO: 21. [00237] 47A. The method of any one of the preceding paragraphs, wherein the antisense RNA nucleotide hybridizes with a wild-type target sequence in an endogenous RNA and comprises a target nucleotide to be edited. [00238] 48A. The method of any one of the preceding paragraphs, wherein the target nucleotide to be edited induces a beneficial mutation in the wild-type target sequence. [00239] 49A. The method of any one of the preceding paragraphs, wherein the antisense RNA nucleotide hybridizes with a mutant target sequence in an endogenous RNA and comprises a target nucleotide to be edited. [00240] 50A. The method of any one of the preceding paragraphs, wherein the target nucleotide to be edited eliminates a detrimental mutation in the mutant target sequence. Attorney Docket No.: 33791/41005 [00241] 51A. The method of any one of the preceding paragraphs, wherein the target nucleotide is a genetic mutation associated with a genetic disease or disorder. [00242] 52A. The method of any one of the preceding paragraphs, wherein the genetic mutation of the target nucleotide causes a premature termination codon (PTC) or an in-frame stop codon. [00243] 53A. The method of any one of the preceding paragraphs, wherein the genetic disease or disorder is caused by a U-to-C nucleotide mutation. [00244] 54A. The method of any one of the preceding paragraphs, wherein the antisense RNA oligonucleotide hybridizes with an RNA molecule comprising the target nucleotide in endogenous RNA of the cell. [00245] 55A. The method of any one of the preceding paragraphs, wherein the antisense RNA oligonucleotide has perfect base-pairing complementarity with the RNA molecule comprising the target nucleotide. [00246] 56A. The method of any one of the preceding paragraphs, wherein the antisense RNA oligonucleotide comprises a one or more mismatches with the RNA molecule comprising the target nucleotide. [00247] 57A. The method of any one of the preceding paragraphs, wherein the antisense RNA oligonucleotide sequence comprises from 1 to 15 mismatches, e.g. about 1, or about 2, or about 3, or about 4, or about 5, or about 7, or about 10, or about 15 mismatches. [00248] 58A. The method of any one of the preceding paragraphs, wherein the antisense RNA oligonucleotide sequence is at least 80% complementary with the target sequence. [00249] 59A. The method of any one of the preceding paragraphs, wherein the 5' end of the antisense RNA oligonucleotide begins before the target nucleotide to be edited. [00250] 60A. The method of any one of the preceding paragraphs, wherein the 3' end of the oligonucleotide extends from 2-22 nucleotides 5' from the target nucleotide to be edited. [00251] 61A. The method of any one of the preceding paragraphs, wherein the antisense RNA oligonucleotide is linked to at least 2, 3, or 4 hairpin RNA oligonucleotides. [00252] 62A. The method of any one of the preceding paragraphs, wherein the hairpin RNA oligonucleotide comprises a nucleic acid sequence located from about 2-20 nucleotide residues 5' of the target mutation. Attorney Docket No.: 33791/41005 [00253] 63A. The method of any one of the preceding paragraphs, wherein the hairpin RNA oligonucleotide comprises a nucleic acid sequence located from about 2-20 nucleotide residues 3' of the target mutation. [00254] 64A. The method of any one of the preceding paragraphs, wherein the hairpin RNA oligonucleotide is a BoxB hairpin RNA oligonucleotide. [00255] 65A. The method of any one of the preceding paragraphs, wherein the BoxB hairpin RNA oligonucleotide is the cognate hairpin oligonucleotide of the mutant λ N-peptide. [00256] 66A. The method of any one of the preceding paragraphs, wherein the BoxB hairpin RNA oligonucleotide comprises a nucleic acid sequence of SEQ ID NO: 10 or SEQ ID NO: 11, or mutants thereof. [00257] 67A. The method of any one of the preceding paragraphs, wherein the mutant λ N peptide interacts with a λ BoxB hairpin RNA oligonucleotide comprising a nucleic acid sequence of SEQ ID NO: 10 or SEQ ID NO: 11, or mutant thereof. [00258] 68A. The method of any one of the preceding paragraphs, wherein the mutant λ N peptide and λ BoxB hairpin RNA oligonucleotide interaction adopts a 4-out GNRA-like pentaloop. [00259] 69A. The method of any one of the preceding paragraphs, wherein the nucleic acid sequence comprises at least one mutation selected from missense mutation, nonsense mutation, insertion, deletion, duplication, frameshift mutation, and repeat expansion. [00260] 70A. The method of any one of the preceding paragraphs, wherein the λ BoxB hairpin RNA oligonucleotide comprises a nucleic acid sequence having sequence identity to SEQ ID NO: 10 or SEQ ID NO: 11, and further comprises from 1 to 15 nucleotide mutations selected from one or more of nucleotide substitutions, nucleotide deletions, and nucleotide additions. [00261] 71A. The method of any one of the preceding paragraphs, wherein the one or more nucleotide mutations take(s) place at one or more of nucleotide residue positions 1 to 15, relative to the wild-type λ BoxB hairpin RNA oligonucleotide. [00262] 72A. The method of any one of the preceding paragraphs, wherein the λ BoxB hairpin RNA oligonucleotide comprises a nucleic acid sequence of one or more of SEQ ID NOs: 12-17. [00263] 73A. The method of any one of the preceding paragraphs, wherein components (i) and (ii) are within a plasmid, vector, mRNA, or lipid nanoparticle. [00264] 74A. The method of any one of the preceding paragraphs, wherein components (i) and (ii) are within a viral vector. Attorney Docket No.: 33791/41005 [00265] 75A. The method of any one of the preceding paragraphs, wherein the viral vector is an adeno- associated viruses (AAVs), adenoviruses, retroviruses, and lentiviruses vector. [00266] 76A. The method of any one of the preceding paragraphs, wherein the viral vector is an adeno- associated virus (AAV) vector. [00267] 77A. The method of any one of the preceding paragraphs, wherein the AAV vector is selected from AAV1, or AAV2, or AAV3, or AAV4, or AAV5, or AAV6, or AAV7, or AAV8, or AAV9, or AAV10, or AAV11, and AAV12. [00268] Additional