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USRE49362E1 - Dye compounds and the use of their labelled conjugates - Google Patents

Dye compounds and the use of their labelled conjugates Download PDF

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USRE49362E1
USRE49362E1 US16/917,713 US200716917713A USRE49362E US RE49362 E1 USRE49362 E1 US RE49362E1 US 200716917713 A US200716917713 A US 200716917713A US RE49362 E USRE49362 E US RE49362E
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alkyl
group
substituted
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Colin Barnes
Nikolai Nikolaevich Romanov
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Illumina Cambridge Ltd
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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/58—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving labelled substances
    • G01N33/582—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving labelled substances with fluorescent label
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K49/00—Preparations for testing in vivo
    • A61K49/001—Preparation for luminescence or biological staining
    • A61K49/0013—Luminescence
    • A61K49/0017—Fluorescence in vivo
    • A61K49/0019—Fluorescence in vivo characterised by the fluorescent group, e.g. oligomeric, polymeric or dendritic molecules
    • A61K49/0021—Fluorescence in vivo characterised by the fluorescent group, e.g. oligomeric, polymeric or dendritic molecules the fluorescent group being a small organic molecule
    • A61K49/0041—Xanthene dyes, used in vivo, e.g. administered to a mice, e.g. rhodamines, rose Bengal
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K49/00—Preparations for testing in vivo
    • A61K49/001—Preparation for luminescence or biological staining
    • A61K49/0013—Luminescence
    • A61K49/0017—Fluorescence in vivo
    • A61K49/005—Fluorescence in vivo characterised by the carrier molecule carrying the fluorescent agent
    • A61K49/0052—Small organic molecules
    • C—CHEMISTRY; METALLURGY
    • C09—DYES; PAINTS; POLISHES; NATURAL RESINS; ADHESIVES; COMPOSITIONS NOT OTHERWISE PROVIDED FOR; APPLICATIONS OF MATERIALS NOT OTHERWISE PROVIDED FOR
    • C09B—ORGANIC DYES OR CLOSELY-RELATED COMPOUNDS FOR PRODUCING DYES, e.g. PIGMENTS; MORDANTS; LAKES
    • C09B11/00—Diaryl- or thriarylmethane dyes
    • C09B11/04—Diaryl- or thriarylmethane dyes derived from triarylmethanes, i.e. central C-atom is substituted by amino, cyano, alkyl
    • C09B11/10—Amino derivatives of triarylmethanes
    • C09B11/24—Phthaleins containing amino groups ; Phthalanes; Fluoranes; Phthalides; Rhodamine dyes; Phthaleins having heterocyclic aryl rings; Lactone or lactame forms of triarylmethane dyes
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10S—TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10S436/00—Chemistry: analytical and immunological testing
    • Y10S436/80—Fluorescent dyes, e.g. rhodamine

Definitions

  • the present invention provides novel rhodamine dye compounds, labelled conjugates comprising the dyes and methods for their use.
  • the dyes and labelled conjugates are useful as molecular probes in a variety of applications, such as in assays involving staining of cells, protein binding, and analysis of nucleic acids, such as hybridization assays and nucleic acid sequencing. More particularly the invention relates to the use of such dyes in solid phase sequencing by synthesis.
  • Non-radioactive detection of nucleic acids utilizing fluorescent labels is an important technology in molecular biology. Many procedures employed in recombinant DNA technology previously relied heavily on the use of nucleotides or polynucleotides radioactively labelled with, for example 32 P. Radioactive compounds permit sensitive detection of nucleic acids and other molecules of interest. However, there are serious limitations in the use of radioactive isotopes such as their expense, limited shelf life and more importantly safety considerations. Eliminating the need for radioactive labels enhances safety whilst reducing the environmental impact and costs associated with, for example, reagent disposal. Methods amenable to non-radioactive fluorescent detection include by way of non-limiting example, automated DNA sequencing, hybridization methods, real-time detection of polymerase-chain-reaction products and immunoassays.
  • multiple spectrally distinguishable fluorescent labels in order to achieve independent detection of a plurality of spatially overlapping analytes.
  • the number of reaction vessels may be reduced simplifying experimental protocols and facilitating the production of application-specific reagent kits.
  • multiplex fluorescent detection allows for the analysis of multiple nucleotide bases in a single electrophoresis lane thereby increasing throughput over single-colour methods and reducing uncertainties associated with inter-lane electrophoretic mobility variations.
  • multiplex fluorescent detection can be problematic and there are a number of important factors which constrain selection of fluorescent labels.
  • simultaneous excitation may be difficult because the absorption bands of the dyes are usually widely separated.
  • Many excitation methods use high power lasers and therefore the dye must have sufficient photo-stability to withstand such laser excitation.
  • a final consideration of particular importance in molecular biology methods is that the fluorescent dyes must be compatible with the reagent chemistries used such as for example DNA synthesis solvents and reagents, buffers, polymerase enzymes and ligase enzymes.
  • the invention provides rhodamine dye compounds of the formula (I):
  • X is a sulfo- or sulfonato- group, SO 3 H or SO 3 ⁇ , M + is a common counter ion, k, n, m are independently integers of from 1 to 6,
  • R 1 is H or an alkyl or substituted alkyl group
  • R 2 is H, alkyl or substituted alkyl group, halogen, carboxy, carboxamide, hydroxy- or alkoxy group, or R 2 together with R 1 or R 5 is a carbon or heterosubstituted chain forming a ring
  • R 3 is H, alkyl or substituted alkyl group, halogen, carboxy, carboxamide, hydroxy- or alkoxy group or R 3 together with R 4 or R 6 is a carbon or heterosubstituted chain forming a ring
  • R 4 is H, or an alkyl or substituted alkyl group
  • R 5 and R 6 are H, alkyl or substituted alkyl group, halogen,
  • the compounds of the present invention can be conjugated with a variety of substrate moieties such as, for example, nucleosides, nucleotides, polynucleotides, polypeptides, carbohydrates, ligands, particles and surfaces.
  • substrate moieties such as, for example, nucleosides, nucleotides, polynucleotides, polypeptides, carbohydrates, ligands, particles and surfaces.
  • dye compounds comprising linker groups to enable, for example, covalent attachment to such substrate moieties.
  • nucleoside or nucleotide compound defined by the formula: N-L-Dye
  • N is a nucleotide
  • L is an optional linker moiety
  • Dye is a compound according to the present invention and wherein said compound is a fluorescent compound.
  • the invention includes methods of sequencing using the dye compounds of the present invention.
  • kits comprising dye compounds of the invention (free or in conjugate form) which may be used in various immunological assays, oligonucleotide and nucleic acid labelling and for DNA sequencing by synthesis.
  • the invention provides kits comprising dye ‘sets’ particularly suited to cycles of sequencing by synthesis on an automated instrument platform.
  • the invention relates to novel rhodamine dye compounds particularly suitable for methods of fluorescence detection and sequencing by synthesis.
  • X is SO 3 H or SO 3 ⁇ , k, n, m are independently integers of from 1 to 6, M + is a common counter ion.
  • the term “common counter ion” includes well known cations such as by way of non-limiting example Na + , K + , Li + and NH 4 + , NEt 3 H + , and the like. See, Whitten, K. W., and Gailey, K. D., General Chemistry, Saunders College Publishing, p. 167, 1981 and James E. Huheey, Inorganic Chemistry, 3rd ed., Harper & Row, pp. A-97-A-103, 1983, which are incorporated herein by reference. In some cases, the compounds include such a common counter ion to help balance the charge of the molecule.
