WO2017040181A1 - Structural nucleic acid nanotechnology in energy applications - Google Patents

Abstract

The present disclosure relates, in some embodiments, to the use of nucleic acid structures (e.g., nanostructures and/or microstructures) in energy applications.

Description

STRUCTURAL NUCLEIC ACID

NANOTECHNOLOGY IN ENERGY APPLICATIONS

RELATED APPLICATIONS

This application claims the benefit under 35 U.S.C. § 119(e) of U.S. provisional application number 62/211,193, filed August 28, 2015, which is incorporated by reference herein in its entirety.

BACKGROUND

Photovoltaic (PV) devices generate electricity directly from sunlight via an electronic process that occurs naturally in certain types of material, such as semiconductors. Photons strike and ionize semiconductor material on the solar panel, causing outer electrons to break free of their atomic bonds. Due to the semiconductor structure, the electrons are forced in one direction creating a flow of electrical current. Carbon nanotubes (CNTs), for example, possess (i) a wide range of direct bandgaps matching the solar spectrum, (ii) strong photoabsorption (from infrared to ultraviolet), (iii) high carrier mobility and (iv) reduced carrier transport scattering, which make CNTs ideal photovoltaic material.

SUMMARY

The methods provided herein, in some embodiments, use nanotrenches on micron- scale DNA brick crystals to spatially confine the directional deposition of CNTs mediated by DNA hybridization, which can be used for the production of photovoltaic and other energy storage devices. Using methods of the present disclosure, parallel carbon nanotube (CNT) arrays were constructed with uniform programmable pitches (ranging, e.g. , from 10.5 nm to 25.2 nm). The methods provided herein enable 2-nm spatial resolution and sub-2 nm precision for programming inter-CNT pitch over millimeter scale.

Generally, the present disclosure provides, at least in part, to the use of structural nucleic acid (e.g. , DNA) nanotechnology in energy applications, such as energy storage and energy generation (e.g. , batteries, photovoltaic s, etc.).

In some embodiments, nucleic acid structures (e.g. , nucleic acid nanostructures) are assembled in lithium (Li) (e.g. , lithium chloride) solution, for example, following epitaxial growth. In some embodiments, supercapacitors are provided. For example, supercapacitors may be produced by depositing Li-based DNA "brick" nanostructures or other 2D or 3D nucleic acid structures (e.g. , nucleic acid nanostructures) onto a substrate comprising (or consisting of) an atomic film, such as graphene or graphite. DNA "bricks" and other DNA nanostructures for use as provided herein are described in International Publication Number WO 2014/018675 Al (PCT/US2013/051891) and International Publication Number WO 2014/186440 A3 (PCT/US2015/032198), each of which is incorporated by reference herein in its entirety. In some embodiments, a capacitor is a double-layer capacitor formed between the electrons charged into graphene and lithium ions adsorbed (e.g. , or intercalated) within DNA brick nanostructures (crystals).

In some embodiments, lithium-containing DNA carbon nanotube (CNT) arrays are provided herein. For example, metallic CNTs may be "trapped" within DNA nanostructures (e.g. , trenches), forming a CNT array with prescribed periodicity surrounded by lithium ions. The array may be prepared, in some embodiments, in LiCl solution.

In some embodiments, a supercapacitor comprises or is produced from a single CNT array. A supercapacitor, in some embodiments, may also be constructed from the Li- containing CNT arrays. In some embodiments, a double-layer capacitor is formed between electrons charged into metallic CNTs and lithium ions adsorbed within DNA brick nanostructures (crystals).

In some embodiments, the orientations and spacings of CNT arrays are

"programmed" with DNA nanostructures (crystals). DNA brick crystals, for example, may be used as templates.

In some embodiments, a photovoltaics device is constructed from a single (or double) CNT array. For examples, a patterned semiconducting CNT may be transferred onto a substrate (e.g. , Si surface or glass surface), followed by, for example, the construction of top metal electrodes and back contacts, which produces photovoltaics from single CNT arrays. The photo-generated charge carriers within CNTs flow, in some embodiments, into electrodes on the top and on the bottom, which converts the sunlight into electric current.

Some embodiments of the present disclosure provide compositions that include an nucleic acid structure having parallel nucleic acid nanotrenches that each include two sidewalls, a bottom layer and a longitudinal axis, wherein each of the nanotrenches comprises a semiconducting nanotube. Some embodiments of the present disclosure provide methods that include depositing, into each parallel nucleic acid nanotrench of a nucleic acid structure, a semiconducting nanotube, wherein each of the nucleic acid nanotrenches includes two sidewalls, a bottom layer and a longitudinal axis.

Also provided herein are uses of nucleic acid structures (e.g. , nucleic acid

nanostructures) in at least one energy application.

In some embodiments, the nucleic acid structures (e.g. , nucleic acid nanostructures) comprise lithium ions (e.g. , obtained from LiCl).

In some embodiments, the energy application is energy storage.

In some embodiments, the energy application is energy generation.

BRIEF DESCRIPTION OF DRAWINGS

The accompanying drawings are not intended to be drawn to scale. For purposes of clarity, not every component may be labeled in every drawing.

Figs. 1A and IB depict Li-DNA nanostructures (crystals). DNA structures are folded in lithium solution (2M) following epitaxial growth (protected). Zoom-out view image (Fig. 1A) shows the high sample density of the final structure. Zoom-in view image (Fig. IB) shows the high structural quality as design. These Li-based DNA structures are typically stable over a wide concentration range, e.g. , from 300 mM or 400 mM LiCl to 3M LiCl.

Fig. 2 depicts a supercapacitor from DNA covered graphene. Based on the high capacity of Li stored within the DNA brick crystals, supercapacitors are constructed by depositing Li-based DNA brick crystals onto graphene. Fig. 2 shows a double-layer capacitor formed between the electrons charged into graphene and lithium ions adsorbed within DNA brick nanostructures (crystals).

Fig. 3 depicts Li-based DNA-CNT arrays, CNT arrays within lithium solution. With

450 mM LiCl as buffer, metallic CNTs could be trapped within the DNA trenches, forming the CNT arrays with prescribed 25 nm periodicity. The array was prepared in 450 mM LiCl solution.

Fig. 4 depicts a supercapacitor from single CNT array. A supercapacitor could also be constructed from the Li-containing CNT arrays. Fig. 4 shows the double-layer capacitor formed between the electrons charged into metallic carbon nanotubes and lithium ions adsorbed within DNA brick crystals. Figs. 5A-5C depict programming CNT array with DNA crystals. DNA brick crystals were used as templates; the rational programming of CNT pitches were initially reported from 16.8 nm to 10.5 nm (protected).

Fig. 6 depicts photovoltaics from a single CNT array. Transferring the patterned semiconducting CNTs onto Si surface, followed by the construction of top metal electrodes and back contacts, also produces photovoltaics at single CNT arrays. The photo-generated charge carriers within CNTs flow into metal electrodes on the top and the bottom, which converts the sunlight into electric current. DETAILED DESCRIPTION

An example of a general method of the present disclosure follows with reference to Fig. 5A. A DNA brick crystal template is first designed and assembled with parallel nanotrenches. Within each trench, multiple single-stranded DNA (ssDNA) handles project out of the bottom layer. Using a two-step assembly method, the CNT surface is wrapped with ssDNA anti-handles (sequence complementary to the DNA handles) through non- covalent interactions. At mild conditions, the hybridization between the ssDNA handles within the DNA nanotrenches and the anti-handles on CNTs mediates the CNT deposition into the DNA nano-trenches and produces parallel CNT arrays at prescribed inter-CNT pitch. Nucleic Acid Structures (e.g., Nanostructures), also referred to as "Crystals"

Aspects of the present disclosure relate to two-dimensional or three-dimensional nucleic acid nanostructures and microstructures for patterning of substrates. A "nucleic acid structure" is a rationally-designed, artificial (e.g., non-naturally occurring) structure self- assembled from individual nucleic acids.

In some embodiments, a self-assembled one-, two- or three-dimensional nucleic acid structure (e.g., nanostructure or micro structure), referred to herein as a "crystal," may be a substrate. It should be understood that the terms "nucleic acid nanostructure" and "nucleic acid crystal" (or simply "crystal") may be used herein interchangeably. Crystals also include, in some embodiments, larger nucleic acid microstructures or macrostructures.

In some embodiments, a has a length in each spatial dimension, depending on whether it is a ID, 2D or 2D structure, and is rationally designed to self-assemble (is programmed) into a pre-determined, defined shape that would not otherwise assemble in nature. The use of nucleic acids to build nanostructures is enabled by strict nucleotide base pairing rules (e.g. , A binds to T, G binds to C, A does not bind to G or C, T does not bind to G or C), which result in portions of strands with complementary base sequences binding together to form strong, rigid structures. This allows for the rational design of nucleotide base sequences that will selectively assemble (self-assemble) to form nanostructures.

Nucleic acid structures (e.g. , nucleic acid nanostructures) (crystals) are typically nanometer- scale or micrometer-scale structures (e.g. , having a length scale of 1 to 1000 nanometers (nm), or 1 to 10 micrometers (μιη)). In some instances, a micrometer- scale structures is assembled from more than one nanometer- scale or micrometer- scale structure. In some embodiments, a nucleic acid nanostructure (and, thus, a crystal) has a length scale of 1 to 1000 nm, 1 to 900 nm, 1 to 800 nm, 1 to 700 nm, 1 to 600 nm, 1 to 500 nm, 1 to 400 nm, 1 to 300 nm, 1 to 200 nm, 1 to 100 nm or 1 to 50 nm. In some embodiments, a nucleic acid nanostructure has a length scale of 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 μιη. In some embodiments, a nucleic acid nanostructure has a length scale of greater than 1000 nm. In some embodiments, a nucleic acid nanostructure has a length scale of 1 μιη to 2 μιη. In some embodiments, a nucleic acid nanostructure has a length scale of 200 nm to 2 μιη, or more.