embodiments: [00269] 1B. A method of site-specific editing of a target nucleotide within an RNA molecule in a cell comprising: (a) contacting the cell with: (i) a deaminase linked to a lamboid P22 bacteriophage N-peptide, and (ii) an antisense RNA oligonucleotide linked to a hairpin RNA oligonucleotide, wherein: the antisense RNA oligonucleotide comprises a region complementary to an RNA molecule comprising the target nucleotide; the N-peptide and hairpin interact; and the deaminase domain causes editing of the target nucleotide to induce a base change. [00270] 2B. A method of treating a disease or disorder by editing a target nucleotide within an RNA molecule in a cell, the method comprising contacting the cell with: (i) a deaminase linked to a lamboid P22 bacteriophage N-peptide, and (ii) an antisense RNA oligonucleotide linked to a hairpin RNA oligonucleotide, wherein: the antisense RNA oligonucleotide comprises a region complementary to an RNA molecule comprising the target nucleotide; the N-peptide and hairpin interact; and the deaminase domain causes editing of the target nucleotide to induce a base change. [00271] 3B. The method of any one of the preceding paragraphs, wherein the deaminase is cytidine deaminase or adenosine deaminase. [00272] 4B. The method of any one of the preceding paragraphs, wherein the adenosine deaminase yields a uracil (U) nucleotide. [00273] 5B. The method of any one of the preceding paragraphs, wherein the adenosine deaminase is selected from adenosine deaminase RNA specific 1 (ADAR1), adenosine deaminase RNA specific 2 Attorney Docket No.: 33791/41005 (ADAR2), adenosine deaminase RNA specific B1 (ADARB1), adenosine deaminase like (ADAL), adenosine deaminase 2 (ADA2), adenosine monophosphate deaminase 1 (AMPD1), adenosine monophosphate deaminase 2 (AMPD2), adenosine monophosphate deaminase 3 (AMPD3), adenosine deaminase domain containing 1 (ADAD1), adenosine deaminase domain containing 2 (ADAD2), adenosine deaminase tRNA specific 1 (ADAT1), adenosine deaminase tRNA specific 2 (ADAT2), adenosine deaminase tRNA specific 3 (ADAT3), TadA or fragments or variants thereof. [00274] 6B. The method of any one of the preceding paragraphs, wherein the adenosine deaminase is ADAR1 or ADAR2. [00275] 7B. The method of any one of the preceding paragraphs, wherein the adenosine deaminase is a fragment, the fragment comprising the catalytic domain of the adenosine deaminase. [00276] 8B. The method of any one of the preceding paragraphs, wherein the adenosine deaminase is a fragment, the fragment comprising a catalytic domain and one or more mutations. [00277] 9B. The method of any one of the preceding paragraphs, wherein the ADAR1 or ADAR2 comprises a fragment that comprises a catalytic domain. [00278] 10B. The method of any one of the preceding paragraphs, wherein the catalytic domain is the deaminase domain of human ADAR2, comprising an amino acid sequence having at least 90% sequence identity with SEQ ID NO: 18. [00279] 11B. The method of any one of the preceding paragraphs, wherein the ADAR2 comprises the amino acid sequence of SEQ ID NO: 18. [00280] 12B. The method of any one of the preceding paragraphs, wherein the ADAR induces a cytidine (C) to uridine (U) nucleotide mutation, optionally wherein the ADAR comprises one or more mutations that allow the ADAR to induce the C to U nucleotide mutation, optionally wherein the ADAR mutation(s) is selected from a substitution at one or more positions E396, C451, V351, R455, T375, K376, S486, Q488, R510, K594, R348, G593, S397, H443, L444, Y445, F442, E438, T448, A353, V355, T339, P539, V525 and I520, optionally relative to SEQ ID NO: 18 or SEQ ID NO: 19. [00281] 13B. The method of any one of the preceding paragraphs, wherein the cytidine deaminase yields a uridine (U) nucleotide. [00282] 14B. The method of any one of the preceding paragraphs, wherein the cytidine deaminase is selected from APOBEC1, activation-induced cytidine deaminase (AID), APOBEC2, APOBEC3A, APOBEC3B, APOBEC3C, APOBEC3D, APOBEC3E, APOBEC3F, APOBEC3G, APOBEC3H, pmCDA1, and ACF1/ASE, or fragments or variants thereof. Attorney Docket No.: 33791/41005 [00283] 15B. The method of any one of the preceding paragraphs, wherein the cytidine deaminase is a fragment, the fragment comprising the catalytic domain of the cytidine deaminase. [00284] 16B. The method of any one of the preceding paragraphs, wherein the cytidine deaminase is a fragment, the fragment comprising a catalytic domain and one or more mutations. [00285] 17B. The method of any one of the preceding paragraphs, wherein the lambdoid bacteriophage N-peptide is derived from the P22 lambdoid bacteriophage. [00286] 18B. The method of any one of the preceding paragraphs, wherein the P22 N-peptide is a variant that is the wild-type amino-terminal domain P22 N-peptide and comprises the amino acid sequence of SEQ ID NO: 53. [00287] 19B. The method of any one of the preceding paragraphs, wherein the amino-terminal domain P22 N-peptide comprises an arginine-rich motif. [00288] 20B. The method of any one of the preceding paragraphs, wherein the amino-terminal domain P22 N-peptide comprises an Ala at position 5 and an arginine at each of positions 8, 12, and 13 of SEQ ID NO: 53. [00289] 21B. The method of any one of the preceding paragraphs, wherein the amino-terminal domain P22 N-peptide variant comprises at least one mutation as compared to the wild type amino-terminal domain P22 N-peptide. [00290] 22B. The method of any one of the preceding paragraphs, wherein the mutation is selected from one or more of an amino acid substitution, deletion, and addition. [00291] 23B. The method of any one of the preceding paragraphs, wherein the amino-terminal domain P22 N-peptide variant comprises from 1 to 21 amino acid residue substitutions. [00292] 24B. The method of any one of the preceding paragraphs, wherein the amino acid substitution takes place at one or more of amino acid residue positions 1 to 21, relative to the wild type amino- terminal domain P22 N-peptide sequence (SEQ ID NO: 53). [00293] 25B. The method of any one of the preceding paragraphs, wherein the