  • R 1 is H or an alkyl group or substituted alkyl group
  • R 2 is H, halogen, alkyl group or substituted alkyl group, hydroxy- or alkoxy
  • R 3 is H, halogen or alkyl group or substituted alkyl group, hydroxy- or alkoxy
  • R 4 is H or a alkyl or substituted alkyl group
  • R 8 is H, halogen, hydroxy- or alkoxy groups, alkyl or substituted alkyl
  • R 9 is H, halogen, hydroxy- or alkoxy groups, alkyl or substituted alkyl
  • R 1 and R 2 or R 8 and/or R 4 and R 3 or R 9 and/or R 2 and R 5 and/or R 3 and R 6 can be connected to form carbo- or heterocyclic rings, an example being five or six membered aliphatic rings, which may contain one or more double bonds.
  • R 5 and R 6 are H, alkyl or substituted alkyl, halogen, hydroxyl- or alkoxy
  • R 7 may be OH
  • OR 10 where R 10 is alkyl or substituted alkyl, or NR 11 R 12 where R 11 and R 12 are independently H, alkyl or a substituted alkyl, or may be joined together in the form of cyclic or substituted cyclic rings
  • Z is a H, halogen, amino or substituted amino, hydroxy-, alkoxy-, carboxy, carboxamido or substituted carboxamido, SO 3 H or SO 3 ⁇ and a is 0 to 4.
  • alkyl refers to C 1 -C 20 hydrocarbon and may include C 3 -C 10 non-aromatic carbocyclic rings.
  • the alkyl groups are C 1 -C 6 alkyl which refers to saturated, straight- or branched-chain hydrocarbon radicals containing between one and six carbon atoms, respectively.
  • alkenyl as used herein represents C 1 -C 20 hydrocarbon containing at least one double bond and may include C 3 -C 10 non-aromatic carbocyclic rings.
  • alkynyl represents C 1 -C 20 hydrocarbon containing at least one triple bond and may include C 3 -C 10 non-aromatic carbocyclic rings.
  • aryl as used herein represents an aromatic carbocyclic ring optionally selected from but not limited to phenyl optionally substituted with common aromatic substituents.
  • halogen refers to fluoro—(hereafter designated as F), chloro—(hereafter designated as Cl), bromo—(hereafter designated as Br) or iodo—(hereafter designated as I), and usually relates to substitution for a hydrogen atom in an organic compound, this substitution is optionally a full substitution for the hydrogen.
  • substituted alkyl refers to alkyl, alkenyl or alkynyl groups as defined above where they may optionally be further substituted with, but not limited to, Halo, Cyano, SO 3 ⁇ , SR 12 , OR 12 , NR 13 R 14 , oxo, CONR 13 R 14 , COOH and COOR 13 .
  • R 13 and R 14 are each independently selected from H, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl and substituted aryl.
  • substituted alkyl, substituted alkenyl and substituted alkynyl may optionally be interrupted by at least one hetero atom or group selected from O, NR 12 , S(O), wherein t is 0 to 2, and the like.
  • Substituted alkyl also covers group such as benzyl where the alkyl groups is comprises a further aryl or substituted aryl moiety.
  • X is SO 3 ⁇
  • n is 3
  • R 1 and R 2 form a six membered ring
  • R 3 and R 4 form a six membered ring
  • R 5 , R 6 , R 8 and R 9 are H
  • a is 0
  • R 7 is OH.
  • Dyes according to the present invention may be synthesised from a variety of different starting materials, including N-sulfonatoalkyl derivatives of 3-aminophenol, 5-hydroxy-1,2,3,4-tetrahydroquinoline or 7-hydroxy-1,2,3,4-tetrahydroquinoline. Condensation of these compounds with substituted or unsubstituted phthalic anhydrides gives the dyes as described.
  • the condensation reaction is typically carried out at high temperature with or without suitable solvent, and is assisted by the use of microwave irradiation.
  • ionic liquids for example 1-ethyl-3-methylimidazolium, as solvent in said condensation reactions is especially advantageous.
  • the reaction can be catalysed by Lewis acids, for example zinc chloride.
  • N-sulfonatoalkyl-5-hydroxy-1,2,3,4-tetrahydroquinoline or N-sulfonatoalkyl-7-hydroxy-1,2,3,4-tetrahydroquinoline can be carried out using catalytic hydrogenation, for example using Raney Nickel as a catalyst.
  • catalytic hydrogenation for example using Raney Nickel as a catalyst.
  • an organic or inorganic base for example triethylamine, greatly enhances the rate of reaction.
  • Mono N-alkylation of 3-aminophenols with alkylsultones can be carried out using one equivalent or more of the aminophenol.
  • Di-alkylation of 3-amino phenol can be achieved using more equivalents of the alkylsultone.
  • Both of the resultant phenolic derivatives can be condensed with phthalic anhydride to make fluorophores as described.
  • dye compounds suitable for attachment to substrate moieties particularly comprising linker groups to enable attachment to substrate moieties.
  • Substrate moieties can be virtually any molecule or substance to which the dyes of the invention can be conjugated and, by way of non-limiting example, may include nucleosides, nucleotides, polynucleotides, carbohydrates, ligands, particles, solid surfaces, organic and inorganic polymers and combinations or assemblages thereof, such as chromosomes, nuclei, living cells and the like.
  • the dyes can be conjugated by an optional linker by a variety of means including hydrophobic attraction, ionic attraction and covalent attachment.
  • the dyes are conjugated to the substrate by covalent attachment. More particularly the covalent attachment is by means of a linker group.
  • the dyes according to the invention may include a reactive linker group at one of the substituent positions for covalent attachment of the dye to another molecule.
  • Reactive linking groups are moieties capable of forming a covalent bond.
  • the linker may be a cleavable linker.
  • Use of the term “cleavable linker” is not meant to imply that the whole linker is required to be removed.
  • the cleavage site can be located at a position on the linker that ensures that part of the linker remains attached to the dye and/or substrate moiety after cleavage.
  • Cleavable linkers may be, by way of non-limiting example, electrophilically cleavable linkers, nucleophilically cleavable linkers, photocleavable linkers, cleavable under reductive conditions (for example disulfide or azide containing linkers), oxidative conditions, cleavable via use of safety-catch linkers and cleavable by elimination mechanisms.
  • electrophilically cleavable linkers nucleophilically cleavable linkers, photocleavable linkers, cleavable under reductive conditions (for example disulfide or azide containing linkers), oxidative conditions, cleavable via use of safety-catch linkers and cleavable by elimination mechanisms.
  • linker groups may be found in pending patent application number WO2004/018493 (herein incorporated by reference) wherein the present inventors have found that certain linkers which connect the bases of nucleotides to labels such as, for example, dyes according to the present invention, may be cleaved using water-soluble phosphines or water-soluble transition metal catalysts formed from a transition metal and at least partially water-soluble ligands. In aqueous solution the latter form at least partially water-soluble transition metal complexes.
  • the linker comprises a spacer group of formula —((CH 2 ) 2 O) n — wherein n is an integer between 2 and 50, as described in applicants pending application number GB0517097.2 (WO07020457).
  • the present invention further provides conjugates of nucleosides and nucleotides labelled with dyes according to the invention (modified nucleotides).
