US20110014611A1 - Design and synthesis of cleavable fluorescent nucleotides as reversible terminators for dna sequences by synthesis - Google Patents

Design and synthesis of cleavable fluorescent nucleotides as reversible terminators for dna sequences by synthesis Download PDF

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US20110014611A1
US20110014611A1 US12/734,227 US73422708A US2011014611A1 US 20110014611 A1 US20110014611 A1 US 20110014611A1 US 73422708 A US73422708 A US 73422708A US 2011014611 A1 US2011014611 A1 US 2011014611A1
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nucleic acid
dntp
dna
fluorophore
primer
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Jingyue Ju
Huanyan Cao
Zengmin Li
Qinglin Meng
Jia Guo
Shenglong Zhang
Lin Yu
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Columbia University of New York
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Publication of US20110014611A1 publication Critical patent/US20110014611A1/en
Assigned to NATIONAL INSTITUTES OF HEALTH (NIH), U.S. DEPT. OF HEALTH AND HUMAN SERVICES (DHHS), U.S. GOVERNMENT reassignment NATIONAL INSTITUTES OF HEALTH (NIH), U.S. DEPT. OF HEALTH AND HUMAN SERVICES (DHHS), U.S. GOVERNMENT CONFIRMATORY LICENSE (SEE DOCUMENT FOR DETAILS). Assignors: COLUMBIA UNIV NEW YORK MORNINGSIDE
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    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869—Methods for sequencing
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
    • C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
    • C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
    • C07H19/06—Pyrimidine radicals
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
    • C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
    • C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
    • C07H19/06—Pyrimidine radicals
    • C07H19/10—Pyrimidine radicals with the saccharide radical esterified by phosphoric or polyphosphoric acids
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
    • C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
    • C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
    • C07H19/14—Pyrrolo-pyrimidine radicals
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
    • C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
    • C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
    • C07H19/16—Purine radicals
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
    • C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
    • C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
    • C07H19/16—Purine radicals
    • C07H19/20—Purine radicals with the saccharide radical esterified by phosphoric or polyphosphoric acids
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    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12Q2525/00—Reactions involving modified oligonucleotides, nucleic acids, or nucleotides
    • C12Q2525/30—Oligonucleotides characterised by their secondary structure
    • C12Q2525/301—Hairpin oligonucleotides
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    • C12Q2537/00—Reactions characterised by the reaction format or use of a specific feature
    • C12Q2537/10—Reactions characterised by the reaction format or use of a specific feature the purpose or use of
    • C12Q2537/157—A reaction step characterised by the number of molecules incorporated or released

Definitions

  • a composition having a first, second and third portion wherein the second portion has the following structure:
  • ⁇ represents a point of attachment to the first portion and ⁇ represents a point of attachment to the third portion.
  • a method for determining the identity of each of a series of consecutive nucleotide residues in a nucleic acid comprising:
  • a method for determining the identity of each of a series of consecutive nucleotide residues in a self-priming nucleic acid comprising:
  • a kit for use in sequencing a nucleic acid comprising:
  • An array comprising a nucleic acid attached to a solid surface, wherein the nucleic acid comprises an azidomethyl group attached to a 3′ atom thereof and a molecule having the structure:
  • ⁇ represents a point of attachment to a 3′ base of the nucleic acid and ⁇ represents a point of attachment to a detectable marker.
  • An array comprising a self-priming nucleic acid attached to a solid surface, wherein the nucleic acid comprises an azidomethyl group attached to a 3′ atom thereof and a molecule having the structure:
  • ⁇ represents a point of attachment to a 3′ base of the nucleic acid and ⁇ represents a point of attachment to a detectable marker.