In some embodiments, a nucleic acid nanostructure (i.e. , crystal) assembles from a plurality of different nucleic acids (e.g. , single-stranded nucleic acids). For example, a nucleic acid nanostructure may assemble from at least 10, at least 20, at least 30, at least 40, at least 50, at least 60, at least 70, at least 80, at least 90 or at least 100 nucleic acids. In some embodiments, a nucleic acid nanostructure assembles from at least 100, at least 200, at least 300, at least 400, at least 500, or more, nucleic acids. The term "nucleic acid" encompasses "oligonucleotides," which are short, single-stranded nucleic acids (e.g. , DNA) having a length of 10 nucleotides to 100 nucleotides. In some embodiments, an oligonucleotide has a length of 10 to 20 nucleotides, 10 to 30 nucleotides, 10 to 40 nucleotides, 10 to 50

nucleotides, 10 to 60 nucleotides, 10 to 70 nucleotides, 10 to 80 nucleotides or 10 to 90 nucleotides. In some embodiments, an oligonucleotide has a length of 20 to 50, 20 to 75 or 20 to 100 nucleotides. In some embodiments, an oligonucleotide has a length of 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49 or 50 nucleotides.

In some embodiments, a nucleic acid nanostructure (i.e. , crystal) is assembled from single-stranded nucleic acids, double- stranded nucleic acids, or a combination of single- stranded and double- stranded nucleic acids. Nucleic acid structures (e.g., nucleic acid nanostructures) (crystals) may assemble, in some embodiments, from a plurality of heterogeneous nucleic acids (e.g., oligonucleotides). "Heterogeneous" nucleic acids may differ from each other with respect to nucleotide sequence. For example, in a heterogeneous plurality that includes nucleic acids A, B and C, the nucleotide sequence of nucleic acid A differs from the nucleotide sequence of nucleic acid B, which differs from the nucleotide sequence of nucleic acid C. Heterogeneous nucleic acids may also differ with respect to length and chemical compositions (e.g., isolated v.

synthetic).

The fundamental principle for designing self-assembled nucleic acid structures (e.g., nucleic acid nanostructures) (crystals) is that sequence complementarity in nucleic acid strands is encoded such that, by pairing up complementary segments, the nucleic acid strands self-organize into a predefined nanostructure under appropriate physical conditions. From this basic principle (see, e.g., Seeman N.C. J. Theor. Biol. 99: 237, 1982, incorporated by reference herein), researchers have created diverse synthetic nucleic acid structures (e.g., nucleic acid nanostructures) (see, e.g., Seeman N.C. Nature 421: All , 2003; Shih W.M. et al. Curr. Opin. Struct. Biol. 20: 276, 2010, each of which is incorporated by reference herein). Examples of nucleic acid (e.g., DNA) nanostructures, and methods of producing such structures, that may be used in accordance with the present disclosure are known and include, without limitation, lattices (see, e.g., Winfree E. et al. Nature 394: 539, 1998; Yan H. et al. Science 301: 1882, 2003; Yan H. et al. Proc. Natl. Acad. ofSci. USA 100; 8103, 2003; Liu D. et al. J. Am. Chem. Soc. 126: 2324, 2004; Rothemund P.W.K. et al. PLoS Biology 2: 2041, 2004, each of which is incorporated by reference herein), ribbons (see, e.g. , Park S.H. et al. Nano Lett. 5: 729, 2005; Yin P. et al. Science 321: 824, 2008, each of which is incorporated by reference herein), tubes (see, e.g., Yan H. Science, 2003; P. Yin, 2008, each of which is incorporated by reference herein), finite two-dimensional and three dimensional objects with defined shapes (see, e.g., Chen J. et al. Nature 350: 631, 1991; Rothemund P. W. K., Nature, 2006; He Y. et al. Nature 452: 198, 2008; Ke Y. et al. Nano. Lett. 9: 2445, 2009; Douglas S. M. et al. Nature 459: 414, 2009; Dietz H. et al. Science 325: 725, 2009; Andersen E. S. et al. Nature 459: 73, 2009; Liedl T. et al. Nature Nanotech. 5: 520, 2010; Han D. et al. Science 332: 342, 2011, each of which is incorporated by reference herein), and macroscopic crystals (see, e.g., Meng J. P. et al. Nature 461: 74, 2009, incorporated by reference herein). Examples of nucleic acid (e.g., DNA) nanostructures include, but are not limited to, DNA origami structures, in which a long scaffold strand (e.g., at least 500 nucleotides in length) is folded by hundreds (e.g., 100, 200, 200, 400, 500 or more) of short (e.g., less than 200, less than 100 nucleotides in length) auxiliary strands into a complex shape (Rothemund, P. W. K. Nature 440, 297-302 (2006); Douglas, S. M. et al. Nature 459, 414-418 (2009); Andersen, E. S. et al. Nature 459, 73-76 (2009); Dietz, H. et al. Science 325, 725-730 (2009); Han, D. et al. Science 332, 342-346 (2011); Liu, Wei al. Angew. Chem. Int. Ed. 50, 264-267 (2011); Zhao, Z. et al. Nano Lett. 11, 2997-3002 (2011); Woo, S. & Rothemund, P. Nat. Chem. 3, 620-627 (2011); T0rring, T. et al. Chem. Soc. Rev. 40, 5636-5646 (2011).

Nucleic acid structures (e.g., nucleic acid nanostructures) (crystals) of the present disclosure may be two-dimensional or three-dimensional. Two-dimensional nucleic acid structures (e.g., nucleic acid nanostructures) are single-layer planar structures that can be measured along an x-axis and a y-axis. A "layer" of a nucleic acid structure (e.g., nucleic acid nanostructure) refers to a planar arrangement of nucleic acids that is uniform in height. "Height" refers to a measurement of the vertical distance (e.g., along the y-axis) of a structure. "Maximum height" refers to a measurement of the greatest vertical distance of a structure (e.g., distance between the highest point of the structure and the lowest point of the structure). In some embodiments, a nucleic acid layer has a maximum height less than 3 nm (e.g., 1 nm, 1.5 nm, 2 nm, 2.5 nm). A two-dimensional nucleic acid nanostructure is a single- layer structure, thus, in some embodiments, a two-dimensional nucleic acid nanostructure has a planar arrangement of nucleic acids that is uniform in height and has a maximum height less than 3 nm. In some embodiments, a two-dimensional nucleic acid nanostructure has a maximum height of less than 2.5 nm. In some embodiments, a two-dimensional nucleic acid nanostructure has a maximum height of 1 nm to 2.9 nm, or 1 nm to 2.5 nm. In some embodiments, a two-dimensional nucleic acid nanostructure has a maximum height of 1 nm, 1.5 nm, 2 nm or 2.5 nm. Non-limiting examples of two-dimensional nucleic acid structures (e.g., nucleic acid nanostructures) include nucleic acid lattices, tiles and nanoribbons (see, e.g., Rothemund P.W.K., Nature 440: 297, 2006; and Jungmann R. et al., Nanotechnology 22(27): 275301, 2011, each of which is incorporated by reference herein).

Three-dimensional nucleic acid structures (e.g., nucleic acid nanostructures) (crystals) can be measured along an x-axis, a y-axis and a z-axis. A three-dimensional nucleic acid nanostructure, in some embodiments, has a maximum height equal to or greater than 3 nm. In some embodiments, a three-dimensional nucleic acid nanostructure has a maximum height of greater than 4 nm, greater than 5 nm, greater than 6 nm, greater than 7 nm, greater than 8 nm, greater than 9 nm or greater than 10 nm. In some embodiments, a three-dimensional nucleic acid nanostructure has a maximum height of 3 nm to 50 nm, 3 nm to 100 nm, 3 nm to 250 nm or 3 nm to 500 nm. In some embodiments, a three-dimensional nanostructure may be a multi-layer structure. In some embodiments, a three-dimensional nucleic acid

nanostructure comprises 2 to 200, or more, nucleic acid layers. In some embodiments, a three-dimensional nucleic acid nanostructure includes greater than 2, greater than 3, greater than 4, or greater than 5 nucleic acid layers. In some embodiments, a three-dimensional nucleic acid nanostructure comprises 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 35, 40, 45 or 50 or more nucleic acid layers. A three-dimensional nanostructure may be uniform in height or it may be non-uniform in height. Non-limiting examples of three-dimensional nucleic acid structures (e.g. , nucleic acid nanostructures) include nucleic acid cubes and other abstract and/or irregular three-dimensional shapes (see, e.g. , Douglas S. M, et al. Nature 459: 414, 2009; Andersen E.D. et al. Nature 459: 73, 2009; Han D. et al. Science 332: 342, 2011 ; Ke Y. et al. , 2011 ; Wei B., 2012, each of which is incorporated by reference herein).

Conceptually, a single-layer two-dimensional nucleic acid nanostructure (i.e. , crystal), in some embodiments, can be constructed by "extraction" of a layer from a three-dimensional nucleic acid nanostructure (see, e.g. , Ke Y. et al. , 2012; see also Wei B., et al. Nature 485: 623, 2012, each of which is incorporated by reference herein). A three-dimensional nucleic acid nanostructure, in some embodiments, may be assembled from more than one two- dimensional nucleic acid nanostructure (e.g. , more than one layer of nucleic acids) or more than one three-dimensional nucleic acid nanostructure (e.g. , more than one "pre-assembled" nucleic acid nanostructure that is linked to one or more other "pre-assembled" nucleic acid nanostructure).