  • Labelled nucleosides and nucleotides are useful for labelling polynucleotides formed by enzymatic synthesis, such as, by way of non-limiting example, in PCR amplification, isothermal amplification or solid phase amplification, polynucleotide sequencing including solid phase sequencing, nick translation reactions and the like.
  • Nucleosides and nucleotides may be labelled at sites on the sugar or nucleobase.
  • a “nucleotide” consists of a nitrogenous base, a sugar, and one or more phosphate groups.
  • the sugar is ribose and in DNA is a deoxyribose, i.e. a sugar lacking a hydroxyl group that is present in ribose.
  • the nitrogenous base is a derivative of purine or pyrimidine.
  • the purines are adenine (A) and guanine (G), and the pyrimidines are cytosine (C) and thymine (T) or in the context of RNA, uracil (U).
  • the C-1 atom of deoxyribose is bonded to N-1 of a pyrimidine or N-9 of a purine.
  • a nucleotide is also a phosphate ester of a nucleoside, with esterification occurring on the hydroxyl group attached to the C-3 or C-5 of the sugar. Nucleotides are usually mono, di- or triphosphates.
  • nucleoside is structurally similar to a nucleotide but is missing the phosphate moieties.
  • An example of a nucleoside analog would be one in which the label is linked to the base and there is no phosphate group attached to the sugar molecule.
  • the base is usually referred to as a purine or pyrimidine, the skilled person will appreciate that derivatives and analogues are available which do not alter the capability of the nucleotide or nucleoside to undergo Watson-Crick base pairing.
  • “Derivative” or “analogue” means a compound or molecule whose core structure is the same as, or closely resembles that of a parent compound but which has a chemical or physical modification, such as, for example, a different or additional side group, which allows the derivative nucleotide or nucleoside to be linked to another molecule.
  • the base may be a deazapurine.
  • the derivatives should be capable of undergoing Watson-Crick pairing.
  • “Derivative” and “analogue” also mean a synthetic nucleotide or nucleoside derivative having modified base moieties and/or modified sugar moieties. Such derivatives and analogues are discussed in, for example, Scheit, Nucleotide analogs (John Wiley & Son, 1980) and Uhlman et al., Chemical Reviews 90:543-584, 1990. Nucleotide analogues can also comprise modified phosphodiester linkages including phosphorothioate, phosphorodithioate, alkyl-phosphonate, phosphoranilidate, phosphoramidate linkages and the like.
  • the dye may be attached to any position on the nucleotide base, through a linker, provided that Watson-Crick base pairing can still be carried out.
  • Particular nucleobase labelling sites include the C5 position of a pyrimidine base or the C7 position of a 7-deaza purine base.
  • a linker group may be used to covalently attach a dye to the nucleoside or nucleotide.
  • the labelled nucleoside or nucleotide may be enzymatically incorporable and enzymatically extendable.
  • a linker moiety may be of sufficient length to connect the nucleotide to the compound such that the compound does not significantly interfere with the overall binding and recognition of the nucleotide by a nucleic acid replication enzyme.
  • the linker can also comprise a spacer unit. The spacer distances, for example, the nucleotide base from a cleavage site or label.
  • Dye is a dye compound according to the present invention
  • B is a nucleobase, such as, for example uracil, thymine, cytosine, adenine, guanine and the like and L is an optional linker group which may or may not be present.
  • R 14 can be H, monophosphate, diphosphate, triphosphate, thiophosphate, a phosphate ester analog, 'O— attached to a reactive phosphorous containing group or —O— protected by a blocking group.
  • R 15 can be H, OH, a phosphoramidite or a 3′OH blocking group and R 16 is H or OH.
  • R 14 is an acid-cleavable hydroxyl protecting group which allows subsequent monomer coupling under automated synthesis conditions.
  • the blocking group is separate and independent of the dye compound, i.e. not attached to it.
  • the dye may comprise all or part of the 3′OH blocking group.
  • R 15 can be a 3′OH blocking group which may or may not comprise the dye compound.
  • there is no blocking group on the 3′ carbon of the pentose sugar and the dye (or dye and linker construct) attached to the base can be of a size or structure sufficient to act as a block to the incorporation of a further nucleotide from a point other than the 3′ site.
  • the block can be due to steric hindrance or can be due to a combination of size, charge and structure.
  • a blocking group allows polymerisation to be controlled, such as by stopping extension when a modified nucleotide is incorporated. If the blocking effect is reversible, for example by way of non-limiting example by changing chemical conditions or by removal of a chemical block, extension can be stopped at certain points and then allowed to continue.
  • a 3′OH blocking group will comprise moieties disclosed in WO2004/018497 (herein incorporated by reference) for example of the formula:
  • linker and blocking group are both present and are separate moieties which are both cleavable under substantially similar conditions.
  • deprotection and deblocking processes may be more efficient since only a single treatment will be required to remove both the dye compound and the block.
  • the invention also encompasses polynucleotides incorporating dye compounds according to the present invention.
  • polynucleotides may be DNA or RNA comprised respectively of deoxyribonucleotides or ribonucleotides joined in phosphodiester linkage.
  • Polynucleotides according to the invention may comprise naturally occurring nucleotides, non-naturally occurring (or modified) nucleotides other than the modified nucleotides of the invention or any combination thereof, provided that at least one modified nucleotide, i.e. labelled with a dye compound, according to the invention is present.
  • Polynucleotides according to the invention may also include non-natural backbone linkages and/or non-nucleotide chemical modifications. Chimeric structures comprised of mixtures of ribonucleotides and deoxyribonucleotides comprising at least one modified nucleotide according to the invention are also contemplated.
  • Modified nucleotides comprising a dye compound according to the invention may be used in any method of analysis which requires detection of a fluorescent label attached to a nucleotide or nucleoside, whether on its own or incorporated into or associated with a larger molecular structure or conjugate.
  • incorporated into a polynucleotide requires that the 5′ phosphate is joined in phosphodiester linkage to the 3′ hydroxyl group of a second (modified or unmodified) nucleotide, which may itself form part of a longer polynucleotide chain.
  • the invention provides a method of detecting a modified nucleotide incorporated into a polynucleotide which comprises:
  • This method requires two essential steps: a synthetic step (a) in which one or more modified nucleotides according to the invention are incorporated into a polynucleotide and a detection step (b) in which one or more modified nucleotide(s) incorporated into the polynucleotide are detected by detecting or quantitatively measuring their fluorescence.
  • the at least one modified nucleotide is incorporated into a polynucleotide in the synthetic step by the action of a polymerase enzyme.
  • a polymerase enzyme for example chemical oligonucleotide synthesis or ligation of labelled oligonucleotides to unlabelled oligonucleotides.
  • the synthetic step may comprise incubating a template polynucleotide strand with a reaction mixture comprising fluorescently labelled modified nucleotides of the invention and a polymerase under conditions which permit formation of a phosphodiester linkage between a free 3′ hydroxyl group on a polynucleotide strand annealed to said template polynucleotide strand and a 5′ phosphate group on said modified nucleotide.
  • This embodiment comprises a synthetic step in which formation of a polynucleotide strand is directed by complementary base-pairing of nucleotides to a template strand.
  • the detection step may be carried out whilst the polynucleotide strand into which the modified nucleotides are incorporated is annealed to a template strand, or after a denaturation step in which the two strands are separated. Further steps, for example chemical or enzymatic reaction steps or purification steps, may be included between the synthetic step and the detection step.