amino acid substitution is selected from any one of the amino acid substitutions listed in Table 2. [00294] 26B. The method of any one of the preceding paragraphs, wherein the amino-terminal domain P22 N-peptide variant comprises the amino acid sequence of any one of SEQ ID NO: 54 to SEQ ID NO: 78. Attorney Docket No.: 33791/41005 [00295] 27B. The method of any one of the preceding paragraphs, wherein the affinity of the P22 N- peptide variant for the BoxB hairpin RNA is greater than the affinity of the wild type P22 N-peptide for the BoxB hairpin RNA. [00296] 28B. The method of any one of the preceding paragraphs, wherein the affinity is greater by at least 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 15-fold, 20-fold, 25-fold, 30-fold, 35-fold, 40-fold, 45-fold, 50-fold, or 100-fold. [00297] 29B. The method of any one of the preceding paragraphs, wherein the substituted amino acid residue of the lambdoid bacteriophage N-peptide is any naturally-occurring amino acid. [00298] 30B. The method of any one of the preceding paragraphs, wherein the naturally-occurring amino acid is hydrophilic, hydrophobic, or non-classical. [00299] 31B. The method of any one of the preceding paragraphs, wherein the hydrophilic amino acid is selected from a polar and positively charged hydrophilic amino acid, a polar and neutral of charge hydrophilic amino acid, and polar and negatively charged hydrophilic amino acid, and an aromatic, polar and positively charged hydrophilic amino acid. [00300] 32B. The method of any one of the preceding paragraphs, wherein the polar and positively charged hydrophilic amino acid is arginine (R) or lysine (K). [00301] 33B. The method of any one of the preceding paragraphs, wherein the polar and neutral of charge hydrophilic amino acid is asparagine (N), glutamine (Q), serine (S), threonine (T), proline (P), or cysteine (C). [00302] 34B. The method of any one of the preceding paragraphs, wherein the polar and negatively charged hydrophilic amino acid is aspartate (D) or glutamate (E). [00303] 35B. The method of any one of the preceding paragraphs, wherein the aromatic, polar and positively charged hydrophilic amino acid is histidine. [00304] 36B. The method of any one of the preceding paragraphs, wherein the hydrophobic amino acid is selected from a hydrophobic, aliphatic amino acid and a hydrophobic, aromatic amino acid. [00305] 37B. The method of any one of the preceding paragraphs, wherein the hydrophobic, aliphatic amino acid is glycine (G), alanine (A), leucine (L), isoleucine (I), methionine (M), or valine (V). [00306] 38B. The method of any one of the preceding paragraphs, wherein the hydrophobic, aromatic amino acid is phenylalanine (F), tryptophan (W), or tyrosine (Y). [00307] 39B. The method of any one of the preceding paragraphs, wherein the non-classical amino acid is selected from selenocysteine, pyrrolysine, N-formylmethionine β-alanine, GABA, δ- Attorney Docket No.: 33791/41005 Aminolevulinic acid, 4-Aminobenzoic acid (PABA), D-isomers of the common amino acids, 2,4- diaminobutyric acid, α-amino isobutyric acid, 4-aminobutyric acid, Abu, 2-amino butyric acid, γ-Abu, ε- Ahx, 6-amino hexanoic acid, Aib, 2-amino isobutyric acid, 3-amino propionic acid, ornithine, norleucine, norvaline, hydroxyproline, sarcosme, citrulline, homocitrulline, cysteic acid, t-butylglycine, t-butylalanine, phenylglycine, cyclohexylalanine, β-alanine, fluoroamino acids, designer amino acids such as β methyl amino acids, C α-methyl amino acids, N α -methyl amino acids, and amino acid analogs in general. [00308] 40B. The method of any one of the preceding paragraphs, wherein the deaminase and the lambdoid bacteriophage N-peptide are a fusion protein. [00309] 41B. The method of any one of the preceding paragraphs, wherein the deaminase and the lambdoid bacteriophage N-peptide are a connected by a chemical linker. [00310] 42B. The method of any one of the preceding paragraphs, wherein the deaminase is linked to at least 2, at least 3, or at least 4 lambdoid bacteriophage N-peptides. [00311] 43B. The method of any one of the preceding paragraphs, wherein the bacteriophage N- peptide is linked to at least 2, at least 3, or at least 4 deaminases. [00312] 44B. The method of any one of the preceding paragraphs, wherein the deaminase and the lambdoid bacteriophage N-peptide comprise a nuclear localization signal. [00313] 45B. The method of any one of the preceding paragraphs, wherein the deaminase and the lambdoid bacteriophage N-peptide comprise a nuclear localization signal and the RNA molecule comprising the target nucleotide is in the nucleus of the cell. [00314] 46B. The method of any one of the preceding paragraphs, wherein the nuclear localization signal is the SV40 Large T-antigen nuclear localization signal. [00315] 47B. The method of any one of the preceding paragraphs, wherein SV40 Large T-antigen nuclear localization signal comprises the amino acid sequence of SEQ ID NO: 21i. [00316] 48B. The method of any one of the preceding paragraphs, wherein the antisense RNA nucleotide hybridizes with a wild-type target sequence in an endogenous RNA and comprises a target nucleotide to be edited. [00317] 49B. The method of any one of the preceding paragraphs, wherein the target nucleotide to be edited induces a beneficial mutation in the wild-type target sequence. [00318] 50B. The method of any one of the preceding paragraphs, wherein the antisense RNA nucleotide hybridizes with a mutant target sequence in an endogenous RNA and comprises a target nucleotide to be edited. Attorney Docket No.: 33791/41005 [00319] 51B. The method of any one of the preceding paragraphs, wherein the target nucleotide to be edited eliminates a detrimental mutation in the mutant target sequence. [00320] 52B. The method of any one of the preceding paragraphs, wherein the target nucleotide is a genetic mutation associated with a genetic disease or disorder. [00321] 53B. The method of any one of the preceding paragraphs, wherein the genetic mutation of the target nucleotide causes a premature termination codon (PTC) or an in-frame stop codon. [00322] 54B. The method