  • a method for increasing a read length of DNA sequencing by synthesis comprising (a) providing deoxynucleotide triphosphate analogues wherein the deoxynucleotide triphosphate analogues differ from deoxynucleotide triphosphates by having a methylazido group attached to a 3′ atom thereof and by having a detectable marker attached to a 1 nitrogen or a 9 nitrogen of a base thereof through a linker comprising the structure
  • a method for determining the identity of each of a series of consecutive nucleotide residues in a nucleic acid comprising:
  • a method for determining the identity of each of a series of consecutive nucleotide residues in a self-priming nucleic acid comprising:
  • a method for determining the identity of each of a series of consecutive nucleotide residues in a plurality of nucleic acids comprising, the same series of consecutive nucleotides comprising:
  • a method for determining the identity of consecutive nucleotide residues in a self-priming nucleic acid comprising:
  • a kit for use in sequencing a nucleic acid comprising:
  • An array comprising a nucleic acid attached to a solid surface, wherein the nucleic acid comprises an azidomethyl group attached to a 3′ atom thereof and a molecule having the structure:
  • An array comprising a self-priming nucleic acid attached to a solid surface, wherein the nucleic acid comprises an azidomethyl group attached to a 3′ atom thereof and a molecule having the structure:
  • a method for increasing a read length of DNA sequencing by synthesis coupled with Sanger dideoxynucleotide terminating reaction (a) providing deoxynucleotide triphosphate analogues wherein the deoxynucleotide triphosphate analogues differ from deoxynucleotide triphosphates by having a methylazido group attached to a 3′ atom thereof and providing dideoxynucleotide triphosphate analogues wherein the dideoxynucleotide triphosphate analogues differ from dideoxynucleotide triphosphates by having a detectable marker attached to a 1 nitrogen or a 9 nitrogen of a base thereof through a linker comprising the structure
  • FIG. 1 Staudinger reduction with TCEP.
  • FIG. 2 3′-O-Azido-dNTPs-Azido-Dye.
  • FIG. 3 Staudinger Reduction of the Azido Linker.
  • FIG. 4 3′-O-Azido-dNTP-PC-Dye.
  • FIG. 5 The hybrid DNA sequencing approach between the Sanger dideoxy chain-terminating reaction and sequencing by synthesis.
  • four nucleotides (3′-O—R 1 -dNTPs) modified as reversible terminators by capping the 3′-OH with a small reversible moiety R1 so that they are still recognized by DNA polymerase as substrates, are used in combination with a small percentage of four cleavable fluorescent dideoxynucleotides (ddNTP-R 2 -fluorophores) to perform SBS.
  • DNA sequences are determined by the unique fluorescence emission of each fluorophore on the DNA products terminated by ddNTPs.
  • the polymerase reaction reinitiates to continue the sequence determination.
  • FIG. 6 3′-O-Azido-dNTPs.
  • FIG. 7 Solution Incorporation and reduction of 3′-O-Azido-dNTPs: polymerase extension and TCEP reduction scheme.
  • FIG. 8 MALDI-TOF MS spectra of incorporation products (left column), and MALDI-TOF MS spectra of reduction products (right column).
  • FIG. 9 Solution incorporation and reduction scheme of 3′-O-Azido-dNTPs-Azido-Dye.
  • FIG. 10 MALDI-TOF MS spectra results for incorporation shown in FIG. 9 .
  • FIG. 11 SBS scheme for 3′-O-Azido-dNTPs-Azido-Dye.
  • FIG. 12 Results for incorporation shown in FIG. 11 .
  • FIG. 13 Mechanisms to cleave the 3′-O-azidomethyl group and the azidolinker-fluorophore from the DNA extension products.
  • FIG. 15 Synthesis of ddCTP-N 3 -Bodipy-FL-510
  • FIG. 16 Synthesis of ddUTP-N 3 -R6G
  • FIG. 17 Synthesis of ddATP-N 3 -ROX
  • FIG. 18 Synthesis of ddGTP-N 3 -Cy5
  • FIG. 19 A detailed scheme (left half of fig.) of polymerase reaction using all four 3′-O—N 3 -dNTPs to extend with an “3′-O—N 3 -dATP”, “3′-O—N 3 -dCTP”, “3′-O—N 3 -dGTP” and “3′-O—N 3 -dTTP” and the subsequent cleavage reaction to cleave off the azidomethyl moiety capping the 3′-OH of the DNA extension product.
  • MALDI-TOF MS spectra verifying base specific incorporation of: (A) 3′-O—N 3 -dCTP (peak at 8,310 m/z), (B) the corresponding cleavage product (8,255 m/z); (C) 3′-O—N 3 -dGTP (peak at 8,639 m/z), (D) the corresponding cleavage product (8,584 m/z); (E) 3′-O—N 3 -dATP (peak at 8,952 m/z), (F) the corresponding cleavage product (8,897 m/z); (G) 3′-O—N 3 -dTTP (peak at 9,256 m/z) and (H) the corresponding cleavage product (9,201 m/z).
  • the azidomethyl moiety capping the 3′-OH group of the DNA extension products is completely removed by TCEP aqueous solution to continue the polymerase reaction.