  • the target strand incorporating the modified nucleotide(s) may be isolated or purified and then processed further or used in a subsequent analysis.
  • target polynucleotides labelled with modified nucleotide(s) according to the invention in a synthetic step may be subsequently used as labelled probes or primers.
  • the product of the synthetic step (a) may be subject to further reaction steps and, if desired, the product of these subsequent steps purified or isolated.
  • Suitable conditions for the synthetic step will be well known to those familiar with standard molecular biology techniques.
  • the synthetic step may be analogous to a standard primer extension reaction using nucleotide precursors, including modified nucleotides according to the invention, to form an extended target strand complementary to the template strand in the presence of a suitable polymerase enzyme.
  • the synthetic step may itself form part of an amplification reaction producing a labelled double stranded amplification product comprised of annealed complementary strands derived from copying of the target and template polynucleotide strands.
  • Other exemplary “synthetic” steps include nick translation, strand displacement polymerisation, random primed DNA labelling etc.
  • the polymerase enzyme used in the synthetic step must be capable of catalysing the incorporation of modified nucleotides according to the invention. Otherwise, the precise nature of the polymerase is not particularly limited but may depend upon the conditions of the synthetic reaction. By way of example, if the synthetic reaction is carried out using thermocycling then a thermostable polymerase is required, whereas this may not be essential for standard primer extension reactions.
  • thermostable polymerases which are capable of incorporating the modified nucleotides according to the invention include those described in WO 2005/024010 or WO06120433.In synthetic reactions which are carried out at lower temperatures such as 37° C., polymerase enzymes need not necessarily be thermostable polymerases, therefore the choice of polymerase will depend on a number of factors such as reaction temperature, pH, strand-displacing activity and the like.
  • the invention encompasses use of the modified nucleotides or nucleosides labelled with dyes according to the invention in a method of nucleic acid sequencing, re-sequencing, whole genome sequencing, single nucleotide polymorphism scoring, any other application involving the detection of the modified nucleotide or nucleoside when incorporated into a polynucleotide, or any other application requiring the use of polynucleotides labelled with the modified nucleotides comprising fluorescent dyes according to the invention.
  • the invention provides use of modified nucleotides comprising dye compounds according to the invention in a polynucleotide “sequencing-by-synthesis” reaction.
  • Sequencing-by-synthesis generally involves sequential addition of one or more nucleotides or oligonucleotides to a growing polynucleotide chain in the 5′ to 3′ direction using a polymerase or ligase in order to form an extended polynucleotide chain complementary to the template nucleic acid to be sequenced.
  • the identity of the base present in one or more of the added nucleotide(s) is determined in a detection or “imaging” step. The identity of the added base may be determined after each nucleotide incorporation step.
  • the sequence of the template may then be inferred using conventional Watson-Crick base-pairing rules.
  • the use of the modified nucleotides labelled with dyes according to the invention for determination of the identity of a single base may be useful, for example, in the scoring of single nucleotide polymorphisms, and such single base extension reactions are within the scope of this invention.
  • the sequence of a template polynucleotide is determined by detecting the incorporation of one or more nucleotides into a nascent strand complementary to the template polynucleotide to be sequenced through the detection of fluorescent label(s) attached to the incorporated nucleotide(s). Sequencing of the template polynucleotide is primed with a suitable primer (or prepared as a hairpin construct which will contain the primer as part of the hairpin), and the nascent chain is extended in a stepwise manner by addition of nucleotides to the 3′ end of the primer in a polymerase-catalysed reaction.
  • each of the different nucleotide triphosphates is labelled with a unique fluorophore and also comprises a blocking group at the 3′ position to prevent uncontrolled polymerisation.
  • the polymerase enzyme incorporates a nucleotide into the nascent chain complementary to the template polynucleotide, and the blocking group prevents further incorporation of nucleotides. Any unincorporated nucleotides are removed and the fluorescent signal from each incorporated nucleotide is “read” optically by suitable means, such as a charge-coupled device using laser excitation and suitable emission filters.
  • U.S. Pat. No. 5,302,509 discloses a method to sequence polynucleotides immobilised on a solid support. The method relies on the incorporation of fluorescently labelled, 3′-blocked nucleotides A, G, C and T into a growing strand complementary to the immobilised polynucleotide, in the presence of DNA polymerase.
  • the polymerase incorporates a base complementary to the target polynucleotide, but is prevented from further addition by the 3′-blocking group.
  • the label of the incorporated base can then be determined and the blocking group removed by chemical cleavage to allow further polymerisation to occur.
  • the nucleic acid template to be sequenced in a sequencing-by-synthesis reaction may be any polynucleotide that it is desired to sequence.
  • the nucleic acid template for a sequencing reaction will typically comprise a double stranded region having a free 3′ hydroxyl group which serves as a primer or initiation point for the addition of further nucleotides in the sequencing reaction.
  • the region of the template to be sequenced will overhang this free 3′ hydroxyl group on the complementary strand.
  • the overhanging region of the template to be sequenced may be single stranded but can be double-stranded, provided that a “nick is present” on the strand complementary to the template strand to be sequenced to provide a free 3′ OH group for initiation of the sequencing reaction.
  • sequencing may proceed by strand displacement.
  • a primer bearing the free 3′ hydroxyl group may be added as a separate component (e.g. a short oligonucleotide) which hybridises to a single-stranded region of the template to be sequenced.
  • the primer and the template strand to be sequenced may each form part of a partially self-complementary nucleic acid strand capable of forming an intra-molecular duplex, such as for example a hairpin loop structure.
  • Hairpin polynucleotides and methods by which they may be attached to solid supports are disclosed in applicant's co-pending International application publication nos. WO0157248 and WO 2005/047301. Nucleotides are added successively to the free 3′hydroxyl group, resulting in synthesis of a polynucleotide chain in the 5′ to 3′ direction. The nature of the base which has been added may be determined, particularly but not necessarily after each nucleotide addition, thus providing sequence information for the nucleic acid template.
  • incorporation of a nucleotide into a nucleic acid strand (or polynucleotide) in this context refers to joining of the nucleotide to the free 3′ hydroxyl group of the nucleic acid strand via formation of a phosphodiester linkage with the 5′ phosphate group of the nucleotide.
  • the nucleic acid template to be sequenced may be DNA or RNA, or even a hybrid molecule comprised of deoxynucleotides and ribonucleotides.
  • the nucleic acid template may comprise naturally occurring and/or non-naturally occurring nucleotides and natural or non-natural backbone linkages, provided that these do not prevent copying of the template in the sequencing reaction.
  • the nucleic acid template to be sequenced may be attached to a solid support via any suitable linkage method known in the art, for example via covalent attachment.
  • template polynucleotides may be attached directly to a solid support (e.g. a silica-based support).
  • the surface of the solid support may be modified in some way so as to allow either direct covalent attachment of template polynucleotides, or to immobilise the template polynucleotides through a hydrogel or polyelectrolyte multilayer, which may itself be non-covalently attached to the solid support.
  • Arrays in which polynucleotides have been directly attached to silica-based supports are those for example disclosed in WO00006770, wherein polynucleotides are immobilised on a glass support by reaction between a pendant epoxide group on the glass with an internal amino group on the polynucleotide.
  • a still further example of solid-supported template polynucleotides is where the template polynucleotides are attached to hydrogel supported upon silica-based or other solid supports.