of any one of the preceding paragraphs, wherein the genetic disease or disorder is caused by a C nucleotide substitution in place of U nucleotide mutation. [00323] 55B. The method of any one of the preceding paragraphs, wherein the antisense RNA oligonucleotide hybridizes with an RNA molecule comprising the target nucleotide in endogenous RNA of the cell. [00324] 56B. The method of any one of the preceding paragraphs, wherein the antisense RNA oligonucleotide has perfect base-pairing complementarity with the RNA molecule comprising the target nucleotide. [00325] 57B. The method of any one of the preceding paragraphs, wherein the antisense RNA oligonucleotide comprises a one or more mismatches with the RNA molecule comprising the target nucleotide. [00326] 58B. The method of any one of the preceding paragraphs, wherein the antisense RNA oligonucleotide sequence comprises from 1 to 15 mismatches, e.g. about 1, or about 2, or about 3, or about 4, or about 5, or about 7, or about 10, or about 15 mismatches. [00327] 59B. The method of any one of the preceding paragraphs, wherein the antisense RNA oligonucleotide sequence is at least 80% complementary with the target sequence. [00328] 60B. The method of any one of the preceding paragraphs, wherein the 5' end of the antisense RNA oligonucleotide begins before the target nucleotide to be edited. [00329] 61B. The method of any one of the preceding paragraphs, wherein the 3' end of the antisense RNA oligonucleotide extends from 2-22 nucleotides 5' from the target nucleotide to be edited. [00330] 62B. The method of any one of the preceding paragraphs, wherein the antisense RNA oligonucleotide is linked to at least 2, 3, or 4 hairpin RNA oligonucleotides. [00331] 63B. The method of any one of the preceding paragraphs, wherein the hairpin RNA oligonucleotide is located from about 2-20 nucleotide residues 5' of the target mutation. Attorney Docket No.: 33791/41005 [00332] 64B. The method of any one of the preceding paragraphs, wherein the hairpin RNA oligonucleotide is located from about 2-20 nucleotide residues 3' of the target mutation. [00333] 65B. The method of any one of the preceding paragraphs, wherein the hairpin RNA oligonucleotide is a BoxB hairpin RNA oligonucleotide. [00334] 66B. The method of any one of the preceding paragraphs, wherein the BoxB hairpin RNA oligonucleotide is the cognate hairpin oligonucleotide of the N-peptide. [00335] 67B. The method of any one of the preceding paragraphs, wherein the BoxB hairpin RNA oligonucleotide comprises a nucleic acid sequence of any one of SEQ ID NOs: 79-80, or variants thereof. [00336] 68B. The method of any one of the preceding paragraphs, wherein the P22 N peptide interacts with a P22 BoxB hairpin RNA oligonucleotide comprising the nucleic acid sequence of SEQ ID NO: 79 or SEQ ID NO: 80, or variant thereof. [00337] 69B. The method of any one of the preceding paragraphs, wherein the P22 N peptide and P22 BoxB hairpin RNA oligonucleotide interaction adopts a 3-out GNRA-like pentaloop. [00338] 70B. The method of any one of the preceding paragraphs, wherein the hairpin RNA oligonucleotide comprises at least one mutation selected from missense mutation, nonsense mutation, insertion, deletion, duplication, frameshift mutation, and repeat expansion. [00339] 71B. The method of any one of the preceding paragraphs, wherein the P22 BoxB hairpin RNA oligonucleotide comprises the nucleic acid sequence of SEQ ID NO: 79 or SEQ ID NO: 80, and further comprises from 1 to 17 nucleotide mutations selected from one or more of nucleotide substitutions, nucleotide deletions, and nucleotide additions. [00340] 72B. The method of any one of the preceding paragraphs, wherein the one or more nucleotide mutations take(s) place at one or more of nucleotide residue positions 1 to 17, relative to the wild type P22 BoxB hairpin RNA oligonucleotide. [00341] 73B. The method of any one of the preceding paragraphs, wherein components (i) and (ii) are within a plasmid, vector, mRNA, or lipid nanoparticle. [00342] 74B. The method of any one of the preceding paragraphs, wherein components (i) and (ii) are within a viral vector. [00343] 75B. The method of any one of the preceding paragraphs, wherein the viral vector is an adeno- associated viruses (AAVs), adenoviruses, retroviruses, and lentiviruses vector. Attorney Docket No.: 33791/41005 [00344] 76B. The method of any one of the preceding paragraphs, wherein the viral vector is an adeno- associated virus (AAV) vector. [00345] 77B. The method of any one of the preceding paragraphs, wherein the AAV vector is selected from AAV1, or AAV2, or AAV3, or AAV4, or AAV5, or AAV6, or AAV7, or AAV8, or AAV9, or AAV10, or AAV11, and AAV12. [00346] Further embodiments: [00347] 1C. A method of site-specific editing of a target nucleotide within an RNA molecule in a cell comprising: (a) contacting the cell with: (i) a deaminase linked to a lamboid P21 bacteriophage N-peptide, and (ii) an antisense RNA oligonucleotide linked to a hairpin RNA oligonucleotide, wherein: the antisense RNA oligonucleotide comprises a region complementary to an RNA molecule comprising the target nucleotide; the N-peptide and hairpin interact; and the deaminase domain causes editing of the target nucleotide to induce a base change. [00348] 2C. A method of treating a disease or disorder by editing a target nucleotide within an RNA molecule in a cell, the method comprising contacting the cell with: (i) a deaminase linked to a lamboid P21 bacteriophage N-peptide, and (ii) an antisense RNA oligonucleotide linked to a hairpin RNA oligonucleotide, wherein: the antisense RNA oligonucleotide comprises a region complementary to an RNA molecule comprising the target nucleotide; the N-peptide and hairpin interact; and the deaminase domain causes editing of the target nucleotide to induce a base change. [00349] 3C. The method of any one of the preceding paragraphs, wherein the deaminase is cytidine deaminase or adenosine deaminase. [00350] 4C. The method of any one of the preceding paragraphs, wherein the adenosine deaminase yields a uracil (U) nucleotide. [00351] 5C. The method