Thus, contemplated herein are composite nucleic acid structures (e.g. , nucleic acid nanostructures) (crystals). In some embodiments, a composite nucleic acid nanostructure comprises nucleic acid structures (e.g. , nucleic acid nanostructures) linked to each other using linkers. The linkers are typically not integral to the nucleic acid structures (e.g. , nucleic acid nanostructures), although they may be attached to the structures through suitable functional groups. The ability to attach two or more nucleic acid structures (e.g. , nucleic acid nanostructures) together allows structures of greater size (e.g. , micrometer size) and complexity to be made. The dimensions of these composite structures may range, for example, from 500 nm to 100 μιη, 1 μιη to 1000 μιη, 1 μιη to 5 μιη, 1 μιη to 10 μιη, 1 μιη to 20 μιη, or more. Thus, in some embodiments, composite nanostructures encompass microstructures. In some embodiments, the nucleic acid structure, comprising nanotrenches, is a nucleic acid microstructure.

Examples of linkers for use in accordance with the present disclosure include, without limitation, chemical crosslinkers (e.g. , glutaraldehyde), biomolecules (e.g. , avidin-biotin), and ligand-functionalized nanoparticles/moieties (e.g. , single- stranded-nucleic acid- functionalized nanoparticles). In some instances, the linkers may involve click chemistry or coordinating interaction (Ni2+/polyhistidine).

In some embodiments, a nucleic acid nanostructure (i.e. , crystal) is assembled using a nucleic acid (e.g. , DNA) origami approach. With a DNA origami approach, for example, a long "scaffold" nucleic acid strand is folded to a predesigned shape through interactions with relatively shorter "staple" strands. Thus, in some embodiments, a single-stranded nucleic acid for assembly of a nucleic acid nanostructure has a length of at least 500 base pairs, at least 1 kilobase, at least 2 kilobases, at least 3 kilobases, at least 4 kilobases, at least 5 kilobases, at least 6 kilobases, at least 7 kilobases, at least 8 kilobases, at least 9 kilobases, or at least 10 kilobases. In some embodiments, a single-stranded nucleic acid for assembly of a nucleic acid nanostructure has a length of 500 base pairs to 10 kilobases, or more. In some embodiments, a single-stranded nucleic acid for assembly of a nucleic acid nanostructure has a length of 7 to 8 kilobases. In some embodiments, a single-stranded nucleic acid for assembly of a nucleic acid nanostructure comprises the M13 viral genome.

In some embodiments, a nucleic acid nanostructure (i.e. , crystal) is assembled from single-stranded tiles (SSTs) (see, e.g. , Wei B. et al. Nature 485: 626, 2012, incorporated by reference herein) or nucleic acid "bricks" (see, e.g. , Ke Y. et al. Science 388: 1177, 2012;

International Publication Number WO 2014/018675 Al, published January 30, 2014, each of which is incorporated by reference herein). For example, single-stranded 2- or 4-domain oligonucleotides self-assemble, through sequence- specific annealing, into two- and/or three- dimensional nanostructures in a predetermined (e.g. , predicted) manner. As a result, the position of each oligonucleotide in the nanostructure is known. In this way, a nucleic acid nanostructure may be modified, for example, by adding, removing or replacing

oligonucleotides at particular positions. The nanostructure may also be modified, for example, by attachment of moieties, at particular positions. This may be accomplished by using a modified oligonucleotide as a starting material or by modifying a particular oligonucleotide after the nanostructure is formed. Therefore, knowing the position of each of the starting oligonucleotides in the resultant nanostructure provides addressability to the nanostructure.

"Self-assembly" refers to the ability of nucleic acids (and, in some instances, preformed nucleic acid structures (e.g. , nucleic acid nanostructures) (crystals)) to anneal to each other, in a sequence- specific manner, in a predicted manner and without external control. In some embodiments, nucleic acid nanostructure self-assembly methods include combining nucleic acids (e.g. , single- stranded nucleic acids, or oligonucleotides) in a single vessel and allowing the nucleic acids to anneal to each other, based on sequence complementarity. In some embodiments, this annealing process involves placing the nucleic acids at an elevated temperature and then reducing the temperature gradually in order to favor sequence-specific binding. Various nucleic acid structures (e.g. , nucleic acid nanostructures) or self-assembly methods are known and described herein.

Nucleic acids of the present disclosure include DNA such as D-form DNA and Inform DNA and RNA, as well as various modifications thereof. Nucleic acid modifications include base modifications, sugar modifications, and backbone modifications. Non-limiting examples of such modifications are provided below.

Examples of modified DNA nucleic acids (e.g. , DNA variants) that may be used in accordance with the present disclosure include, without limitation, L-DNA (the backbone enantiomer of DNA, known in the literature), peptide nucleic acids (PNA) bisPNA clamp, a pseudocomplementary PNA, locked nucleic acid (LNA), and co-nucleic acids of the above such as DNA-LNA co-nucleic acids. Thus, the present disclosure contemplates

nanostructures that comprise DNA, RNA, LNA, PNA or combinations thereof. It is to be understood that the nucleic acids used in methods and compositions of the present disclosure may be homogeneous or heterogeneous in nature. As an example, nucleic acids may be completely DNA in nature or they may be comprised of DNA and non-DNA (e.g. , LNA) monomers or sequences. Thus, any combination of nucleic acid elements may be used. The nucleic acid modification may render the nucleic acid more stable and/or less susceptible to degradation under certain conditions. For example, in some embodiments, nucleic acids are nuclease-resistant. Nucleic acids of the present disclosure, in some embodiments, have a homogenous backbone (e.g. , entirely phosphodiester or entirely phosphorothioate) or a heterogeneous (or chimeric) backbone. Phosphorothioate backbone modifications may render an

oligonucleotide less susceptible to nucleases and thus more stable (as compared to a native phosphodiester backbone nucleic acid) under certain conditions. Other linkages that may provide more stability to a nucleic acid of the present disclosure include, without limitation, phosphorodithioate linkages, methylphosphonate linkages, methylphosphorothioate linkages, boranophosphonate linkages, peptide linkages, alkyl linkages and dephospho-type linkages. Thus, in some embodiments, nucleic acids have non-naturally occurring backbones.

In some embodiments, nucleic acids of the present disclosure do not encode a product

(e.g. , a protein).

Nucleic acids of the present disclosure, in some embodiments, additionally or alternatively comprise modifications in their sugars. For example, a β-ribose unit or a β-ϋ-2'- deoxyribose unit can be replaced by a modified sugar unit, wherein the modified sugar unit is, for example, selected from β-D-ribose, oc-D-2'-deoxyribose, L-2'-deoxyribose, 2'-F-2'- deoxyribose, arabinose, 2'-F-arabinose, 2'-0-(Ci-C₆)alkyl-ribose, preferably 2'-0-(Ci- C₆)alkyl-ribose is 2'-0-methylribose, 2'-0-(C₂-C₆)alkenyl-ribose, 2'-[0-(Ci-C₆)alkyl-0-(Ci- C₆)alkyl]-ribose, 2'-NH₂-2'-deoxyribose, β-D-xylo-furanose, a-arabinofuranose, 2,4-dideoxy- β-D-erythro-hexo-pyranose, and carbocyclic (see, e.g. , Froehler J. Am. Chem. Soc. 114:8320, 1992, incorporated by reference herein) and/or open-chain sugar analogs (see, e.g. ,

Vandendriessche et al. Tetrahedron 49:7223, 1993, incorporated by reference herein) and/or bicyclosugar analogs (see, e.g. , Tarkov M. et al. Helv. Chim. Acta. 76:481 , 1993,

incorporated by reference herein).

Nucleic acids of the present disclosure, in some embodiments, comprise modifications in their bases. Modified bases include, without limitation, modified cytosines (such as 5- substituted cytosines (e.g. , 5-methyl-cytosine, 5-fluoro-cytosine, 5-chloro-cytosine, 5-bromo- cytosine, 5-iodo-cytosine, 5-hydroxy-cytosine, 5-hydroxymethyl-cytosine, 5-difluoromethyl- cytosine, and unsubstituted or substituted 5-alkynyl-cytosine), 6-substituted cytosines, N4- substituted cytosines (e.g. , N4-ethyl-cytosine), 5-aza-cytosine, 2-mercapto-cytosine, isocytosine, pseudo-isocytosine, cytosine analogs with condensed ring systems (e.g. , Ν,Ν'- propylene cytosine or phenoxazine), and uracil and its derivatives (e.g. , 5-fluoro-uracil, 5- bromo-uracil, 5-bromovinyl-uracil, 4-thio-uracil, 5-hydroxy-uracil, 5-propynyl-uracil), modified guanines such as 7-deazaguanine, 7-deaza-7-substituted guanine (such as

7- deaza-7-(C2-C6)alkynylguanine), 7-deaza-8-substituted guanine, hypoxanthine, N2- substituted guanines (e.g. N2-methyl-guanine), 5-amino-3-methyl-3H,6H-thiazolo[4,5- d]pyrimidine-2,7-dione, 2,6-diaminopurine, 2-aminopurine, purine, indole, adenine, substituted adenines (e.g. N6-methyl-adenine, 8-oxo-adenine) 8-substituted guanine (e.g.

8- hydroxyguanine and 8-bromoguanine), and 6-thioguanine. The nucleic acids may comprise universal bases (e.g. 3-nitropyrrole, P-base, 4-methyl-indole, 5-nitro-indole, and K-base) and/or aromatic ring systems (e.g. fluorobenzene, difluorobenzene, benzimidazole or dichloro-benzimidazole, 1 -methyl- 1H-[1, 2,4] triazole-3-carboxylic acid amide). A particular base pair that may be incorporated into the oligonucleotides of the present disclosure is a dZ and dP non-standard nucleobase pair reported by Yang et al. NAR, 2006, 34(21):6095-6101. dZ, the pyrimidine analog, is 6-amino-5-nitro-3-(l'-P-D-2'-deoxyribofuranosyl)-2(lH)- pyridone, and its Watson-Crick complement dP, the purine analog, is 2-amino-8-( -P-D-l'- deoxyribofuranosyl)-imidazo[ 1 ,2-a] - 1 ,3 ,5-triazin-4(8H)-one.