  • Silica-based supports are typically used to support hydrogels and hydrogel arrays as described in W000/31148, W001/01143, W002/12566, W003/014392, U.S. Pat. No. 6,465,178 and W000/53812.
  • a particular surface to which template polynucleotides may be immobilised is a polyacrylamide hydrogel.
  • Polyacrylamide hydrogels are described in the prior art, some of which is discussed above. However, a particular hydrogel is described in WO2005/065814.
  • DNA template molecules can be attached to beads or microparticles for the purposes of sequencing; for example as described in U.S. Pat. No. 6,172,218. Further examples of the preparation of bead libraries where each bead contains different DNA sequences can be found in the prior art (Nature. 437, 376-380 (2005); Science. 309, 5741, 1728-1732 (2005)). Sequencing of arrays of such beads using nucleotides as described is within the scope of the invention.
  • the template(s) to be sequenced may form part of an “array” on a solid support, in which case the array may take any convenient form.
  • the method of the invention is applicable to all types of “high density” arrays, including single-molecule arrays, clustered arrays and bead arrays.
  • Modified nucleotides labelled with dye compounds of the invention may be used for sequencing templates on essentially any type of array formed by immobilisation of nucleic acid molecules on a solid support, and more particularly any type of high-density array.
  • the modified nucleotides labelled with dye compounds of the invention are particularly advantageous in the context of sequencing of clustered arrays.
  • distinct regions on the array comprise multiple polynucleotide template molecules.
  • the term “clustered array” refers to an array wherein distinct regions or sites on the array comprise multiple polynucleotide molecules that are not individually resolvable by optical means. Depending on how the array is formed each site on the array may comprise multiple copies of one individual polynucleotide molecule or even multiple copies of a small number of different polynucleotide molecules (e.g. multiple copies of two complementary nucleic acid strands).
  • Multi-polynucleotide or clustered arrays of nucleic acid molecules may be produced using techniques generally known in the art.
  • WO 98/44151 and WO00/18957 both describe methods of amplification of nucleic acids wherein both the template and amplification products remain immobilised on a solid support in order to form arrays comprised of clusters or “colonies” of immobilised nucleic acid molecules.
  • the nucleic acid molecules present on the clustered arrays prepared according to these methods are suitable templates for sequencing using the modified nucleotides labelled with dye compounds of the invention.
  • the modified nucleotides labelled with dye compounds of the invention are also useful in sequencing of templates on single molecule arrays.
  • the term “single molecule array” or “SMA” as used herein refers to a population of polynucleotide molecules, distributed (or arrayed) over a solid support, wherein the spacing of any individual polynucleotide from all others of the population is such that it is possible to effect individual resolution of the polynucleotides.
  • the target nucleic acid molecules immobilised onto the surface of the solid support should thus be capable of being resolved by optical means. This means that, within the resolvable area of the particular imaging device used, there must be one or more distinct signals, each representing one polynucleotide.
  • each molecule is individually resolvable and detectable as a single molecule fluorescent point, and fluorescence from said single molecule fluorescent point also exhibits single step photobleaching.
  • the terms “individually resolved” and “individual resolution” are used herein to specify that, when visualised, it is possible to distinguish one molecule on the array from its neighbouring molecules. Separation between individual molecules on the array will be determined, in part, by the particular technique used to resolve the individual molecules.
  • the general features of single molecule arrays will be understood by reference to published applications WO00/06770 and WO 01/57248.
  • one use of the modified nucleotides of the invention is in sequencing-by-synthesis reactions, the utility of the modified nucleotides is not limited to such methods. In fact, the nucleotides may be used advantageously in any sequencing methodology which requires detection of fluorescent labels attached to nucleotides incorporated into a polynucleotide.
  • the modified nucleotides labelled with dye compounds of the invention may be used in automated fluorescent sequencing protocols, particularly fluorescent dye-terminator cycle sequencing based on the chain termination sequencing method of Sanger and co-workers.
  • Such methods generally use enzymes and cycle sequencing to incorporate fluorescently labelled dideoxynucleotides in a primer extension sequencing reaction.
  • So called Sanger sequencing methods, and related protocols rely upon randomised chain termination with labelled dideoxynucleotides.
  • the invention also encompasses modified nucleotides labelled with dye compounds according to the invention which are dideoxynucleotides lacking hydroxyl groups at both of the 3′ and 2′ positions, such modified dideoxynucleotides being suitable for use in Sanger type sequencing methods and the like.
  • Modified nucleotides labelled with dye compounds of the present invention incorporating 3′ blocking groups may also be of utility in Sanger methods and related protocols since the same effect achieved by using modified dideoxy nucleotides may be achieved by using modified nucleotides having 3′-OH blocking groups: both prevent incorporation of subsequent nucleotides.
  • nucleotides according to the present invention and having a 3′ blocking group are to be used in Sanger-type sequencing methods it will be appreciated that the dye compounds or detectable labels attached to the nucleotides need not be connected via cleavable linkers, since in each instance where a labelled nucleotide of the invention is incorporated; no nucleotides need to be subsequently incorporated and thus the label need not be removed from the nucleotide.
  • kits including modified nucleosides and/or nucleotides labelled with dyes according to the invention.
  • Such kits will generally include at least one modified nucleotide or nucleoside labelled with a dye according to the invention together with at least one further component.
  • the further component(s) may be further modified or unmodified nucleotides or nucleosides.
  • modified nucleotides labelled with dyes according to the invention may be supplied in combination with unlabelled or native nucleotides, and/or with fluorescently labelled nucleotides or any combination thereof.
  • the kits may comprise modified nucleotides labelled with dyes according to the invention and modified nucleotides labelled with other, for example, prior art dye compounds. Combinations of nucleotides may be provided as separate individual components or as nucleotide mixtures.
  • kits comprise a plurality, particularly two, more particularly four, modified nucleotides labelled with a dye compound
  • the different nucleotides may be labelled with different dye compounds.
  • the different nucleotides are labelled with different dye compounds it is a feature of the kits that said dye compounds are spectrally distinguishable fluorescent dyes.
  • the term “spectrally distinguishable fluorescent dyes” refers to fluorescent dyes that emit fluorescent energy at wavelengths that can be distinguished by fluorescent detection equipment (for example, a commercial capillary based DNA sequencing platform) when two or more such dyes are present in one sample.
  • the spectrally distinguishable fluorescent dyes can be excited at the same wavelength, such as, for example by the same laser.
  • four modified nucleotides labelled with fluorescent dye compounds are supplied in kit form, it is a feature of the invention that two of the spectrally distinguishable fluorescent dyes can both be excited at one wavelength and the other two spectrally distinguishable dyes can both be excited at another wavelength.
  • Particular excitation wavelengths are 532 nm, 630 nm to 700 nm, particularly 660 nm.
  • a kit comprises a modified nucleotide labelled with ‘DYE 2’ and a second modified nucleotide labelled with a second dye wherein the dyes have a difference in absorbance maximum of at least 10 nm, particularly 20 nm is to 50 nm. More particularly the two dye compounds have Stokes shifts of between 15-40 nm where “Stokes shift” is the distance between the peak absorption and peak emission wavelengths.
  • the modified nucleotides are labelled with ‘Dye 1’ and ‘Dye 2’.
  • modified nucleotides are labelled with ‘Dye 2’ and an alternative dye that excites at 532 nm (such as Atto 532 (Atto-tec catalogue number AD532-3), as described in WO 04055117; or Alexa 532 (Molecular Probes catalogue number A20001, patent U.S. Pat. No. 6,130,101).