of any one of the preceding paragraphs, wherein the adenosine deaminase is selected from adenosine deaminase RNA specific 1 (ADAR1), adenosine deaminase RNA specific 2 (ADAR2), adenosine deaminase RNA specific B1 (ADARB1), adenosine deaminase like (ADAL), adenosine deaminase 2 (ADA2), adenosine monophosphate deaminase 1 (AMPD1), adenosine Attorney Docket No.: 33791/41005 monophosphate deaminase 2 (AMPD2), adenosine monophosphate deaminase 3 (AMPD3), adenosine deaminase domain containing 1 (ADAD1), adenosine deaminase domain containing 2 (ADAD2), adenosine deaminase tRNA specific 1 (ADAT1), adenosine deaminase tRNA specific 2 (ADAT2), adenosine deaminase tRNA specific 3 (ADAT3), TadA or fragments or variants thereof. [00352] 6C. The method of any one of the preceding paragraphs, wherein the adenosine deaminase is ADAR1 or ADAR2. [00353] 7C. The method of any one of the preceding paragraphs, wherein the adenosine deaminase is a fragment, the fragment comprising the catalytic domain of the adenosine deaminase. [00354] 8C. The method of any one of the preceding paragraphs, wherein the adenosine deaminase is a fragment, the fragment comprising a catalytic domain and one or more mutations. [00355] 9C. The method of any one of the preceding paragraphs, wherein the ADAR1 or ADAR2 comprises a fragment that comprises a catalytic domain. [00356] 10C. The method of any one of the preceding paragraphs, wherein the catalytic domain is the deaminase domain of human ADAR2, comprising an amino acid sequence having at least 90% sequence identity with SEQ ID NO: 18. [00357] 11C. The method of any one of the preceding paragraphs, wherein the ADAR2 comprises the amino acid sequence of SEQ ID NO: 19. [00358] 12C. The method of any one of the preceding paragraphs, wherein the ADAR induces a cytidine (C) to uridine (U) nucleotide mutation, optionally wherein the ADAR comprises one or more mutations that allow the ADAR to induce the C to U nucleotide mutation, optionally wherein the ADAR mutation(s) is selected from a substitution at one or more positions E396, C451, V351, R455, T375, K376, S486, Q488, R510, K594, R348, G593, S397, H443, L444, Y445, F442, E438, T448, A353, V355, T339, P539, V525 and I520, optionally relative to SEQ ID NO: 18 or SEQ ID NO: 19. [00359] 13C. The method of any one of the preceding paragraphs, wherein the cytidine deaminase yields a uridine (U) nucleotide. [00360] 14C. The method of any one of the preceding paragraphs, wherein the cytidine deaminase is selected from APOBEC1, activation-induced cytidine deaminase (AID), APOBEC2, APOBEC3A, APOBEC3B, APOBEC3C, APOBEC3D, APOBEC3E, APOBEC3F, APOBEC3G, APOBEC3H, pmCDA1, and ACF1/ASE, or fragments or variants thereof. [00361] 15C. The method of any one of the preceding paragraphs, wherein the cytidine deaminase is a fragment, the fragment comprising the catalytic domain of the cytidine deaminase. Attorney Docket No.: 33791/41005 [00362] 16C. The method of any one of the preceding paragraphs, wherein the cytidine deaminase is a fragment, the fragment comprising a catalytic domain and one or more mutations. [00363] 17C. The method of any one of the preceding paragraphs, wherein the lambdoid bacteriophage N-peptide is derived from the P21 lambdoid bacteriophage. [00364] 18C. The method of any one of the preceding paragraphs, wherein the P21 N-peptide is the wild-type amino-terminal domain P21 N-peptide and comprises the amino acid sequence of SEQ ID NO: 95. [00365] 19C. The method of any one of the preceding paragraphs, wherein the amino-terminal domain P21 N-peptide comprises an arginine-rich motif. [00366] 20C. The method of any one of the preceding paragraphs, wherein the amino-terminal domain P21 N-peptide comprises an Ala at position 5 and an arginine at each of positions 8, 12, and 13 of SEQ ID NO: 95. [00367] 21C. The method of any one of the preceding paragraphs, wherein the amino-terminal domain P21 N-peptide variant comprises at least one mutation as compared to the wild type amino-terminal domain P21 N-peptide. [00368] 22C. The method of any one of the preceding paragraphs, wherein the mutation is selected from one or more of an amino acid substitution, deletion, and addition. [00369] 23C. The method of any one of the preceding paragraphs, wherein the amino-terminal domain P21 N-peptide variant comprises from 1 to 21 amino acid residue substitutions. [00370] 24C. The method of any one of the preceding paragraphs, wherein the amino acid substitution takes place at one or more of amino acid residue positions 1 to 21, relative to the wild type amino- terminal domain P21 N-peptide sequence (SEQ ID NO: 95). [00371] 25C. The method of any one of the preceding paragraphs, wherein the amino-terminal domain P21 N-peptide variant comprises one or mutations at positions R13 and I17 with reference to SEQ ID NO: 95. [00372] 26C. The method of any one of the preceding paragraphs, wherein the amino-terminal domain P21 N-peptide variant is not mutated at position R13 and/or I17 with reference to SEQ ID NO: 95. [00373] 27C. The method of any one of the preceding paragraphs, wherein the amino acid substitution is selected from any one of the amino acid substitutions listed in Table 3. Attorney Docket No.: 33791/41005 [00374] 28C. The method of any one of the preceding paragraphs, wherein the affinity of the P21 N- peptide variant for the BoxB hairpin RNA is greater than the affinity of the wild type P21 N-peptide for the BoxB hairpin RNA. [00375] 29C. The method of any one of the preceding paragraphs, wherein the affinity is greater by at least 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 15-fold, 20-fold, 25-fold, 30-fold, 35-fold, 40-fold, 45-fold, 50-fold, or 100-fold. [00376] 30C. The method of any one of the preceding paragraphs, wherein the substituted amino acid residue of the lambdoid bacteriophage N-peptide is any naturally-occurring amino acid. [00377] 31C. The method of any one of the preceding paragraphs, wherein the naturally-occurring amino acid is hydrophilic, hydrophobic, or non-classical. [00378] 32C. The method of any one of the preceding paragraphs, wherein the