Nucleic acids of the present disclosure, in some embodiments, are synthesized in vitro. Thus, in some embodiments, nucleic acids are synthetic (e.g., not naturally-occurring). Methods for synthesizing nucleic acids, including automated nucleic acid synthesis, are known. For example, nucleic acids having modified backbones, such as backbones comprising phosphorothioate linkages, and including those comprising chimeric modified backbones, may be synthesized using automated techniques employing either

phosphoramidate or H-phosphonate chemistries (see, e.g., F. E. Eckstein, "Oligonucleotides and Analogues - A Practical Approach" IRL Press, Oxford, UK, 1991; and Matteucci M. D. et al. Tetrahedron Lett. 21: 719, 1980). Synthesis of nucleic acids with aryl- and

alkyl-phosphonate linkages are also contemplated (see, e.g., U.S. Patent No. 4,469,863). In some embodiments, nucleic acids with alkylphosphotriester linkages (in which the charged oxygen moiety is alkylated, e.g., as described in U.S. Patent No. 5,023,243 and European Patent No. 092,574) are prepared by automated solid phase synthesis using commercially available reagents. Methods for making other DNA backbone modifications and

substitutions have been described (see, e.g., Uhlmann E. et al. Chem. Rev. 90:544, 1990; Goodchild J. Bioconjugate Chem. 1: 165, 1990; Crooke S.T. et al. Annu. Rev. Pharmacol. Toxicol. 36: 107, 1996; and Hunziker J. et al. Mod Synth Methods 7:331, 1995, each of which is incorporated by reference) and may be used in accordance with the present disclosure.

Some aspects of the present disclosure are directed to assembling nucleic acid structures {e.g., nucleic acid nanostructures) using annealing processes. In some

embodiments, nucleic acids are combined, in a single vessel such as, but not limited to, a tube, a well or a vial. The molar amounts of nucleic acids that are used may depend on the frequency of each nucleic acid in the nanostructure desired and the amount of nanostructure desired. In some embodiments, the nucleic acids may be present in equimolar concentrations. In some embodiments, each nucleic acid {e.g., oligonucleotide) may be present at a concentration of about 200 nM. In some embodiments, the nucleic acids are placed in a solution. The solution may be buffered, although the annealing reaction can also occur in the absence of buffer. The solution may further comprise divalent cations such as, but not limited, to Mg²⁺. The cation or salt concentration may vary. An exemplary concentration is about 490 mM. The solution may also comprise EDTA or other nuclease inhibitors in order to prevent degradation of the nucleic acids.

An annealing reaction is carried out, in some embodiments, by heating the solution containing nucleic acids and then allowing the solution to slowly cool down {e.g., heated and then placed in a room temperature environment). The temperature of the reaction should be sufficiently high to melt any undesirable secondary structure such as hairpin structures and to ensure that the nucleic acids are not bound incorrectly to other non-complementary nucleic acids. The temperature, therefore, may be initially raised to any temperature below or equal to 100 °C. For example, the temperature may be initially raised to 100 °C, 95 °C, 90 °C, 85 °C, 80 °C, 75 °C, 70 °C, 65 °C or 60 °C. The temperature may be raised by placing the vessel in a hot water bath, heating block or a device capable of temperature control, such as a thermal cycler {e.g., polymerase chain reaction (PCR) machine). The vessel may be kept in that environment for seconds or minutes. In some embodiments, an incubation time of about 1-10 minutes is sufficient.

Once nucleic acid incubation at an elevated temperature is complete, the temperature may be dropped in a number of ways. The temperature may be dropped, for example, in an automated manner using a computer algorithm that drops the temperature by a certain amount and maintains that temperature for a certain period of time before dropping the temperature again. Such automated methods may involve dropping the temperature by a degree in each step or by a number of degrees at each step. The vessel may thus be heated and cooled in the same device. As another example, the heated solution may be placed at room temperature to cool. An exemplary process for dropping temperature is as follows. To effect a drop in temperature from about 80 °C to about 24 °C, the temperature is changed from 80 °C to 61 °C in one degree increments at a rate of 3 minutes per degree (e.g. , 80 °C for 3 minutes, 79 °C for 3 minutes, etc.). The temperature is then changed from 60 °C to 24 °C in one degree increments and at a rate of about 120 minutes per degree (e.g. , 60 °C for 120 minutes, 59 °C for 210 minutes, etc.). The total annealing time for this process is about 17 hours. In accordance with the present disclosure, under these conditions, nucleic acids (e.g. , oligonucleotides) self-assemble into a nanostructure (i.e. , crystal) of predetermined and desired shape and size.

An example of a specific annealing process uses one hundred different 200 nM oligonucleotides in solution (e.g. , 5 mM Tris- 1 mM EDTA (TE), 40 mM MgCi₂) and the solution is heated to about 90 °C and then cooled to about 24 °C over a period of about 73 hours, as described above with a 3 minute per degree drop between 80 °C and 61 °C, and a 120 minute per degree drop between 60 °C and 24 °C. It should be understood that the foregoing annealing process is exemplary and that other annealing processes may be used in accordance with the present disclosure.

The disclosure provides nucleic acid structures (e.g. , nucleic acid nanostructures) generated using epitaxial growth processes. Epitaxial-grown nucleic acid structures (e.g. , nucleic acid nanostructures) (to be used as DNA templates, for example) may be formed through a seed-mediated nucleic acid (e.g. , DNA) growth process starting from a pre-formed nucleic acid (e.g. , DNA) seed. The seed may comprise one or more single- stranded DNAs with longer binding domains (such as 16 nucleotides compared with a typical 8 nucleotides per domain) or it may be a pre-formed DNA structure, without limitation. Epitaxial growth creates a single-crystalline interface between the seed and the resulting grown structure. In contrast to existing seed-mediated DNA growth, epitaxial growth does not require sequence design for specific growth pathway, and can be used for 3D structures. Additionally, using epitaxial growth, the seed-mediated DNA formation can start either along π-π stacking direction (helical direction) or perpendicular to the helical direction.

In some embodiments, nucleic acid structures (e.g. , nucleic acid nanostructures) are assembled in lithium (Li) (e.g. , lithium chloride) solution (lithium ions are adsorbed onto nucleic acid structures). Assembly of nucleic acid (e.g. , DNA) structures (e.g. , having nanotrenches) may be performed, for example, using multi-staged incubation reaction. For example, nucleic acid structures (e.g. , nucleic acid nanostructures) (e.g. , 100 nM-1000 nM concentration of oligonucleotide "bricks" single- stranded oligonucleotides programmed to self-assemble into nanostructures) may be combined with a solution containing buffer, such as Tris, EDTA, LiCl (e.g. , 1-5 M) and subjected to a multi-stage incubation at 65-85 °C for 10-30 min, 40-50 °C for 10-14 h, 30-40 °C for 70-74 h, and 25-35 °C for 6- 10 h, sequentially.

In some embodiments, semiconducting nanotubes (e.g. , CNTs) are assembled in lithium solution. For example, 'DNA-wrapped' semiconducting nanotubes (e.g. , CNTs linked to single-stranded handles (or anti-handles)) may be combined with oligonucleotide "bricks" (e.g. , lOx dilution into 500 mM LiCl solution) and incubated at 30-40 °C for 8-10 h, and then stored at 4 °C .

Nanotrenches

The methods and compositions of the present disclosure enable precise deposition of semiconducting nanotubes (e.g. , carbon nanotubes, CNTs) into nucleic acid nanotrenches at prescribed inter-nanotube pitch. Thus, in some embodiments, the distance between two semiconducting nanotubes (e.g. , between two adjacent nanotubes) is between 5 nm and 100 nm. For example, the distance between two semiconducting nanotubes may be between 5 nm and 50 nm, or between 5 nm and 25 nm. In some embodiments, the distance between two semiconducting nanotubes is 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 or 30 nm. In some embodiments, the distance between two

semiconducting nanotubes is 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10.0, 10.1, 10.2, 10.3, 10.4, 10.5, 10.6, 10.7, 10.8, 10.9, 11.0, 11.1, 11.2, 11.3, 11.4, 11.5, 11.6, 11.7, 11.8, 11.9, 12.0, 12.1, 12.2, 12.3, 12.4, 12.5, 12.6, 12.7, 12.8, 12.9, 13.0, 13.1, 13.2, 13.3, 13.4, 13.5, 13.6, 13.7, 13.8, 13.9, 14.0, 14.1, 14.2, 14.3, 14.4, 14.5, 14.6, 14.7, 14.8, 14.9, 15.0, 15.1, 15.2, 15.3, 15.4, 15.5, 15.6, 15.7, 15.8, 15.9, 16.0, 16.1, 16.2, 16.3, 16.4, 16.5, 16.6, 16.7, 16.8, 16.9, 17.0, 17.1, 17.2, 17.3, 17.4, 17.5, 17.6, 17.7, 17.8, 17.9, 18.0, 18.1, 18.2, 18.3, 18.4, 18.5, 18.6, 18.7, 18.8, 18.9, 19.0, 19.1, 19.2, 19.3, 19.4, 19.5, 19.6, 19.7, 19.8, 19.9, 20.0, 20.1, 20.2, 20.3, 20.4, 20.5, 20.6, 20.7, 20.8, 20.9, 21.0, 21.1, 21.2, 21.3, 21.4, 21.5, 21.6, 21.7, 21.8, 21.9, 22.0, 22.1, 22.2, 22.3, 22.4, 22.5, 22.6, 22.7, 22.8, 22.9, 23.0, 23.1, 23.2, 23.3, 23.4, 23.5, 23.6, 23.7, 23.8, 23.9, 24.0, 24.1, 24.2, 24.3, 24.4, 24.5, 24.6, 24.7, 24.8, 24.9, 25.0, 25.1, 25.2, 25.3, 25.4, 25. 5, 25.6, 25.7, 25.8 or 25.9 nm. In some embodiments, the distance between two semiconducting nanotubes is between 10.0 nm and 25 nm. In some embodiments, the distance between two semiconducting nanotubes is 10.4 nm, 12.6 nm or 16.8 nm. In some embodiments, the distance between two semiconducting nanotubes is 9- 12 nm, 10-15 nm or 14- 18 nm. In some embodiments, the distance between two semiconducting nanotubes is 10.4+0.5 nm, 12.6+0.5 nm or 16.8+0.5 nm. In some embodiments, the distance between two semiconducting nanotubes is 10.4+1.0 nm, 12.6+1.0 nm or 16.8+1.0 nm.