  • an alternative dye that excites at 532 nm such as Atto 532 (Atto-tec catalogue number AD532-3), as described in WO 04055117; or Alexa 532 (Molecular Probes catalogue number A20001, patent U.S. Pat. No. 6,130,101).
  • said kit further comprises two other modified nucleotides labelled with fluorescent dyes wherein said dyes are excited by the same laser at 600 nm to 700 nm, particularly 630 nm to 700 nm, more particularly 660 nm.
  • the dyes have a difference in absorbance maximum of at least 10 nm, particularly 20 nm to 50 nm. More particularly the two dye compounds have Stokes shifts of between 20-40 nm. Still yet more particularly the two dye compounds have a different absorbance maximum above 600 nm, particularly above 640 nm.
  • Particular dyes which are spectrally distinguishable from ‘DYE 1’ and ‘DYE 2’ and which meet the above criteria are polymethine analogues as described in U.S. Pat.
  • the invention provides a set of four nucleotides (A, C, G and T) each labelled with one of the following spectrally distinguishable fluorescent dye compounds: ‘Dye 2’, atto 532, a dicarbocyanine (Cy5) analogue such as Ferrania S-07181, and Dy681 (U.S. Pat. No. 6,924,372).
  • Another particular embodiment of so the invention provides a set of four nucleotides (A, C, G and T) each labelled with one of the following spectrally distinguishable dye compounds: ‘DYE 2’, ‘DYE 1’, a dicarbocyanines such as Ferrania S-07181, and Dy 681. Yet more particularly the set of four nucleotides further each comprise a 3′OH blocking group. Still yet more particularly both the dye compound and the 3′OH group are removable under the same reaction conditions. Synthesis of an exemplary set of four dye-nucleotide structures is given in the examples section below.
  • the Dyomics compound Dy681 can be substituted by a number of commercially available, structurally similar analogues also detailed in U.S. Pat. No. 6,924,372.
  • dyes such as Dy675, Dy676, Dy677, Dy680, Dy682, Dy700, Dy701 (also available from Dyomics) may also be used.
  • the pentamethine cyanine analogue used contains a sulphonamide moiety on the aromatic ring, and can be obtained from Ferrania Imaging technologies (Italy).
  • This-material can be substituted with a number of other commercially available materials that have a spectral similarity, for example Cy5 (GE Healthcare; PA15100), Alexa 647 (Molecular Probes; A20106), Atto 647 (Atto-tec; AD647-3), Dy647, Dy648, Dy650, Dy651 or Dy652 (Dyomics).
  • kits may include a polymerase enzyme capable of catalyzing incorporation of the modified nucleotides into a polynucleotide.
  • Other components to be included in such kits may include buffers and the like.
  • the modified nucleotides labelled with dyes according to the invention, and other any nucleotide components including mixtures of different nucleotides, may be provided in the kit in a concentrated form to be diluted prior to use. In such embodiments a suitable dilution buffer may also be included.
  • reaction was performed according to Example 2; step 3 using triethylammonium 3-[(5-hydroxy-2-methyl-phenyl)amino]propanesulfonate instead of triethylammonium 3-(7-hydroxy-3,4-dihydro-quinoline-1-yl)-propanesulfonate.
  • the reaction mixture was cooled to room temperature, solid mass treated with acetonitrile and the product was filtered off then under vacuum to give quantitative yield of DYE 1 as a purple powder.
  • This compound is prepared from 7-hydroxyquinoline and 1,3-propanesultone as published (GB 1,122,704) for 3-(8-hydroxyquinolinio-1-yl)propanesulfonate.
  • step two The product of step two (0.05 g, 0.13 mmole) was combined with 0.05 g (0.34 mmole) of phthalic anhydride, 0.3 ml 1-ethyl-3-methylimidazolium chloride (ionic liquid) and 0.02 g of anhydrous ZnCl 2 .
  • the resulting mixture was heated in an oil bath at 140° C. for 3 hours and then cooled to room temperature.
  • the resultant solid mass was treated with acetonitrile and the product was filtered off under vacuum to give quantitative yield (0.06 g) of (DYE 2) as a purple powder. Absorption max. 560 nm.
  • Triethylammonium 3-(7-hydroxy-3,4-2H-dihydro-quinoline-1-yl)sulfonate (Example 2, step 2) (0.05 g, 0.13 mmole) was combined with 0.05 g (0.26 mmole) of trimellitic anhydride in 0.5 ml of 1-ethyl-3-methylimidazolium chloride and 0.05 g of anhydrous ZnCl 2 . The resulting mixture was heated at 120° C. for 0.5 hour then 5 ml of acetonitrile was added to the reaction mixture. The resulting precipitate is filtered, washed with acetonitrile and dried. Yield: 0.05 g. (92%). Isomers separated by HPLC and structure confirmed by NMR and mass-spectra
  • IL 1-ethyl-3-methylimidazolium chloride
  • ZnCl 2 1-ethyl-3-methylimidazolium chloride
  • Triethylammonio 3-(7-hydroxy-3,4-dihydro-2H-quinoline-1-yl)propanesulfonate (0.74 g, 2 mmole) was combined with solution of 0.5 g ( ⁇ 2 mmole) of 3- or 4-sulfophthalic anhydride in 1 g 1-ethyl-3-methylimidazolium chloride and 1 g of anhydrous ZnCl 2 .
  • the resulting mixture was heated 4 hours at 180° C.
  • the reaction mixture was cooled to room temperature, solid mass treated with mixture acetonitrile-water and applied to a flash column. Dyes prepared as a purple powder.
  • 3-(5-Hydroxy-3,4-dihydro-2H-quinoline-1-yl)propanesulfonic acid triethylamonium salt from step la example 6 (0.025 g, 0.9 mmole) was combined with 0.02 g (0.10 mmole) of trimellitic anhydride and 0.03 g of anhydrous ZnCl 2 .
  • the resulting mixture was heated in an oil bath at 170° C. for 1 hours.
  • the reaction mixture was cooled to room temperature, solid mass pulverized with acetonitrile and the product was filtered off
  • the crude product was purified on silica gel. Yield: 0.005 g. (16%).
  • Target compound molecular formula C 52 H 61 N 8 O 15 S 2 ⁇
  • Target compound molecular formula C 65 H 78 N 14 0 28 P 3 S 2 ⁇
  • Target compound molecular weight 1660.44
  • Alexa647NHS ester (10 mg, 8 ⁇ mol), (Molecular probes A20106), LN3 (8.8 mg, 24 ⁇ mol) and DIPEA (8 ⁇ L, 48 ⁇ mol) were dissolved in anhydrous DMF (4 mL) in a round bottom flask under N 2 .
  • Alexa647LN 3 CO 2 H (3.35 ⁇ mol) was dissolved in anhydrous DMF (1.1 mL) in a 5 mL round bottom flask under N 2 . To this was added DSC (1.28 mg, 5.02 ⁇ mol) and DMAP (0.61 mg, 5.02 ⁇ mol) in 20 ⁇ L each respectively. The reaction mixture was stirred at ambient temperature under N 2 for 5 minutes before analysing by TLC (4:1 acetonitrile: water, Aldrich TLC plates 200 ⁇ layer, 2-25 ⁇ particle size, 60 A pore). Full activation of Alexa647LN 3 CO 2 H (R f 0.48) was observed, generating the activated linker (R f 0.64).