hydrophilic amino acid is selected from a polar and positively charged hydrophilic amino acid, a polar and neutral of charge hydrophilic amino acid, and polar and negatively charged hydrophilic amino acid, and an aromatic, polar and positively charged hydrophilic amino acid. [00379] 33C. The method of any one of the preceding paragraphs, wherein the polar and positively charged hydrophilic amino acid is arginine (R) or lysine (K). [00380] 34C. The method of any one of the preceding paragraphs, wherein the polar and neutral of charge hydrophilic amino acid is asparagine (N), glutamine (Q), serine (S), threonine (T), proline (P), or cysteine (C). [00381] 35C. The method of any one of the preceding paragraphs, wherein the polar and negatively charged hydrophilic amino acid is aspartate (D) or glutamate (E). [00382] 36C. The method of any one of the preceding paragraphs, wherein the aromatic, polar and positively charged hydrophilic amino acid is histidine. [00383] 37C. The method of any one of the preceding paragraphs, wherein the hydrophobic amino acid is selected from a hydrophobic, aliphatic amino acid and a hydrophobic, aromatic amino acid. [00384] 38C. The method of any one of the preceding paragraphs, wherein the hydrophobic, aliphatic amino acid is glycine (G), alanine (A), leucine (L), isoleucine (I), methionine (M), or valine (V). [00385] 39C. The method of any one of the preceding paragraphs, wherein the hydrophobic, aromatic amino acid is phenylalanine (F), tryptophan (W), or tyrosine (Y). [00386] 40C. The method of any one of the preceding paragraphs, wherein the non-classical amino acid is selected from selenocysteine, pyrrolysine, N-formylmethionine β-alanine, GABA, δ- Attorney Docket No.: 33791/41005 Aminolevulinic acid, 4-Aminobenzoic acid (PABA), D-isomers of the common amino acids, 2,4- diaminobutyric acid, α-amino isobutyric acid, 4-aminobutyric acid, Abu, 2-amino butyric acid, γ-Abu, ε- Ahx, 6-amino hexanoic acid, Aib, 2-amino isobutyric acid, 3-amino propionic acid, ornithine, norleucine, norvaline, hydroxyproline, sarcosme, citrulline, homocitrulline, cysteic acid, t-butylglycine, t-butylalanine, phenylglycine, cyclohexylalanine, β-alanine, fluoroamino acids, designer amino acids such as β methyl amino acids, C α-methyl amino acids, N α -methyl amino acids, and amino acid analogs in general. [00387] 41C. The method of any one of the preceding paragraphs, wherein the deaminase and the lambdoid bacteriophage N-peptide are a fusion protein. [00388] 42C. The method of any one of the preceding paragraphs, wherein the deaminase and the lambdoid bacteriophage N-peptide are a connected by a chemical linker. [00389] 43C. The method of any one of the preceding paragraphs, wherein the deaminase is linked to at least 2, at least 3, or at least 4 lambdoid bacteriophage N-peptides. [00390] 44C. The method of any one of the preceding paragraphs, wherein the bacteriophage N- peptide is linked to at least 2, at least 3, or at least 4 deaminases. [00391] 45C. The method of any one of the preceding paragraphs, wherein the deaminase and the lambdoid bacteriophage N-peptide comprise a nuclear localization signal. [00392] 46C. The method of any one of the preceding paragraphs, wherein the deaminase and the lambdoid bacteriophage N-peptide comprise a nuclear localization signal and the RNA molecule comprising the target nucleotide is in the nucleus of the cell. [00393] 47C. The method of any one of the preceding paragraphs, wherein the nuclear localization signal is the SV40 Large T-antigen nuclear localization signal. [00394] 48C. The method of any one of the preceding paragraphs, wherein SV40 Large T-antigen nuclear localization signal comprises the amino acid sequence of SEQ ID NO: 21. [00395] 49C. The method of any one of the preceding paragraphs, wherein the antisense RNA nucleotide hybridizes with a wild-type target sequence in an endogenous RNA and comprises a target nucleotide to be edited. [00396] 50C. The method of any one of the preceding paragraphs, wherein the target nucleotide to be edited induces a beneficial mutation in the wild-type target sequence. [00397] 51C. The method of any one of the preceding paragraphs, wherein the antisense RNA nucleotide hybridizes with a mutant target sequence in an endogenous RNA and comprises a target nucleotide to be edited. Attorney Docket No.: 33791/41005 [00398] 52C. The method of any one of the preceding paragraphs, wherein the target nucleotide to be edited eliminates a detrimental mutation in the mutant target sequence. [00399] 53C. The method of any one of the preceding paragraphs, wherein the target nucleotide is a genetic mutation associated with a genetic disease or disorder. [00400] 54C. The method of any one of the preceding paragraphs, wherein the genetic mutation of the target nucleotide causes a premature termination codon (PTC) or an in-frame stop codon. [00401] 55C. The method of any one of the preceding paragraphs, wherein the genetic disease or disorder is caused by a C nucleotide substitution in place of U nucleotide mutation. [00402] 56C. The method of any one of the preceding paragraphs, wherein the antisense RNA oligonucleotide hybridizes with an RNA molecule comprising the target nucleotide in endogenous RNA of the cell. [00403] 57C. The method of any one of the preceding paragraphs, wherein the antisense RNA oligonucleotide has perfect base-pairing complementarity with the RNA molecule comprising the target nucleotide. [00404] 58C. The method of any one of the preceding paragraphs, wherein the antisense RNA oligonucleotide comprises a one or more mismatches with the RNA molecule comprising the target nucleotide. [00405] 59C. The method of any one of the preceding paragraphs, wherein the antisense RNA oligonucleotide sequence comprises from 1 to 15 mismatches, e.g. about 1, or about 2, or about 3, or about 4, or about 5, or about 7, or about 10, or about 15 mismatches. [00406] 60C. The method of any one of the preceding paragraphs, wherein the antisense RNA oligonucleotide sequence is at least 80% complementary with the target sequence. [00407] 61C. The method of any one