As depicted in Fig. 5A, each nanotrench has a bottom layer and at least one sidewall, which form a compartment into which a semiconducting nanotube may be deposited. In some embodiments, the bottom layer and/or the sidewall(s) of each of the nanotrenches comprises single- stranded oligonucleotides (e.g. , having a length of less than 200 nucleotides, or less than 100 nucleotides), referred to as "handles." The number of handles attached (covalently or non-covalently) to a nanotrench surface (e.g. , bottom layer and/or sidewall(s)) may vary and may be determined by an ordinary artisan. For example, a nanotrench, or a surface of a nanotrench, may include 10-500 single- stranded handles. In some embodiments, a nanotrench, or a surface of a nanotrench, includes 10-25, 10-50, 10- 100, 10- 125, 10-150, 10-175, 10-200, 10-225, 10-250, 10-275, 10-300, 10-325, 10-350, 10-375, 10-400, 10-425, 10-450, 10-475, 25-50, 25-100, 25- 150, 25-200, 25-250, 25-300, 25-350, 25-400, 25-450, 25- 500, 50-100, 50- 150, 50-200, 50-250, 50-300, 50-350, 50-400, 50-450 or 50-500 single- stranded handles.

To direct deposition of a semiconducting nanotube into a nucleic acid nanotrench, the nanotube is decorated with (directly or indirectly linked to) single- stranded oligonucleotides, each having a nucleotide sequence complementary to a handle located on a nanotrench surface. These single-stranded oligonucleotides are referred to as anti-handles. Note, however, that the use of the terms "handle" and "anti-handle" are somewhat arbitrary and are used to identify a pair of oligonucleotides capable of binding to each other. Thus, single- stranded oligonucleotides located on a surface of a nanotrench may be referred to as anti- handles, while the single- stranded oligonucleotides located on the semiconducting nanotubes may be referred to as handles. The number of anti-handles attached (covalently or non- covalently) to a semiconducting nanotube may vary and depends, at least in part, on the number of handles present within a nanotrench into which the semiconducting nanotube is deposited. For example, a nanotube may include 10-500 single-stranded anti-handles. In some embodiments, a nanotube includes 10-25, 10-50, 10- 100, 10-125, 10-150, 10- 175, 10- 200, 10-225, 10-250, 10-275, 10-300, 10-325, 10-350, 10-375, 10-400, 10-425, 10-450, 10- 475, 25-50, 25- 100, 25-150, 25-200, 25-250, 25-300, 25-350, 25-400, 25-450, 25-500, 50- 100, 50-150, 50-200, 50-250, 50-300, 50-350, 50-400, 50-450 or 50-500 single- stranded anti- handles. As an example, a nanotube comprising about 25 anti-handles may be deposited into a nanotrench that comprises about 25 handles such that the handles and anti-handles bind to each other, thereby directed deposition of the nanotube into the nanotrench.

In some embodiments, a two-step assembly method (Z. Zhao, et al. Org. Biomol.

Chem. , 11 :596-598, 2013, incorporated herein by reference) is used to introduce DNA anti- handles (sequence complementary to the DNA handles within DNA nanotrenches) onto semiconducting nanotubes (e.g., CNTs). First, a nanotube surface is wrapped with two- domain ssDNA (ssDNA- 1), which contained a wrapping domain of repeating GT sequence at the 3' end and a binding domain (e.g. , 016-nt binding domain) at the 5' end to hybridize with a ssDNA anti-handle (ssDNA-2). Wrapping the nanotube with ssDNA- 1 molecules uses non-covalent pi-pi stacking between DNA nucleotides and the nanotube (e.g., CNT) surface. Next, a two-domain ssDNA anti-handle (ssDNA-2) is introduced to hybridize with the ssDNA-1 -wrapped nanotubes (e.g., CNTs). Within the ssDNA-2 molecules, a binding domain (e.g., 16-nt binding domain) is introduced at the 5' end for hybridizing with its complementary domain in the ssDNA-1 wrapped onto the nanotube. An anti-handle domain (e.g., a 14-nt anti-handle domain) at the 3' end of the ssDNA-2 molecules is designed to hybridize with the DNA handles located in nanotrenches of the nucleic acid structures (e.g. , nucleic acid nanostructures).

Nucleic acid structures of the present disclosure include at least 2 nanotrenches. In some embodiments, a nucleic acid structure includes 2-500 nanotrenches, at least 2 of which (or each/all) include a semiconducting nanotubes (e.g. , CNT). For example, a nucleic acid nanostructure may include 2-500, 2-400, 2-300, 2-200, 2- 100, 2-50, 2-25 or 2-10

nanotrenches. In some embodiments, a nucleic acid nanostructure includes 5-500, 5-400, 5- 300, 5-200, 5- 100, 5-50, 5-25 or 5-10 nanotrenches. In some embodiments, a nucleic acid nanostructure includes 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or 100 nanotrenches. In some embodiments, a nucleic acid nanostructure includes 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190 or 200 nanotrenches.

Semiconducting Nanotubes

Photovoltaic devices may be fabricated from thin films of organic semiconductors, such as polymers, small-molecule compounds and nanoparticle, and are typically on the order of 100 nm- 1,000 nm thick. Semiconducting nanotubes (e.g., carbon nanotubes, CNTs) possess a wide range of direct bandgaps matching the solar spectrum, strong photoabsorption, from infrared to ultraviolet, and high carrier mobility and reduced carrier transport scattering, which make themselves ideal photovoltaic material. Photovoltaic effect can be achieved in ideal single wall carbon nanotube diodes, for example. Individual semiconducting nanotubes can b fabricated into typical p-n junction diodes. An ideal behavior is the theoretical limit of performance for any diode, a highly sought after goal in optoelectronic materials

development. Under illumination, semiconducting nanotubes diodes show significant power conversion efficiencies owing to enhanced properties of an ideal diode.

Semiconducting nanotubes (e.g., CNTs) can be directly configured as energy conversion materials to fabricate thin-film solar cells, with nanotubes serving as both photogeneration sites and a charge carriers collecting/transport layer. Solar cells, for example, may include semitransparent thin film of nanotubes conformally coated on a substrate (e.g., n-type crystalline silicon substrate) to create high-density p-n heterojunctions between nanotubes and n-Si to favor charge separation and extract major and minor charge carriers through n-Si and nanotubes.

Thus, in some embodiments, a semiconducting nanotube of the present disclosure is a carbon nanotube, although nanotubes comprising other or additional semiconducting material are encompassed herein. Examples of such semiconducting material include, but are not limited to, Group IV elemental semiconductors, Group IV compound semiconductors, Group VI elemental semiconductors, Group III-V semiconductors, Group II- VI semiconductors, Group I- VII semiconductors, Group IV-VI semiconductors, Group IV- VI semiconductors, Group V-VI semiconductors, Group II- V semiconductors, oxides, layered semiconductors, magnetic semiconductors, organic semiconductors, charge-transfer complexes and

combinations thereof. Specific examples of each Group of semiconductor material are provided below. The width (diameter) of a semiconducting nanotube (e.g. , CNT) is typically 2 nm or less (e.g. , 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9 or 2 nm).