  • DY681NHS ester (5 mg, 5.9 pmol) (Dyomics 681-01) was dissolved in DMF (1.3 ml). A solution of LN3 (6.6 mg, 17.9 ⁇ mol) and DIPEA (6 ⁇ l, 35.9 ⁇ mol) in DMF (0.5 ml) was added. The reaction progress was monitored by TLC (eluting system CH 3 CN:H 2 O 4:1) and by HPLC (5-100 method in 20 min in the semiprep Zorbax column). The reaction was stopped after 4 h. The solvent was evaporated and the reaction crude was redissolved in 0.1 M TEAB. The crude was purified by HPLC using the same method and column aforementioned, retention time 11.5 min. DY681LN3 was obtained in 55% yield.
  • DY681LN3 (3.13 ⁇ mol) was dissolved in DMF (1.5 ml). A solution of TSTU (1.4 mg, 4.7 ⁇ mol) in DMF (120 ⁇ l) was added. The activation progress was monitored by TLC (eluting system CH 3 CN:H 2 O 4:1). DIPEA (2.7 ⁇ l) was added to aid the activation, which had a 80% progress in 20 min. PPPC (9.4 ⁇ mol, 4.87 mM) was co-evaporated with tributylamine (22 ⁇ l, 94 ⁇ mol), re-dissolved in DMF (300 ⁇ l) and added to the reaction mixture.
  • Atto532NHS ester (20 mg, 26.9 ⁇ mol) (Atto-tecAD532-3) was dissolved in DMF (1.5 ml). A solution of H2N-PEG12-COOH (49.8 mg, 80.7 mol) in 0.1 M TEAB (0.5 ml) was added to the reaction. The reaction was monitored by TLC (eluting system CH 3 CN:H 2 O 4:1) and reached completion in 90 min. It was quenched with 2 ml of 0.1 M TEAB and concentrated to dryness. The crude reaction mixture was purified by doing a Sephadex column (1 ⁇ 10 cm).
  • Atto532PEG (21.6 mg, 17.4 ⁇ mol) was dissolved in DMF (1.8 ml).
  • a solution of TSTU (7.8 mg, 26.1 ⁇ mol) in DMF was added to the reaction.
  • DIPEA (15 ⁇ l, 87 ⁇ mol) was added.
  • the activation was completed in 30 min and LN3 (15.9 mg, 43.5 ⁇ mol) dissolved in DMF was added.
  • the reaction was left stirring for 16 h, after which it was quenched with 10 ml of 0.1 M TEAB and vacuumed off.
  • the crude reaction mixture was purified by HPLC (5-50 method in 20 min in the semiprep Zorbax column), retention time 14.9 min. The product was obtained in 66% yield.
  • Atto532PEGLN3 (18 mg, 11.3 ⁇ mol) was dissolved in DMF (3 ml). A solution of TSTU (5.1 mg, 17 ⁇ mol) in DMF (200 ⁇ l) was added. The progress of the reaction was monitored by TLC (eluting system CH 3 CN:H 2 O 4:1 and DIPEA (10 ⁇ l) was added. After 30 min, the TLC shows that the activation was completed. PPPG (34 ⁇ mol, 2.25 mM) was co-evaporated with tributylamine (81 ⁇ l) and redissolved in 0.1 M TEAB (0.5 ml). After 30 min, TLC showed that the reaction had gone to completion (eluting system CH 3 CN: H 2 O 4:1).
  • reaction was quenched with 10 ml of 0.1 M TEAB at 0° C. and vacuumed off.
  • the reaction crude was purified by HPLC (5-50 method in 20 min in the semiprep Zorbax column), retention time 14.8 min. The product was obtained in 57% yield.
  • the solid supports used are typically 8-channel glass chips such as those provided by Silex Microsystems (Sweden). However, the experimental conditions and procedures are readily applicable to other solid supports.
  • Chips were washed as follows: neat Decon for 30 min, milliQ H 2 O for 30 min, NaOH 1N for 15 min, milliQ H 2 O for 30 min, HCl 0.1N for 15 min, milliQ H 2 O for 30 min.
  • the 10 ml solution of acrylamide was first degas sed with argon for 15 min.
  • the solutions of BRAPA, TEMED and potassium persulfate were successively added to the acrylamide solution.
  • the mixture was then quickly vortexed and immediately used. Polymerization was then carried out for 1 h 30 min(?) at RT. Afterwards the channels were washed with milliQ H 2 O for 30 min and filled with 0.1 M potassium phosphate buffer for storage until required.
  • N-Boc-1,5-diaminopentane p-toluenesulfonate was obtained from Novabiochem.
  • the bromoacetyl chloride and acryloyl chloride were obtained from Fluka. All other reagents were Aldrich products.
  • N-[5-(t-Bytoxycarbonyl)aminopentyl]acrylamide (2.56 g, 10 mmol) was dissolved in mixture of trifluoroacetic acid and dichloromethane (1:9, 100 ml) and stirred at room temperature. The progress of the reaction was monitored by TLC (dichloromethane:methanol 9:1). On completion, the reaction mixture was evaporated to dryness, the residue co-evaporated three times with toluene and then purified by flash chromatography (neat dichloromethane followed by a gradient of methanol up to 20%). Product was obtained as a white powder (2.43 g, 9 mmol, 90%).
  • a peristaltic pump Ismatec IPC equipped with tubing Ismatec Ref 070534-051 (orange/yellow, 0.51 mm internal diameter) is used.
  • the pump is run in the forward direction (pulling fluids).
  • a waste dish is installed to collect used solution at the outlet of the peristaltic pump tubing.
  • the different solutions used are dispensed into 8 tube microtube strips, using 1 tube per chip inlet tubing, in order to monitor the correct pumping of the solutions in each channel. The volume required per channel is specified for each step.
  • the Silex chip is mounted on top of an MJ-Research thermocycler.
  • the chip sits on top of a custom made copper block, which is attached to the flat heating block of the thermocycler.
  • the chip is covered with a small Perspex block and is held in place by adhesive tape.
  • thermocycler Both pump and thermocycler are controlled by computer run scripts, which prompt the user to change solutions between each step.
  • An SFA coated chip is placed onto a modified MJ-Research thermocycler and attached to a peristaltic pump as described above. Grafting mix consisting of 0.5 ⁇ M of a forward primer and 0.5 ⁇ M of a reverse primer in 10 mM phosphate buffer (pH 7.0) is pumped into the channels of the chip at a flow rate of 60 ⁇ l/min for 75 s at 20° C. The thermocycler is then heated up to 51.6° C., and the chip is incubated at this temperature for 1 hour.
  • the grafting mix undergoes 18 cycles of pumping: grafting mix is pumped in at 15 ⁇ l/min for 20 s, then the solution is pumped back and forth (5 s forward at 15 ⁇ l/min, then 5 s backward at 15 ⁇ l/min) for 180 s. After 18 cycles of pumping, the chip is washed by pumping in 5 ⁇ SSC/5 mM EDTA at 15 ⁇ l/min for 300 s at 51.6° C. The thermocycler is then cooled to 20° C.
  • the DNA templates to be hybridised to the grafted chip are diluted to the required concentration (currently 0.5-2 pM) in 5 ⁇ SSC/0.1% Tween.
  • the diluted DNA is heated on a heating block at 100° C. for 5 min to denature the double stranded DNA into single strands suitable for hybridisation.