of the preceding paragraphs, wherein the 5' end of the antisense RNA oligonucleotide begins before the target nucleotide to be edited. [00408] 62C. The method of any one of the preceding paragraphs, wherein the 3' end of the antisense RNA oligonucleotide extends from 2-22 nucleotides 5' from the target nucleotide to be edited. [00409] 63C. The method of any one of the preceding paragraphs, wherein the antisense RNA oligonucleotide is linked to at least 2, 3, or 4 hairpin RNA oligonucleotides. [00410] 64C. The method of any one of the preceding paragraphs, wherein the hairpin RNA oligonucleotide is located from about 2-20 nucleotide residues 5' of the target mutation. Attorney Docket No.: 33791/41005 [00411] 65C. The method of any one of the preceding paragraphs, wherein the hairpin RNA oligonucleotide is located from about 2-20 nucleotide residues 3' of the target mutation. [00412] 66C. The method of any one of the preceding paragraphs, wherein the hairpin RNA oligonucleotide is a BoxB hairpin RNA oligonucleotide. [00413] 67C. The method of any one of the preceding paragraphs, wherein the BoxB hairpin RNA oligonucleotide is the cognate hairpin oligonucleotide of the N-peptide. [00414] 68C. The method of any one of the preceding paragraphs, wherein the BoxB hairpin RNA oligonucleotide comprises a nucleic acid sequence of any one of SEQ ID NOs: 96-97, or variants thereof. [00415] 69C. The method of any one of the preceding paragraphs, wherein the P21 N peptide interacts with a P21 BoxB hairpin RNA oligonucleotide comprising the nucleic acid sequence of SEQ ID NO: 96 or SEQ ID NO: 97, or variant thereof. [00416] 70C. The method of any one of the preceding paragraphs, wherein the P21 N-peptide and P21 BoxB hairpin RNA oligonucleotide interaction adopts a non-GNRA U-turn with respect to the apical four nucleotides of the P21 BoxB hairpin RNA oligonucleotide. [00417] 71C. The method of any one of the preceding paragraphs, wherein the hairpin RNA oligonucleotide comprises at least one mutation selected from missense mutation, nonsense mutation, insertion, deletion, duplication, frameshift mutation, and repeat expansion. [00418] 72C. The method of any one of the preceding paragraphs, wherein the P21 BoxB hairpin RNA oligonucleotide comprises the nucleic acid sequence of SEQ ID NO: 96 or SEQ ID NO: 97, and further comprises from 1 to 20 nucleotide mutations selected from one or more of nucleotide substitutions, nucleotide deletions, and nucleotide additions. [00419] 73C. The method of any one of the preceding paragraphs, wherein the one or more nucleotide mutations take(s) place at one or more of nucleotide residue positions 1 to 20, relative to the wild type P21 BoxB hairpin RNA oligonucleotide. [00420] 74C. The method of any one of the preceding paragraphs, wherein components (i) and (ii) are within a plasmid, vector, mRNA, or lipid nanoparticle. [00421] 75C. The method of any one of the preceding paragraphs, wherein components (i) and (ii) are within a viral vector. [00422] 76C. The method of any one of the preceding paragraphs, wherein the viral vector is an adeno-associated viruses (AAVs), adenoviruses, retroviruses, and lentiviruses vector. Attorney Docket No.: 33791/41005 [00423] 77C. The method of any one of the preceding paragraphs, wherein the viral vector is an adeno-associated virus (AAV) vector. [00424] 78C. The method of any one of the preceding paragraphs, wherein the AAV vector is selected from AAV1, or AAV2, or AAV3, or AAV4, or AAV5, or AAV6, or AAV7, or AAV8, or AAV9, or AAV10, or AAV11, and AAV12.

Claims

Attorney Docket No.: 33791/41005 CLAIMS What is claimed is: 1. A method of site-specific editing of a target nucleotide within an RNA molecule in a cell comprising: (a) contacting the cell with: (i) a deaminase linked to a mutant λ bacteriophage N-peptide, a lamboid P21 bacteriophage N-pepeptide, or a lamboid P22 bacteriophage N-peptide (“a bacteriophage N-peptide”), and (ii) an antisense RNA oligonucleotide linked to a hairpin RNA oligonucleotide, wherein: the antisense RNA oligonucleotide comprises a region complementary to an RNA molecule comprising the target nucleotide; the bacteriophage N-peptide and hairpin interact; and the deaminase domain causes editing of the target nucleotide to induce a base change. 2. A method of treating a disease or disorder by editing a target nucleotide within an RNA molecule in a cell, the method comprising contacting the cell with: (i) a deaminase linked to a mutant λ bacteriophage N-peptide, a lamboid P21 bacteriophage N-peptide, a lamboid P22 bacteriophage N-peptide (“a bacteriophage N-peptide”), and (ii) an antisense RNA oligonucleotide linked to a hairpin RNA oligonucleotide, wherein: the antisense RNA oligonucleotide comprises a region complementary to an RNA molecule comprising the target nucleotide; the bacteriophage N-peptide and hairpin interact; and the deaminase domain causes editing of the target nucleotide to induce a base change. 3. The method of any one of the preceding claims, wherein the deaminase is cytidine deaminase or adenosine deaminase. 4. The method of any one of the preceding claims, wherein the adenosine deaminase yields an uracil (U) nucleotide. 5. The method of any one of the preceding claims, wherein the adenosine deaminase is selected from adenosine deaminase RNA specific 1 (ADAR1), adenosine deaminase RNA specific 2 (ADAR2), adenosine deaminase RNA specific B1 (ADARB1), adenosine deaminase like (ADAL), adenosine Attorney Docket No.: 33791/41005 deaminase 2 (ADA2), adenosine monophosphate deaminase 1 (AMPD1), adenosine monophosphate deaminase 2 (AMPD2), adenosine monophosphate deaminase 3 (AMPD3), adenosine deaminase domain containing 1 (ADAD1), adenosine deaminase domain containing 2 (ADAD2), adenosine deaminase tRNA specific 1 (ADAT1), adenosine deaminase tRNA specific 2 (ADAT2), adenosine deaminase tRNA specific 3 (ADAT3), TadA or fragments or variants thereof. 6. The method of any one of the preceding claims, wherein the adenosine deaminase is ADAR1 or ADAR2. 7. The method of any one of the preceding claims, wherein the adenosine deaminase is a fragment, the fragment comprising the catalytic domain of the adenosine deaminase. 