  • FIG. 20 A detailed scheme (top half of fig.) of polymerase reaction using all four ddATP-N 3 -fluorophores to extend with an “ddA”, “ddC”, “ddG” and “ddU” and the subsequent cleavage reaction to cleave off the fluorophore from the DNA extension product.
  • FIG. 21 (A) Reaction scheme of Sanger/sequencing by synthesis hybrid sequencing on a chip using combination of cleavable fluorescent dideoxynucleotides and 3′-O—N 3 -modified nucleotides.
  • FIG. 22 A plot (four-color sequencing data) of raw fluorescence emission intensity obtained by using 3′-O—N3-dNTPs and ddNTP-N3-fluorophores at the four designated emission wavelengths of the four cleavable fluorescent dideoxynucleotides.
  • FIG. 23 “Walking” Strategy 1
  • FIG. 24 Structures of the nucleotide reversible terminators
  • FIG. 25 Structures of cleavable fluorescent dideoxynucleotide terminators
  • FIG. 26 Hybrid SBS scheme
  • FIG. 27 Template “Walking” Method 1
  • FIG. 28 Template “Walking” Method 2
  • FIG. 29 Template “Walking” Method 3
  • FIG. 30 Template “Walking” Method 4
  • FIG. 31 Template “Walking” Method 5
  • FIG. 32 Structures of the nucleotide reversible terminators, 3′-O—N 3 -dATP, 3′-O—N 3 -dCTP, 3′-O—N 3 -dGTP, 3′-O—N 3 -dTTP
  • FIG. 34 (A) Staudinger reaction with TCEP to regenerate the 3′-OH group of the DNA extension product. (B) Staudinger reaction with TCEP to cleave the N 3 -fluorophore from the dideoxynucleotide.
  • FIG. 35 Four-color DNA sequencing by the hybrid SBS approach
  • FIG. 36 Four-color DNA sequencing by the hybrid SBS after template “walking”
  • FIG. 37 General Scheme for SBS with C—F-NRTs
  • FIG. 38 Structure of 3′-O—N 3 -dNTPs-N 3 -fluorophore
  • FIG. 39 Four-color DNA SBS with 3′-O—N 3 -dNTPs-N 3 -fluorophore.
  • FIG. 40 Template “Walking” Method 1 for SBS with C—F-NRTs
  • FIG. 41 Template “Walking” Method 2 for SBS with C—F-NRTs
  • FIG. 42 Template “Walking” Method 3 for SBS with C—F-NRTs
  • FIG. 43 Template “Walking” Method 4 for SBS with C—F-NRTs
  • FIG. 44 Template “Walking” Method 5 for SBS with C—F-NRTs
  • FIG. 45 “Walking” Strategy 2
  • FIG. 46 “Walking” Strategy 3
  • Nucleic acid shall mean any nucleic acid molecule, including, without limitation, DNA, RNA and hybrids thereof.
  • the nucleic acid bases that form nucleic acid molecules can be the bases A, C, G, T and U, as well as derivatives thereof. Derivatives of these bases are well known in the art, and are exemplified in PCR Systems, Reagents and Consumables (Perkin Elmer Catalogue 1996-1997, Roche Molecular Systems, Inc., Branchburg, N.J., USA).
  • Type of nucleotide refers to A, G, C, T or U.
  • Type of base refers to adenine, guanine, cytosine, uracil or thymine.
  • Mass tag shall mean a molecular entity of a predetermined size which is capable of being attached by a cleavable bond to another entity.
  • Solid substrate shall mean any suitable medium present in the solid phase to which a nucleic acid or an agent may be affixed.
  • Non-limiting examples include chips, beads and columns.
  • Hybridize shall mean the annealing of one single-stranded nucleic acid to another nucleic acid based on sequence complementarity.
  • the propensity for hybridization between nucleic acids depends on the temperature and ionic strength of their milieu, the length of the nucleic acids and the degree of complementarity. The effect of these parameters on hybridization is well known in the art (see Sambrook J, Fritsch E F, Maniatis T. 1989. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, New York.)
  • a composition having a first, second and third portion wherein the second portion has the following structure:
  • ⁇ represents a point of attachment to the first portion and ⁇ represents a point of attachment to the third portion.
  • ⁇ may be directly linked to the first portion, e.g. comprising a base, or bonded to the, for example base via, e.g. an alkynylene.
  • ⁇ may be directly linked to the third portion, e.g. a detectable marker, or bonded to the third portion, for example via another group.