In some embodiments, semiconducting nanotubes have a uniform inter-nanotube spacing that may range between 2- 100 nm. "Inter-nanotube spacing" refers to the distance between two adjacent nanotubes (e.g. , measured from the center of each nanotube). Such spacing is considered "uniform" if the distance between multiple adjacent nanotubes is approximately equal (e.g. , spacing distances within less than 5% or less than 10% of each other). For example, semiconducting nanotubes may have an inter-nanotube spacing (e.g. , uniform inter-nanotube spacing) of 2-50 nm, 2-25 nm, 2-10 nm, 5-100 nm, 5-50 nm, 5-25 nm, 5-10 nm, 10-100 nm, 10-50 nm or 10-25 nm. In some embodiments, semiconducting nanotubes have an inter-nanotube spacing of 2, 3, 4, 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 or 30 nm. In some embodiments,

semiconducting nanotubes have an inter-nanotube spacing of 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7,

7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8,

9.9, 10.0, 10.1, 10.2, 10.3, 10.4, 10.5, 10.6, 10.7, 10.8, 10.9, 11.0, 11.1, 11.2, 11.3, 11.4, 11.5, 11.6, 11.7, 11.8, 11.9, 12.0, 12.1, 12.2, 12.3, 12.4, 12.5, 12.6, 12.7, 12.8, 12.9, 13.0, 13.1, 13.2, 13.3, 13.4, 13.5, 13.6, 13.7, 13.8, 13.9, 14.0, 14.1, 14.2, 14.3, 14.4, 14.5, 14.6, 14.7, 14.8, 14.9, 15.0, 15.1, 15.2, 15.3, 15.4, 15.5, 15.6, 15.7, 15.8, 15.9, 16.0, 16.1, 16.2, 16.3, 16.4, 16.5, 16.6, 16.7, 16.8, 16.9, 17.0, 17.1, 17.2, 17.3, 17.4, 17.5, 17.6, 17.7, 17.8, 17.9, 18.0, 18.1, 18.2, 18.3, 18.4, 18.5, 18.6, 18.7, 18.8, 18.9, 19.0, 19.1, 19.2, 19.3, 19.4, 19.5, 19.6, 19.7, 19.8, 19.9, 20.0, 20.1, 20.2, 20.3, 20.4, 20.5, 20.6, 20.7, 20.8, 20.9, 21.0, 21.1, 21.2, 21.3, 21.4, 21.5, 21.6, 21.7, 21.8, 21.9, 22.0, 22.1, 22.2, 22.3, 22.4, 22.5, 22.6, 22.7, 22.8, 22.9, 23.0, 23.1, 23.2, 23.3, 23.4, 23.5, 23.6, 23.7, 23.8, 23.9, 24.0, 24.1, 24.2, 24.3, 24.4, 24.5, 24.6, 24.7, 24.8, 24.9, 25.0, 25.1, 25.2, 25.3, 25.4, 25. 5, 25.6, 25.7, 25.8 or 25.9 nm. In some embodiments, semiconducting nanotubes have an inter-nanotube spacing of 10- 25 nm. In some embodiments, semiconducting nanotubes have an inter-nanotube spacing of 9-12 nm, 10-15 nm or 14-18 nm. In some embodiments, semiconducting nanotubes have an inter-nanotube spacing of 10.4+0.5 nm, 12.6+0.5 nm or 16.8+0.5 nm. In some embodiments, semiconducting nanotubes have an inter-nanotube spacing of 10.4+1.0 nm, 12.6+1.0 nm or 16.8+1.0 nm. The length (along the longitudinal axis) of a semiconducting nanotube (e.g. , CNT) may vary. In some embodiments, semiconducting nanotubes have a length of 25-500 nm. For example, semiconducting nanotubes may have a length of 25-250 nm, 25- 100 nm, 25-50 nm, 50-500 nm, 50-250 nm or 50- 100 nm. In some embodiments, semiconducting nanotubes have a length of 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 225, 250, 375, 300, 350, 400, 450 or 500 nm. In some embodiments, semiconducting nanotubes are longer than 500 nm or shorter than 25 nm.

In some embodiments, the carbon nanotubes are oriented in the same direction (e.g. , are parallel relative to one another) along the longitudinal axis of the nanotrenches. An example of this configuration is depicted in Fig. 5A. The three nanotubes depicted in Fig. 5A are aligned parallel to one another. To demonstrate directionality, if each nanotube included at one end a moiety, then all nanotubes would be considered oriented in the same direction if the nanotubes were aligned such that the ends with the moiety are all facing the same direction.

Substrates

In some embodiments, a nucleic acid nanostructure may be attached to a substrate. In some embodiments, a substrate comprises Si0₂. A substrate refers to a substance (e.g. , a solid planar substance or a nucleic acid nanostructure/crystal) onto which another substance (e.g. , nucleic acid nanostructure/crystal) is applied. For example, moieties, such as nanoparticles, nanowires or nucleic acids, may be applied to a substrate (e.g. , silicon wafer of nucleic acid nanostructure/crystal). Substrates used in accordance with the present disclosure may comprise, without limitation, nucleic acids, silicon, GaN, silicon dioxide (also referred to as silica), aluminum oxide, ITO (indium-tin oxide), sapphire, germanium, gallium arsenide (GaAs), an alloy of silicon and germanium, or indium phosphide (InP). In some instances, the substrates may comprise silicon nitride, carbon, and/or polymer.

A substrate may be inorganic (e.g. , do not contain carbon) or organic (e.g. , contain carbon). In some instances, the substrate may comprise graphene and/or graphite.

In some embodiments, a substrate is a hybrid (e.g. , comprises a mixture) of any two or more materials (e.g. , a hybrid of an inorganic material and an organic material, or a hybrid of two or more different inorganic materials or organic materials), as provided herein. For example, a substrate may comprise a mixture of inorganic and organic materials, a mixture of two or more different inorganic materials, or a mixture of two or more different organic materials. The ratio of one material to another in a hybrid substrate may be, for example, 1: 10, 1:20, 1:30, 1:40, 1:50, 1:60, 1:70, 1:80 or 1:90. Other proportions are contemplated herein. Any two or more different materials may be arranged in the substrate as layers, for example. Other configurations are also contemplated herein.

In some embodiments, a substrate comprises a semiconductor material or a mixture of semiconductor materials. Semiconductor materials include, without limitation, Group IV elemental semiconductors, Group IV compound semiconductors, Group VI elemental semiconductors, Group III-V semiconductors, Group II- VI semiconductors, Group I- VII semiconductors, Group IV- VI semiconductors, Group IV- VI semiconductors, Group V-VI semiconductors, Group II- V semiconductors, oxides, layered semiconductors, magnetic semiconductors, organic semiconductors, charge-transfer complexes and combinations thereof.

In some embodiments, a substrate comprises a Group IV semiconductor material. Examples of Group IV semiconductor materials for use in accordance with the present disclosure include, without limitation, diamond, silicon, germanium, gray tin, silicon carbide and combinations thereof.

In some embodiments, a substrate comprises a Group VI semiconductor material. Examples of Group VI semiconductor materials for use in accordance with the present disclosure include, without limitation, sulfur, gray selenium, tellurium and combinations thereof.

In some embodiments, a substrate comprises a Group III-V semiconductor material. Examples of Group III-V semiconductor materials for use in accordance with the present disclosure include, without limitation, boron nitride, cubic, boron nitride, hexagonal, boron phosphide, boron arsenide, boron arsenide, aluminium nitride, aluminium phosphide, aluminium arsenide, aluminium antimonide, gallium nitride, gallium phosphide, gallium arsenide, gallium antimonide, indium nitride, indium phosphide, indium arsenide, indium antimonide and combinations thereof.

In some embodiments, a substrate comprises a Group II- VI semiconductor material. Examples of Group II- VI semiconductor materials for use in accordance with the present disclosure include, without limitation, cadmium selenide, cadmium sulfide, cadmium telluride, zinc oxide, zinc selenide, zinc sulfide, zinc telluride, cuprous chloride, copper sulfide, lead selenide, lead(ii) sulfide, lead telluride, tin sulfide, tin sulfide, tin telluride, lead tin telluride, thallium tin telluride, thallium germanium telluride, bismuth telluride and combinations thereof.

In some embodiments, a substrate comprises a Group I- VII semiconductor material. Examples of Group I- VII semiconductor materials for use in accordance with the present disclosure include, without limitation, cuprous chloride, copper sulfide and a combination of cuprous chloride and copper sulfide.

In some embodiments, a substrate comprises a Group IV- VI semiconductor material. Examples of Group IV- VI semiconductor materials for use in accordance with the present disclosure include, without limitation, lead selenide, lead(ii) sulfide, lead telluride, tin sulfide, tin sulfide, tin telluride, lead tin telluride, thallium tin telluride, thallium germanium telluride and combinations thereof.

In some embodiments, a substrate comprises a Group V-VI semiconductor material. An example of a Group IV- VI semiconductor material for use in accordance with the present disclosure includes, without limitation, bismuth telluride.

In some embodiments, a substrate comprises a Group II- V semiconductor material. Examples of Group II- V semiconductor materials for use in accordance with the present disclosure include, without limitation, cadmium phosphide, cadmium arsenide, cadmium antimonide, zinc phosphide, zinc arsenide, zinc antimonide and combinations thereof.

In some embodiments, a substrate comprises an oxide. Examples of oxides for use in accordance with the present disclosure include, without limitation, titanium dioxide, anatase, titanium dioxide, rutile, titanium dioxide, brookite, copper(i) oxide, copper(ii) oxide, uranium dioxide, uranium trioxide, bismuth trioxide, tin dioxide, barium titanate, strontium titanate, lithium niobate, lanthanum copper oxide and combinations thereof.

In some embodiments, a substrate comprises a layered semiconductor. Examples of layered semiconductors for use in accordance with the present disclosure include, without limitation, lead(ii) iodide, molybdenum disulfide, gallium selenide, tin sulfide, bismuth sulfide and combinations thereof.

In some embodiments, a substrate comprises a magnetic semiconductor. Examples of magnetic semiconductors for use in accordance with the present disclosure include, without limitation, gallium manganese arsenide, indium manganese arsenide, cadmium manganese telluride, lead manganese telluride, lanthanum calcium manganate, iron(ii) oxide, nickel(ii) oxide, europium(ii) oxide, europium(ii) sulfide, chromium(iii) bromide and combinations thereof.

Other examples of semiconductor materials that may be used in accordance with the present disclosure include, without limitation, copper indium selenide, cis, silver gallium sulfide, zinc silicon phosphide, arsenic sulfide, platinum silicide, bismuth(iii) iodide, mercury(ii) iodide, thallium(i) bromide, silver sulfide, iron disulfide, copper zinc tin sulfide, copper zinc antimony sulfide and combinations thereof.

In some embodiments, a substrate comprises a chalcogenide. A chalcogenide is a chemical compound that includes at least one chalcogen anion and at least one more electropositive element. In some embodiments, the chalcogenide is a sulfide, selenide or a telluride.