  • the DNA is then immediately snap-chilled in an ice/water bath for 3 min.
  • the tubes containing the DNA are briefly spun in a centrifuge to collect any condensation, and then transferred to a pre-chilled 8-tube strip and used immediately.
  • the grafted chip from step 1 is primed by pumping in 5 ⁇ SSC/0.1% Tween at 60 ⁇ l/min for 75 s at 20° C.
  • the thermocycler is then heated to 98.5° C., and the denatured DNA is pumped in at 15 ⁇ l/min for 300 s.
  • An additional pump at 100 ⁇ l/min for 10 s is carried out to flush through bubbles formed by the heating of the hybridisation mix.
  • the temperature is then held at 98.5° C. for 30 s, before being cooled slowly to 40.2° C. over 19.5 min.
  • the chip is then washed by pumping in 0.3 ⁇ SSC/0.1% Tween at 15 ⁇ l/min for 300 s at 40.2° C.
  • the script then runs straight to the next step.
  • the hybridised template molecules are amplified by a bridging polymerase chain reaction using the grafted primers and a thermostable polymerase.
  • PCR buffer consisting of 10 mM Tris (pH 9.0), 50 mM KCl, 1.5 mM MgCl 2 , 1 M betaine and 1.3% DMSO is pumped into the chip at 15 ⁇ l/min for 200 s at 40.2° C. Then PCR mix of the above buffer supplemented with 200 ⁇ M dNTPs and 25 U/ml Taq polymerase is pumped in at 60 ⁇ l/min for 75 s at 40.2° C. The thermocycler is then heated to 74° C. and held at this temperature for 90 s. This step enables extension of the surface bound primers to which the DNA template strands are hybridised. The thermocycler then carries out 50 cycles of amplification by heating to 98.5° C.
  • Linearization mix consisting of 0.1 M sodium periodate and 0.1 M ethanolamine is pumped into the chip at 15 ⁇ l/min for 1 hr at 20° C. The chip is then washed by pumping in water at 15 ⁇ l/min for 300 s at 20° C.
  • This step uses Terminal Transferase to incorporate a dideoxynucleotide onto the free 3′ OH ends of DNA strands (both grafted primers and amplified cluster molecules).
  • Blocking buffer consisting of 50 mM potassium acetate, 20 mM Tris-acetate, 10 mM magnesium acetate, 1 mM dithiothreitol (pH 7.9) and 250 ⁇ M CoCl 2 is pumped into the chip at 15 ⁇ l/min for 200 s at 20° C. Then Blocking Mix of the above buffer supplemented with 2.4 ⁇ M ddNTPs and 250 U/ml Terminal Transferase is pumped in at 15 ⁇ l/min for 300 s at 37.7° C. The thermocycler is held at 37.7° C.
  • d ur i ng w hich time Blocking Mix is pumped into the chip at 15 ⁇ l/min for 20 s every 3 min. After blocking, the chip is then washed by pumping in 0.3 ⁇ SSC/0.1% Tween at 15 ⁇ l/min for 300 s at 20° C.
  • This step uses NaOH to denature and wash away one of the strands of the amplified, linearised and blocked clusters. After a wash to remove the NaOH, the sequencing primer is then hybridised onto the single strands left on the surface.
  • the double stranded DNA in the clusters is denatured by pumping in 0.1N NaOH at 15 ⁇ l/min for 300 s at 20° C.
  • the chip is then washed by pumping in TE (10 mM Tris pH 8.0, 1 mM EDTA) at 15 ⁇ l/min for 300 s at 20° C.
  • Sequencing primer is diluted to 0.5 ⁇ M in 5 ⁇ SSC/0.1% Tween, and pumped into the channels at 15 ⁇ l/min for 300 s at 20° C.
  • the thermocycler is then heated up to 60° C. and held at this temperature for 15 min.
  • the thermocycler is then cooled to 40.2° C. and the chip is washed by pumping in 0.3 ⁇ SSC/0.1% Tween at 15 ⁇ l/min for 300 s.
  • the clusters are now ready for 1 st cycle sequencing enzymology.
  • the DNA sequence used in this process was a single monotemplate sequence of 400 bases, with ends complementary to the grafted primers.
  • the duplex DNA was denatured as described above.
  • the primers are typically 5′-phosphorothioate oligonucleotides incorporating any specific sequences or modifications required for cleavage. Their sequences and suppliers vary according to the experiment they are to be used for, and in this case were complementary to the 5′-ends of the template duplex.
  • the amplified clusters contained a diol linkage in one of the grafted primers.
  • Diol linkages can be introduced by including a suitable linkage into one of the primers used for solid-phase amplification.
  • Suitable primers including any desired template-specific sequence can be manufactured by standard automated DNA synthesis techniques using components available from commercial suppliers (e.g. Fidelity Systems Inc., ATD).
  • a cleavable diol-containing primer would typically have the following structure:
  • sequence represents a sequence of nucleotides capable of hybridising to the template to be amplified.
  • Products containing such diol linkages can be cleaved using periodate as described above, and the resulting single stranded polynucleotides hybridised as described above.
  • a mutant 9° N polymerase enzyme (an exo- variant including the triple mutation L408Y/Y409A/P410V and C223S) was used for the nucleotide incorporation steps.
  • Incorporation mix Incorporation buffer (50 mM Tris-HCl pH 8.0, 6 mM MgSO4, 1 mM EDTA, 0.05% (v/v) Tween 20, 50 mM NaCl) plus 110 nM YAV exo- C223S, and 1 ⁇ M each of the four labelled modified nucleotides, was applied to the clustered templates, and heated to 45° C.
  • Templates were maintained at 45° C. for 30 min, cooled to 20° C. and washed with Incorporation buffer, then with 5 ⁇ SSC/0.05% Tween 20.Templates were then exposed to Imaging buffer (100 mM Tris pH 7.0, 30 mM NaCl, 0.05% Tween 20, 50 mM sodium ascorbate, freshly dissolved).
  • Templates were scanned in 4 colours at room temp.
  • the system comprises a mounted flow cell chip, a fluid direction system that controllably moves various reagents (e.g., buffers, labelled nucleotides wherein each type of nucleotide has its own specific fluorescent moiety, etc.) into contact with the polynucleotides; a temperature control system that regulates the temperature of the substrate and/or of the reagents; a TIRF laser system for exciting the fluorescent moiety; a detector component (e.g., a CCD camera and objective lenses, etc.) that is proximal to the substrate and which detects fluorescence from the laser excited moiety; a computer, connected to the detector, which has instruction sets for acquiring fluorescence data from the detector and optionally for determining sequence of the polynucleotide based on the fluorescence data.
  • various reagents e.g., buffers, labelled nucleotides wherein each type of nucleotide has its own specific fluorescent moiety, etc.
  • a temperature control system
  • each of each chip was recorded in each of the four colours corresponding to the labelled nucleotides.
  • the images were analysed to pick the brightest colour for each cluster, and this image intensity analysis was used to call the base for each cluster at each cycle. Images from each cycle were colocalised to obtain the sequence corresponding to each cluster.
  • the sequence of each cluster is known; and is the same for every cluster in the above experiment, the error rates (i.e. clusters not called as the correct sequence) can be analysed for each cycle of nucleotide incorporation. The error rates were less than 1% for the first 20 cycles of the experiment, meaning the known sequence of the monotemplate was correctly identified.

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