  • the first portion is a deoxynucleotide or a dideoxynucleotide and the third portion is a detectable marker.
  • the detectable marker is a fluorescent dye.
  • the deoxynucleotide or dideoxynucleotide comprises a methylazido group attached to a 3′ atom thereof.
  • the dye in each structure is a fluorescent dye.
  • a method for determining the identity of each of a series of consecutive nucleotide residues in a nucleic acid comprising:
  • a method for determining the identity of each of a series of consecutive nucleotide residues in a self-priming nucleic acid comprising:
  • steps b) and c) can be performed simultaneously, or in the order step b) then step c) or in the order step c) then step b).
  • the nucleic acid is DNA and the nucleic acid polymerase is a 9°N thermopolymerase.
  • the cleavable chemical group is a methylazido group.
  • the four dNTP analogues have the following structures:
  • nucleic acid is immobilized on a solid surface.
  • solid surface is a chip or a bead.
  • a kit for use in sequencing a nucleic acid comprising:
  • An array comprising a nucleic acid attached to a solid surface, wherein the nucleic acid comprises an azidomethyl group attached to a 3′ atom thereof and a molecule having the structure:
  • ⁇ represents a point of attachment to a 3′ base of the nucleic acid and ⁇ represents a point of attachment to a detectable marker.
  • An array comprising a self-priming nucleic acid attached to a solid surface, wherein the nucleic acid comprises an azidomethyl group attached to a 3′ atom thereof and a molecule having the structure:
  • ⁇ represents a point of attachment to a 3′ base of the nucleic acid and ⁇ represents a point of attachment to a detectable marker.
  • the detectable marker is a fluorophore.
  • a method for increasing a read length of DNA sequencing by synthesis comprising (a) providing deoxynucleotide triphosphate analogues wherein the deoxynucleotide triphosphate analogues differ from deoxynucleotide triphosphates by having a methylazido group attached to a 3′ atom thereof and by having a detectable marker attached to a 1 nitrogen or a 9 nitrogen of a base thereof through a linker comprising the structure
  • ⁇ represents a point of attachment to a the base and ⁇ represents a point of attachment to the detectable marker
  • a method for determining the identity of each of a series of consecutive nucleotide residues in a nucleic acid comprising:
  • a method for determining the identity of each of a series of consecutive nucleotide residues in a self-priming nucleic acid comprising:
  • steps b) and c) can be performed simultaneously, or in the order step b) then step c) or in the order step c) then step b).
  • the nucleic acid is DNA and the nucleic acid polymerase is a 9°N thermopolymerase.
  • the cleavable chemical group is a methylazido group.
  • the four dNTP analogues have the following structures:
  • nucleic acid is immobilized on a solid surface.
  • solid surface is a chip or a bead.
  • a method for determining the identity of each of a series of consecutive nucleotide residues in a plurality of nucleic acids comprising, the same series of consecutive nucleotides comprising:
  • a method for determining the identity of consecutive nucleotide residues in a self-priming nucleic acid comprising:
  • steps b) and c) can be performed simultaneously, or in the order step b) then step c) or in the order step c) then step b).
  • the nucleic acid is DNA and the nucleic acid polymerase is a 9°N thermopolymerase.
  • the cleavable chemical group is a methylazido group.
  • the four ddNTP analogues have the following structures:
  • the four dNTPs have the following structures:
  • nucleic acid is immobilized on a solid surface.
  • solid surface is a chip or a bead.
  • a kit for use in sequencing a nucleic acid comprising:
  • An array comprising a nucleic acid attached to a solid surface, wherein the nucleic acid comprises an azidomethyl group attached to a 3′ atom thereof and a molecule having the structure:
  • ⁇ represents a point of attachment to a 3′ base of the nucleic acid and ⁇ represents a point of attachment to a detectable marker.
  • An array comprising a self-priming nucleic acid attached to a solid surface, wherein the nucleic acid comprises an azidomethyl group attached to a 3′ atom thereof and a molecule having the structure:
  • ⁇ represents a point of attachment to a 3′ base of the nucleic acid and ⁇ represents a point of attachment to a detectable marker.
  • the detectable marker is a fluorophore.