In some embodiments, a substrate comprises an electrical insulator. An electric insulator is a material with internal electric charges that do not flow freely, and therefore make it difficult to conduct an electric current under the influence of an electric field.

In some embodiments, a substrate comprises a metal. Examples of metals that may be used in accordance with the present disclosure include, without limitation, aluminium, chromium, titanium, tungsten, tantalum, niobium, platinum, zinc and combinations thereof.

In some embodiments, a substrate comprises carbon, SiC, LiNb0₃, PbZrTi0₃, Hf0₂, Ti0₂, V₂0₅, A1₂0₃, Ta₂0₃ or combinations thereof.

In some embodiments, a substrate comprises a polymer. Examples of polymers that may be used in accordance with the present disclosure include, without limitation, polydimethylsiloxane (PDMS), poly(methyl methacrylate) (PMMA) (e.g. , PMMA resin), and self-assembling polymers. In some embodiments, the substrate comprises poly(methyl methacrylatemethacrylic acid) (e.g. , copolymer P(MMA-MAA)). In some embodiments, the substrate comprises self-assembling block-copolymers.

In some embodiments, a substrate comprises a film such as, for example, a photoresist film, a chemical vapor deposition (CVD) film, a semiconductor film, graphene and/or other single-layer atomic films. In some embodiments, the substrate comprises a physical vapor deposition (PVD) film, an atomic layer deposition (ALD) film and/or an ion implantation film. In some embodiments, a substrate is a polished silicon wafer such as, for example, a plasma treated, or a hot piranha solution treated, silicon wafer (e.g. , 7:3 concentrated H₂S0₄: 35% H₂0₂).

In some embodiments, a moiety is coupled to a surface of a substrate. In some embodiments, a substrate is a substantially planar substance having a top surface onto which moieties are coupled. Substrates may be single-layered or multi-layered (e.g. , multi-layered grapheme/BN/MoS₂, such as ribbon or mesh).

In some embodiments, a substrate has a (e.g. , at least one) layer comprising or consisting of biomolecules. Biomolecules include proteins and nucleic acids, for example. Other biomolecules are contemplated herein, such as polysaccharides and lipids. A substrate, in some embodiments, may contain only proteins (a homogeneous or heterogeneous population), only nucleic acids (a homogeneous or heterogeneous population), or a mixture of proteins and nucleic acids (or other biomolecules). A biomolecular layer of a substrate may be an internal layer (e.g. , sandwiched between two layers) and/or an external layer (e.g. , surface exposed to the surrounding environment).

Energy Storage and Generation Devices

Methods and compositions of the present disclosure may be used to produce energy storage devices, such as supercapacitors and batteries. The methods and compositions may also be used to produce energy generation devices, such as photovoltaic devices (e.g., solar cells).

Energy storage: e.g., Supercapacitor

Patterned semiconducting nanotubes (e.g. , CNTs) store different charges from the environment. Thus, methods and compositions of the present disclosure may be used to produce devices for storing lithium, for example. Lithium-containing (e.g., coated) nucleic acid structures (e.g., DNA brick crystals) may be deposited onto a surface of a substrate (e.g., a graphene surface, e.g. , pre-deposited onto metal electrodes), and metal electrodes may then be placed on the top surface of the lithium-containing nucleic acid structures.

Upon charging, lithium is enriched at the nucleic acid-graphene interface, similar to the negative charged electrons located on the graphene side of the nucleic acid-graphene interface. The presence of nucleic acid structures (e.g., DNA brick crystals) provides a host substrate for accommodating excess lithium during charging. After charging, the excess ions remain in the nucleic acid-graphene interface to store the energy charged. The rapid discharging process of an energy storage device of the present disclosure is similar to commercially available supercapacitors. By connecting the anode and cathode (metal electrodes) with wires, the charge re-balancing through the wires removes the excess lithium and electrons from the interface, and generates an output current.

In some embodiments, metallic nanotubes (e.g., metallic CNTs), instead of graphene, may be used, due to their small diameter and high current density. During charging, an electrical double layer forms between lithium-containing nucleic acid structures (e.g., DNA brick crystals) and metallic nanotubes (e.g., metallic CNTs). The other charging and discharging processes are similar to above. When using the patterned metallic nanotubes (e.g., metallic CNTs) on lithium-containing nucleic acid structures (e.g., DNA brick crystals), densely aligned electrical double layers (down to 8- 10 nm) may be produced to store more charges.

Energy generation: Photovoltaics

Patterned semiconducting nanotubes (e.g. , CNTs) generate charge-carriers when irradiated with photons. Thus, in some embodiments, methods of the present disclosure are used to produce photovoltaic devices, such as solar cells. A solar cell (photovoltaic cell) is a device that converts the energy of light directly into electricity by the photovoltaic effect, which is a physical and chemical phenomenon. It is a form of photoelectric cell having electrical characteristics, such as current, voltage or resistance, that vary when exposed to light.

Patterned semiconducting CNTs (e.g., with spacing down to 8- 10 nm) may be used as the major components of a photovoltaic device, such as a solar cell. In addition to Si, other semiconducting materials having similar device architectures may be used, including, but not limited to, copper zinc tin sulfide (CZTS), copper indium selenide (CIS)/copper indium gallium selenide (CIGS) and/or lead-based perovskite material. As long as their work functions differ from that of the semiconducting nanotubes (e.g., CNTs), the charge separation still works at the semiconducting nanotube (e.g. , CNT) interface.

Thus, in some embodiments, semiconducting nanotubes (e.g., CNTs) may be patterned using nucleic acid structures (e.g., DNA brick crystals). Nanotube (e.g., CNT)- decorated nucleic acid structures (e.g., DNA brick crystals) may be deposited onto semiconducting materials (e.g., Si) that have been previously deposited onto back contacts (e.g., ITO or other metal electrodes patterned on reflective substrates). The nucleic acid nanostructure templates are then be removed, leaving only the patterned semiconducting nanotubes (e.g. , CNTs). Metal electrodes may also be fabricated on top of the

semiconducting nanotubes (e.g. , CNTs) to extract specific charge carriers generated at the nanotube-semiconducting interface. Fabricating the remaining parts of the photovoltaic device (including top glass, reflective layer, etc.) may follow current commercially-available approaches.

Upon photon irradiation, both semiconducting nanotubes (e.g., CNTs) and Si adsorbs photons of selected wavelength, and generate desired major (electron) and minor (hole) charge carriers. Different charge carriers are separated at the interface and diffuse into either top metal electrodes or the back contacts, depending on the materials selection of the electrodes. Because there is only one kind of charge carrier within each electrode, the output current is generated once wiring the top metal electrode and back contacts.

The present disclosure further provides embodiments encompassed by the following numbered paragraphs:

1. A composition comprising a nucleic acid structure having parallel nucleic acid nanotrenches that each include two sidewalls, a bottom layer and a longitudinal axis, wherein each of the nanotrenches comprises a semiconducting nanotube.

2. The composition of paragraph 1, wherein the distance between the

semiconducting nanotubes is between 10 nm and 100 nm.

3. The composition of paragraph 1, wherein the distance between the

semiconducting nanotubes is between 10 nm and 50 nm.

4. The composition of paragraph 1, wherein the distance between the

semiconducting nanotubes is between 10 nm and 25 nm.

5. The composition of any one of paragraphs 1-4, wherein the semiconducting nanotubes are carbon nanotubes.

6. The composition of any one of paragraphs 1-5, wherein semiconducting nanotubes have a width of 2-100 nm and/or a length of 25-500 nm. 7. The composition of any one of paragraphs 1-6, wherein the nucleic acid structure is a three-dimensional nucleic acid nanostructure or microstructure.

8. The composition of any one of paragraphs 1-7, wherein the nucleic acid structure is a DNA structure.

9. The composition of any one of paragraphs 1-8, wherein the nucleic acid structure comprises at least 100 single-stranded oligonucleotides, each having a length of less than 200 nucleotides.

10. The composition of any one of paragraphs 1-8, wherein the carbon nanotubes are oriented in the same direction along the longitudinal axis of the nanotrenches.

11. The composition of any one of paragraphs 1-10, wherein the bottom layer of each of the nanotrenches comprises single- stranded oligonucleotide handles.

12. The composition of paragraph 11, wherein each of the semiconducting nanotubes comprises single- stranded oligonucleotide anti-handles that are complementary to the single- stranded oligonucleotide handles of the nanotrenches.

13. The composition of any one of paragraphs 1-12, further comprise a substrate to which the nucleic acid structure is attached.

14. The composition of paragraph 13, wherein the substrate comprises Si0₂.

15. A method comprising depositing, into each parallel nucleic acid nanotrench of a nucleic acid structure, a semiconducting nanotube, wherein each of the nucleic acid nanotrenches includes two sidewalls, a bottom layer and a longitudinal axis.

16. The method of paragraph 15, wherein the distance between the

semiconducting nanotubes is between 10 nm and 100 nm.

17. The method of paragraph 16, wherein the distance between the

semiconducting nanotubes is between 10 nm and 50 nm.

18. The method of paragraph 17, wherein the distance between the

semiconducting nanotubes is between 10 nm and 25 nm.

19. The method of any one of paragraphs 15-18, wherein the semiconducting nanotubes are carbon nanotubes.

20. The method of any one of paragraphs 15-19, wherein semiconducting nanotubes have a width of 2-100 nm and/or a length of 25-500 nm.

21. The method of any one of paragraphs 15-20, wherein the nucleic acid structure is a three-dimensional nucleic acid nanostructure or microstructure. 22. The method of any one of paragraphs 15-21, wherein the nucleic acid structure is a DNA structure.

23. The method of any one of paragraphs 15-22, wherein the nucleic acid structure comprises at least 100 single- stranded oligonucleotides, each having a length of less than 200 nucleotides.