8. The method of any one of the preceding claims, wherein the adenosine deaminase is a fragment, the fragment comprising a catalytic domain and one or more mutations. 9. The method of any one of the preceding claims, wherein the ADAR1 or ADAR2 comprises a fragment that comprises a catalytic domain. 10. The method of any one of the preceding claims, wherein the catalytic domain is the deaminase domain of human ADAR2, comprising an amino acid sequence having at least 90% amino acid sequence identity with SEQ ID NO: 18. 11. The method of any one of the preceding claims, wherein the ADAR2 comprises the amino acid sequence of SEQ ID NO: 19. 12. The method of any one of the preceding claims, wherein the ADAR induces a cytidine (C) to uridine (U) nucleotide mutation, optionally wherein the ADAR comprises one or more mutations that allow the ADAR to induce the C to U nucleotide mutation, optionally wherein the ADAR mutation(s) is selected from a substitution at one or more positions E396, C451, V351, R455, T375, K376, S486, Q488, R510, K594, R348, G593, S397, H443, L444, Y445, F442, E438, T448, A353, V355, T339, P539, V525 and I520, optionally relative to SEQ ID NO: 18 or SEQ ID NO: 19. 13. The method of any one of the preceding claims, wherein the cytidine deaminase yields a uridine (U) nucleotide. 14. The method of any one of the preceding claims, wherein the cytidine deaminase is selected from APOBEC1, activation-induced cytidine deaminase (AID), APOBEC2, APOBEC3A, APOBEC3B, APOBEC3C, APOBEC3D, APOBEC3E, APOBEC3F, APOBEC3G, APOBEC3H, pmCDA1, and Attorney Docket No.: 33791/41005 ACF1/ASE, or fragments or variants thereof. 15. The method of any one of the preceding claims, wherein the deaminase and the bacteriophage N- peptide are a fusion protein. 16. The method of any one of the preceding claims, wherein the deaminase and the bacteriophage N- peptide are a connected by a chemical linker. 17. The method of any one of the preceding claims, wherein the deaminase is linked to at least 2, at least 3, or at least 4 bacteriophage N-peptides. 18. The method of any one of the preceding claims, wherein the bacteriophage N-peptide is linked to at least 2, at least 3, or at least 4 deaminases, or fragments thereof. 19. The method of any one of the preceding claims, wherein the deaminase and the bacteriophage N- peptide comprise a nuclear localization signal. 20. The method of any one of the preceding claims, wherein the deaminase and the bacteriophage N- peptide comprise a nuclear localization signal and the RNA molecule comprising the target nucleotide is in the nucleus of the cell. 21. The method of any one of the preceding claims, wherein the nuclear localization signal is the SV40 Large T-antigen nuclear localization signal. 22. The method of any one of the preceding claims, wherein SV40 Large T-antigen nuclear localization signal comprises the amino acid sequence of SEQ ID NO: 21. 23. The method of any one of the preceding claims, wherein the antisense RNA nucleotide hybridizes with a wild-type target sequence in an endogenous RNA and comprises a target nucleotide to be edited. 24. The method of any one of the preceding claims, wherein the target nucleotide to be edited induces a beneficial mutation in the wild-type target sequence. 25. The method of any one of the preceding claims, wherein the antisense RNA nucleotide hybridizes with a mutant target sequence in an endogenous RNA and comprises a target nucleotide to be edited. 26. The method of any one of the preceding claims, wherein the target nucleotide to be edited eliminates a detrimental mutation in the mutant target sequence. 27. The method of any one of the preceding claims, wherein the target nucleotide is a genetic mutation associated with a genetic disease or disorder. Attorney Docket No.: 33791/41005 28. The method of any one of the preceding claims, wherein the genetic mutation of the target nucleotide causes a premature termination codon (PTC) or an in-frame stop codon. 29. The method of any one of the preceding claims, wherein the genetic disease or disorder is caused by a U-to-C nucleotide mutation. 30. The method of any one of the preceding claims, wherein the antisense RNA oligonucleotide hybridizes with an RNA molecule comprising the target nucleotide in endogenous RNA of the cell. 31. The method of any one of the preceding claims, wherein the antisense RNA oligonucleotide sequence is at least 80% complementary with the target sequence. 32. The method of any one of the preceding claims, wherein the 5' end of the antisense RNA oligonucleotide begins before the target nucleotide to be edited. 33. The method of any one of the preceding claims, wherein the 3' end of the oligonucleotide extends from 2-22 nucleotides 5' from the target nucleotide to be edited. 34. The method of any one of the preceding claims, wherein the antisense RNA oligonucleotide is linked to at least 2, 3, or 4 hairpin RNA oligonucleotides. 35. The method of any one of the preceding claims, wherein the hairpin RNA oligonucleotide comprises a nucleic acid sequence located from about 2-20 nucleotide residues 5' of the target mutation. 36. The method of any one of the preceding claims, wherein the hairpin RNA oligonucleotide comprises a nucleic acid sequence located from about 2-20 nucleotide residues 3' of the target mutation. 37. The method of any one of the preceding claims, wherein components (i) and (ii) are within a plasmid, vector, mRNA, or lipid nanoparticle. 38. The method of any one of the preceding claims, wherein components (i) and (ii) are within a viral vector. 39. The method of any one of any one of the preceding claims, wherein the bacteriophage N-peptide is a mutant λ bacteriophage N-peptide. 40. The method of any one of any one of the preceding claims, wherein the bacteriophage N-peptide is a lamboid P21 bacteriophage N-pepeptide. 41. The method of any one of any one of the preceding claims, wherein the bacteriophage N-peptide is a lamboid P22 bacteriophage N-peptide.
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