  • a method for increasing a read length of DNA sequencing by synthesis coupled with Sanger dideoxynucleotide terminating reaction (a) providing deoxynucleotide triphosphate analogues wherein the deoxynucleotide triphosphate analogues differ from deoxynucleotide triphosphates by having a methylazido group attached to a 3′ atom thereof and providing dideoxynucleotide triphosphate analogues wherein the dideoxynucleotide triphosphate analogues differ from dideoxynucleotide triphosphates by having a detectable marker attached to a 1 nitrogen or a 9 nitrogen of a base thereof through a linker comprising the structure
  • This invention provides the instant method, wherein the detectable bound to the base via a cleavable linker is a dye, a fluorophore, a chromophore, a combinatorial fluorescence energy transfer tag, a mass tag, or an electrophore.
  • a cleavable linker is a dye, a fluorophore, a chromophore, a combinatorial fluorescence energy transfer tag, a mass tag, or an electrophore.
  • Combinatorial fluorescence energy tags and methods for production thereof are disclosed in U.S. Pat. No. 6,627,748, which is hereby incorporated by reference.
  • This invention also provides the instant method, wherein the primer is a self-priming moiety.
  • This invention also provides the instant method, wherein the DNA is bound to a solid substrate.
  • This invention also provides the instant method, wherein the DNA is bound to the solid substrate via 1,3-dipolar azide-alkyne cycloaddition chemistry.
  • This invention also provides the instant method, wherein the DNA is bound to the solid substrate via a polyethylene glycol molecule.
  • This invention also provides the instant method, wherein the DNA is alkyne-labeled.
  • This invention also provides the instant method, wherein the DNA is bound to the solid substrate via a polyethylene glycol molecule and the solid substrate is azide-functionalized.
  • This invention also provides the instant method, wherein the DNA is immobilized on the solid substrate via an azido linkage, an alkynyl linkage, or biotin-streptavidin interaction. Immobilization of nucleic acids is described in Immobilization of DNA on Chips II, edited by Christine Wittmann (2005), Springer Verlag, Berlin, which is hereby incorporated by reference.
  • This invention also provides the instant methods, wherein the DNA is bound to the solid substrate via a polyethylene glycol molecule and the solid substrate is azide-functionalized or the DNA is immobilized on the solid substrate via an azido linkage, an alkynyl linkage, or biotin-streptavidin interaction.
  • the DNA or nucleic acid is attached/bound to the solid surface by covalent site-specific coupling chemistry compatible with DNA.
  • This invention also provides the instant method, wherein the solid substrate is in the form of a chip, a bead, a well, a capillary tube, a slide, a wafer, a filter, a fiber, a porous media, or a column.
  • the solid substrate is gold, quartz, silica, plastic, glass, nylon, diamond, silver, metal, or polypropylene.
  • This invention also provides the instant method, wherein the solid substrate is porous.
  • Chips or beads may be made from materials common for DNA microarrays, for example glass or nylon. Beads/micro-beads may be in turn immobilized to chips.
  • This invention also provides the instant method, wherein about 1000 or fewer copies of the DNA are bound to the solid substrate.
  • This invention also provides the instant invention wherein 2 ⁇ 10 7 , 1 ⁇ 10 7 , 1 ⁇ 10 6 or 1 ⁇ 10 4 or fewer copies of the DNA are bound to the solid substrate.
  • nucleotide analogues comprise one of the fluorophores Cy5, Bodipy-FL-510, ROX and R6G.
  • DNA polymerase is a 9°N polymerase or a variant thereof.
  • DNA polymerases which can be used in the instant invention include, for example E. Coli DNA polymerase I, Bacteriophage T4 DNA polymerase, SequenaseTM, Taq DNA polymerase and 9°N polymerase (exo-) A485L/Y409V.
  • RNA polymerases which can be used in the instant invention include, for example, Bacteriophage SP6, T7 and T3 RNA polymerases.
  • a method for determining the identity of each of a series of consecutive nucleotide residues in a nucleic acid comprising:
  • linker in each of step a) and j) independently each comprise the structure:
  • a linker is cleaved by contacting the linker with tris(2-carboxyethyl)phosphine.
  • one or more linkers are photocleavable or chemically cleavable.
  • one or more chemical groups are photocleavable or chemically cleavable.
  • R in the structures set forth in steps a) and or j) is independently chosen from a —N 3 group or an allyl group.
  • the cleavable chemical group in step g) is independently chosen from a —N 3 group or an allyl group.
  • a method for determining the identity of each of a series of consecutive nucleotide residues in a nucleic acid comprising:
  • the three types of dNTPs are chosen from the group dATP, dCTP, dGTP, dTTP or dITP.