24. The method of any one of paragraphs 15-23, wherein the carbon nanotubes are oriented in the same direction along the longitudinal axis of the nanotrenches.

25. The method of any one of paragraphs 15-24, wherein the bottom layer of each of the nanotrenches comprises single- stranded oligonucleotide handles.

26. The method of paragraph 25, wherein each of the semiconducting nanotubes comprises single- stranded oligonucleotide anti-handles that are complementary to the single- stranded oligonucleotide handles of the nanotrenches.

27. The method of any one of paragraphs 15-26, further depositing the nucleic acid structure onto a substrate.

28. The method of paragraph 27, wherein the substrate comprises Si0₂.

EXAMPLES

Example 1

Folding DNA brick crystals in Li buffer

Assembling of the designed DNA brick crystals was performed using multi-staged incubation reaction. 90

mixture of unpurified DNA bricks (IDTDNA Inc., pH 7.9, containing 300 - 600 nM of each brick), 5 mM Tris, 1 mM EDTA, and 2M LiCl was subjected to a multi-stage incubation at 80 °C for 15 min, 44 °C for 12 h, 39 °C for 72 h, and 31 °C for 8 h sequentially, without careful adjustment of each brick stoichiometry.

Assembling CNTs in Li buffer

DNA-wrapped CNTs (0.4

diluted DNA brick crystals (lOx dilution into 500 mM LiCl solution) into 6 final solution containing 450 mM LiCl. The reaction buffer was incubated at 33 °C for 9 h, and then stored at 4°C . Example 2

By programming DNA brick crystals with different trench periodicity along the x direction, we further demonstrated the rational scaling of inter-CNT pitch at 16.8 nm, 12.6 nm, and 10.4 nm (Figs. 5A-5C), respectively.

Within each unit cell of the narrow-pitch DNA brick crystals, we used 2 helices x 8 helices x 94 base pairs for the nanotrenches sidewall (Fig. 5A-C, top left); while in the bottom layer of the nanotrenches, 6 helices x 4 helices x 94 base pairs, 4 helices x 4 helices x 94 base pairs, and 3 helices x 4 helices x 94 base pairs were used for designed nanotrench periodicity of 16.8 nm, 12.6 nm, and 10.5 nm, respectively.

The folding condition of the narrow-pitch DNA brick crystals was identical to that of

DNA brick crystal with 25-nm periodicity. After folding, DNA brick crystals exhibited measured trench periodicity of 16.8 +/- 0.4 nm, 12.7 +/- 0.2 nm, and 10.6 +/- 0.1 nm (N = 50 from 10 individual crystals for each design) along x direction (Fig. 5A-C, bottom left).

Slightly twisted DNA trench sidewalls were observed after dried in vacuum, which might be ascribed to the relative small structural stiffness of the narrow trench sidewall (containing two-layer DNA helices in the width direction). However, the average periodicity was not affected by the twisting of the DNA sidewalls.

After CNT deposition, parallel CNTs were aligned within the DNA nano-trenches (designs in Fig. 5A-5C, top right; zoomed-in TEM images in Fig. 5A-5C, bottom right). The inter-CNT pitches varied from 16.8 +/- 1.5 nm, 12.6 +/- 0.6 nm, to 10.5 +/- 0.4 nm (N = 50 from 10 individual crystals for each design. For every two neighboring CNTs, three different positions were measured along the longitudinal axis of CNT), similar to the measured periodicities in the corresponding DNA brick crystal templates, respectively. The range and the percent relative range of the inter-CNT pitch variation were characterized as 5.9 nm and 36%, 2.7 nm and 24%, 1.9 nm and 18% for 16.8 nm 12.6 nm, and 10.4 nm inter-CNT pitches respectively. In the zoomed-out TEM images, the CNT array densities were counted around 0.01 crystal per μπι . The angular deviation were measured less than 2°.

Under CNT assembly conditions, the assembly yields were over 95%, even for narrow trenches, despite the high electrostatic repulsion between negative charged DNA trench sidewalls and CNTs at narrow inter-CNT pitches. In addition, low stiffness of DNA sidewalls (as evidenced by the local twist of the DNA nano-trench sidewalls) did not affect the yield of CNT alignment. Narrower DNA nanotrench improves the precision for CNT alignment. When the width of DNA nano-trench was decreased to around 6 nm (in 10.5-nm pitch CNT arrays), the range value of inter-CNT pitch was decreased to less than 2 nm, compared with the 5.9-nm range value in DNA nanotrench with 12-nm width (in 16.8-nm pitches CNT arrays).

Figs. 5A-5C show an example of programming inter-CNT pitch with DNA brick crystals. Schematic designs (top row) and TEM images (bottom row) of programming CNT arrays with 16.8 nm (Fig. 5A), 12.6 nm (Fig. 5B), and 10.5 nm (Fig. 5C) pitches using DNA brick crystals. Within each panel, top left is the design of DNA brick crystal template. The bundles present a repeating unit of DNA brick crystals with selected periodicity along x direction. The light gray bundles are the sidewalls of DNA nano-trenches. The dark gray bundles are the bottom layer of DNA nanotrenches. Gray curves denote the

DNA handles. The rods represent CNTs. Bottom left is the zoomed-in TEM image (100 nm x 100 nm) of the DNA brick crystals along the x-z projection direction. Bottom right is the zoomed-in TEM image (100 nm x 100 nm) of the CNTs assembled on DNA brick crystals along the x-z projection direction. The arrows indicate the decorated CNTs. The scale bar is 25 nm.

All references, patents and patent applications disclosed herein are incorporated by reference with respect to the subject matter for which each is cited, which in some cases may encompass the entirety of the document.

The indefinite articles "a" and "an," as used herein in the specification and in the claims, unless clearly indicated to the contrary, should be understood to mean "at least one."

It should also be understood that, unless clearly indicated to the contrary, in any methods claimed herein that include more than one step or act, the order of the steps or acts of the method is not necessarily limited to the order in which the steps or acts of the method are recited.

In the claims, as well as in the specification above, all transitional phrases such as "comprising," "including," "carrying," "having," "containing," "involving," "holding," "composed of," and the like are to be understood to be open-ended, i.e., to mean including but not limited to. Only the transitional phrases "consisting of and "consisting essentially of shall be closed or semi-closed transitional phrases, respectively, as set forth in the United States Patent Office Manual of Patent Examining Procedures, Section 2111.03.

Claims

What is claimed is: CLAIMS

1. A composition comprising

a nucleic acid structure having parallel nucleic acid nanotrenches that each include two sidewalls, a bottom layer and a longitudinal axis, wherein each of the nanotrenches comprises a semiconducting nanotube.

2. The composition of claim 1, wherein the distance between the semiconducting nanotubes is between 10 nm and 100 nm.

3. The composition of claim 1, wherein the distance between the semiconducting nanotubes is between 10 nm and 50 nm.

4. The composition of claim 1, wherein the distance between the semiconducting nanotubes is between 10 nm and 25 nm.

5. The composition of claim 1, wherein the semiconducting nanotubes are carbon nanotubes.

6. The composition of claim 1, wherein semiconducting nanotubes have a diameter of 2 nm or less.

7. The composition of claim 1, wherein the nucleic acid structure is a three-dimensional nucleic acid nanostructure or microstructure.

8. The composition of claim 1, wherein the nucleic acid structure is a DNA structure.

9. The composition of claim 1, wherein the nucleic acid structure comprises at least 100 single-stranded oligonucleotides, each having a length of less than 200 nucleotides.

10. The composition of claim 1, wherein the carbon nanotubes are oriented in the same direction along the longitudinal axis of the nanotrenches.

11. The composition of claim 1, wherein the bottom layer of each of the nanotrenches comprises single- stranded oligonucleotide handles.

12. The composition of claim 1, wherein each of the semiconducting nanotubes comprises single-stranded oligonucleotide anti-handles that are complementary to the single-stranded oligonucleotide handles of the nanotrenches.

13. The composition of claim 1, further comprise a substrate to which the nucleic acid structure is attached.

14. The composition of claim 13, wherein the substrate comprises Si or glass.

15. A method comprising

depositing, into each parallel nucleic acid nanotrench of a nucleic acid structure, a semiconducting nanotube, wherein each of the nucleic acid nanotrenches includes two sidewalls, a bottom layer and a longitudinal axis.

16. The method of claim 15, wherein the distance between the semiconducting nanotubes is between 10 nm and 100 nm.

17. The method of claim 16, wherein the distance between the semiconducting nanotubes is between 10 nm and 50 nm.

18. The method of claim 17, wherein the distance between the semiconducting nanotubes is between 10 nm and 25 nm.

19. The method of claim 15, wherein the semiconducting nanotubes are carbon nanotubes.

20. The method of claim 15, wherein semiconducting nanotubes have a diameter of 2nm or less.

21. The method of claim 15, wherein the nucleic acid structure is a three-dimensional nucleic acid nanostructure or microstructure.

22. The method of claim 15, wherein the nucleic acid structure is a DNA structure.

23. The method of claim 15, wherein the nucleic acid structure comprises at least 100 single-stranded oligonucleotides, each having a length of less than 200 nucleotides.

24. The method of claim 15, wherein the carbon nanotubes are oriented in the same direction along the longitudinal axis of the nanotrenches.

25. The method of claim 15, wherein the bottom layer of each of the nanotrenches comprises single- stranded oligonucleotide handles.

26. The method of claim 25, wherein each of the semiconducting nanotubes comprises single-stranded oligonucleotide anti-handles that are complementary to the single-stranded oligonucleotide handles of the nanotrenches.

27. The method of claim 15, further depositing the nucleic acid structure onto a substrate.

28. The method of claim 27, wherein the substrate comprises Si or glass.