  • linker in each of step a) and j) independently each comprise the structure:
  • a linker is cleaved by contacting the linker with tris(2-carboxyethyl)phosphine.
  • one or more linkers are photocleavable or chemically cleavable.
  • one or more chemical groups are photocleavable or chemically cleavable.
  • R in the structures set forth in steps a) and or j) is independently chosen from a —N 3 group or an allyl group.
  • the cleavable chemical group in step g) is independently chosen from a —N 3 group or an allyl group.
  • a method for determining the identity of each of a series of consecutive nucleotide residues in a nucleic acid comprising:
  • step g) the three types of dNTPs are chosen from the group dATP, dCTP, dGTP and dTTP.
  • linker in each of step a) and j) independently each comprise the structure:
  • a linker is cleaved by contacting the linker with tris(2-carboxyethyl)phosphine.
  • one or more linkers are photocleavable or chemically cleavable.
  • one or more chemical groups are photocleavable or chemically cleavable.
  • R in the structures set forth in steps a) and or j) is independently chosen from a —N 3 group or an allyl group.
  • the cleavable chemical group in step g) is independently chosen from the a —N 3 group or an allyl group.
  • the methods described herein can be applied mutatis mutandis to sequencing RNA using the appropriate ddNTPS or analogues thereof and dNTPS and analogues thereof.
  • base-pairing complementarity allows the sequence of the extended primer or of the target nucleic to be readily determined.
  • Hybridize is understood by those skilled in the art to mean to disassociate the hybridized primer (or extended strand thereof) from the target nucleic acid without destroying the target nucleic acid and thus permitting further hybridization of a second primer to the target nucleic acid.
  • Hybridization as used herein in one embodiment means stringent hybridization, for examples as described in Sambrook, J., Russell, D. W., (2000) Molecular Cloning: A Laboratory Manual: Third Edition.
  • Type of dNTP or ddNTP is used to distinguish dNTP or ddNTPs comprising different bases.
  • 3′-O-Allyl-dNTPs and 3′-O-photocleaveble linker(PC)-dNTPs have offered concrete evidence for their implementation in sequencing by synthesis (SBS), a new set of nucleotide analogs, modified with the small azido group (N 3 ), is investigated to seek potential improvement over the current system.
  • SBS sequencing by synthesis
  • N 3 small azido group
  • an azido group can be effectively converted into an amine with phosphine in DNA-friendly aqueous solution (35).
  • This efficient reduction is further enhanced through the utilization of Tris(2-Carboxyethyl) phosphine (TCEP), an odorless and stable agent often used to digest peptide disulfide bonds ( FIG. 1 ).
  • TCEP Tris(2-Carboxyethyl) phosphine
  • nucleotide Similar to allyl and nitrobenzyl alterations previously reported, two positions of the nucleotide need to be modified with the azido moiety to afford a set of 3′-O-Azido-dNTPs-Azido-Dye.
  • the small azido methyl group (—CH 2 —N 3 ) is used to cap the 3′ position of the sugar base while a novel azido linker connects unique fluorophores to the 5′ position of C/U and the 7′ position of A/G (see novel structures in FIG. 2 ).
  • TCEP reagent
  • Staudinger TCEP reduces the azido-methyl capping group to methylamine at the 3′ sugar base. Since the carbon of the methylamine is highly unstable due to its position between two electron-withdrawing elements (oxygen and nitrogen), the methylamine is hydrolyzed in the presence of water that recovers the hydroxyl group at the 3′ position. For the azido linker, the same Straudinger reduction takes place. However immediately after the attachment of TCEP to azido, the intermediate attacks the ester bond to afford total cleavage of the fluorophore ( FIG. 3 ).
  • an alternative approach is to attach the fluorophore via a PC (nitrobenzyl) linker while conserving the 3′ capping with the azido methyl group (3′-O-Azido-dNTPs-PC-Dye, FIG. 4 ) and cleaving the azido again using TCEP.
  • extension and detection steps for this set of nucleotides are analogous to those for 3′-O-Azido-dNTPs-Azido-Dye.
  • An additional photolysis procedure is involved during the deprotection step. This dual cleavage process might offer different advantages for removing the fluorophore than the Staudinger reduction.
  • nucleotides modified as reversible terminators by capping the 3′-OH with a small reversible moiety so that they are still recognized as substrates by DNA polymerase, are used in combination with a small percentage of four cleavable fluorescent dideoxynucleotides to perform SBS.
  • DNA sequences are determined by the unique fluorescence emission of each fluorophore on the DNA products terminated by ddNTPs.
  • the polymerase reaction reinitiates to continue the sequence determination ( FIG. 5 ).
  • primer resetting The fundamental rationale behind primer resetting is to regenerate the original primer site or to insert two or more primer sites of known sequences into the target DNA so SBS can be carried out at each site sequentially.
  • three steps are involved with this approach: 1) annealing of the first primer, 2) performing SBS, 3) denaturing the sequenced section of the template to recover a single-stranded DNA for the second primer annealing. These steps are carried out repeatedly until the target DNA is sequenced in its entirety.
  • the advantage of primer resetting lies in its ability to restore all the templates after the denaturation step, including those that are terminated with ddNTPs, so the next cycle of SBS can restart with potentially the same amount of sequenceable DNA as the previous round.
  • the DNA sequence is reset by reattaching the original primer, extending the chain with natural or minimally modified nucleotides to the end of the first round sequence, and then sequencing from that point.
  • the second strategy relies on annealing of a second round primer that is longer than the first, containing at its 5′ end the same sequence as the original primer, followed by a run of 20 universal nucleotides such as inosine, from which the second round of sequencing can be primed.
  • the two chemically cleavable fluorescent nucleotide analogs were used in an SBS reaction to identify the sequence of a self-primed DNA template (130 base pairs) immobilized on a solid surface.
  • a reaction mixture of 3′-O-Azido-dCTP-Azido-BodipyFL, 3′-O-Azido-dUTP-Azido-R6G, 3′-O-Azido-dATP, and 3′-O-Azido-dGTP were prepared for the incorporation.
  • a synchronization step was performed with the full set of 3′-O-Azido-dNTPs after incorporation to extend any remaining priming strand.
  • sequencing by synthesis of DNA templates attached on solid surface will be carried out.
  • the goal will be the achievement of maximum base read length of each template with high consistency.
  • 3′-O-azidomethyl-modified NRTs (3′-O—N 3 -dNTPs) ( FIG. 6 ) were synthesized and evaluated for the hybrid SBS.
  • the 3′-O-azidomethyl group on the DNA extension product generated by incorporating each of the NRTs was efficiently removed by the Staudinger reaction by using aqueous Tris(2-carboxyethyl) phosphine (TCEP) solution (36,37) followed by hydrolysis to yield a free 3′-OH group for elongating the DNA chain in subsequent cycles of the hybrid SBS ( FIG. 13A ).
  • TCEP Tris(2-carboxyethyl) phosphine
  • ddNTP-N 3 -fluorophores four cleavable fluorescent dideoxynucleotides ddNTP-N 3 -fluorophores (ddCTP-N 3 -Bodipy-FL-510, ddUTP-N 3 -R6G, ddATP-N 3 -ROX, and ddGTP-N 3 -Cy5) were synthesized ( FIGS. 14-22 ). The ddNTP-N 3 -fluorophores would be combined with the 4 NRTs ( FIG. 6 ) to perform the hybrid SBS.
  • Modified DNA polymerases have been shown to be highly tolerant to nucleotide modifications with bulky groups at the 5 position of pyrimidines (C and U) and the 7 position of purines (A and G) (27).
  • C and U pyrimidines
  • a and G purines
  • a unique fluorophore was attached to the 5 position of C/U and the 7 position of A/G through a cleavable linker, which is also based on an azido-modified moiety (37) as a trigger for cleavage, a mechanism that is similar to the removal of the 5′-O-azidomethyl group ( FIG. 13B ).
  • the ddNTP-N 3 -fluorophores are found to efficiently incorporate into the growing DNA strand to terminate DNA synthesis for sequence determination.
  • the fluorophore on a DNA extension product which is generated by incorporation of the cleavable fluorescent ddNTPs, is removed rapidly and quantitatively by TCEP from the DNA extension
  • the MALDI-TOF MS spectrum consist of a distinct peak corresponding to the DNA extension product 5′-primer-C—N 3 3′ (m/z 8,310), which confirms that the NRT can be incorporated base-specifically by DNA polymerase into a growing DNA strand.
  • FIG. 19(B) shows the cleavage result on the DNA extension product. The extended DNA mass peak at m/z 8,310 completely disappeared, whereas the peak corresponding to the cleavage product 5′-primer-C-3′ appears as the sole dominant peak at m/z 8,255, which establishes that TCEP incubation completely cleaves the 3′-O-azidomethyl group with high efficiency.
  • the next extension reaction was carried out by using this cleaved product, which now has a free 3′-OH group, as a primer to yield a second extension product, 5′-primer-CGN 3 -3′ (m/z 8,639; FIG. 19C ).
  • the extension product was cleaved to generate product for further MS analysis yielding a single peak at m/z 8,584 ( FIG. 19(D) ).
  • FIGS. 20 A, C, E, and G Single clear mass peaks at 9,180, 8,915, 9,317, and 9,082 (m/z) corresponding to each primer extension product with no leftover starting materials were produced by using ddNTP-N 3 -fluorophores.
  • FIGS. 20 A, C, E, and G Brief incubation of the DNA extension products in an aqueous TCEP solution led to the cleavage of the linker tethering the fluorophore to the dideoxynucleotide.
  • FIGS. 20 B, D, F, and H shows the cleavage results for the DNA products extended with ddNTP-N 3 -fluorophores.
  • the identity of the incorporated nucleotide is determined by the unique fluorescent emission from the four fluorescent dideoxynucleotide terminators, while the role of the 3′-O-modified NRTs is to further extend the DNA strand to continue the determination of the DNA sequence. Therefore, the ratio between the amount of ddNTP-N 3 -fluorophores and 3′-O—N 3 -dNTPs during the polymerase reaction determines how much of the ddNTP-N 3 -fluorophores incorporate and thus the corresponding fluorescent emission strength.
  • De novo sequencing reaction on the chip was initiated by extending the self-priming DNA by using a solution consisting of four 3′-O—N 3 -dNTPs and four ddNTP-N 3 -fluorophores, and 9°N DNA polymerase.
  • the hybrid SBS allows for the addition of all eight, nucleotide substrates simultaneously to unambiguously determine DNA sequences. This reduces the number of steps needed to complete the sequencing cycle, while increasing the sequencing accuracy because of competition among the substrates in the polymerase reaction.
  • the DNA products extended by ddNTP-N 3 -fluorophores, after fluorescence detection for sequence determination and cleavage, are no longer involved in the subsequent polymerase reaction cycles because they are permanently terminated.
  • a synchronization step was added to reduce the amount of unextended priming strands after the initial extension reaction shown in the scheme of FIG. 21A .
  • a synchronization reaction mixture consisting of just the four 3′-O—N 3 -dNTPs in relatively high concentration was used along with the 9°N DNA polymerase to extend, any remaining priming strands that retain a free 3′-OH group to synchronize the incorporation.
  • FIG. 21B The four-color images from a fluorescence scanner for each step of the hybrid SBS on a chip is shown in FIG. 21B .
  • the surface was immersed in a TCEP solution to cleave both the fluorophore from the DNA product extended with ddNTP-N 3 -fluorophores and the 3′-O-azidomethyl group from the DNA product extended with 3′-O—N 3 -dNTPs.
  • walking The fundamental rationale behind this template “walking” strategy is the removal of the sequenced strand and reattaching of the original primer to allow the extension, or walking, of the template with a combination of natural and modified nucleotides to the end of the first round sequence so that SBS can be carried out from that point. Since the original sequenced strand is stripped away, including those terminated with ddNTPs, all the templates become available for “walking”. Given that “walking” is carried out with either natural or 3′-modified nucleotides, the subsequent round of SBS is performed on nascent DNA strands for maximum read length.
  • the advantage of template “walking” is its ability to restore all the templates after the denature step, includes those that are terminated with ddNTPs, so the next cycle of SBS can restart with potentially the same amount of nascent DNA as the previous round.
  • the “walking” methodology is applicable to both hybrid SBS and SBS with C—F-NRTs, and has the potential to dramatically increase the read lengths of these SBS technologies ( FIG. 23 ).
  • DNA sequencing by synthesis offers a paradigm to efficiently decipher multiple DNA sequences in parallel.
  • Hybrid SBS is a hybrid DNA sequencing method between the Sanger dideoxy chain terminating reaction and SBS.
  • four nucleotides FIG. 24
  • four nucleotides FIG. 24
  • FIG. 25 a small percentage of four cleavable fluorescent dideoxynucleotides
  • Sequences are determined by the unique fluorescence emission of each fluorophore on the DNA products terminated by ddNTPs, while the role of the 3′-O-modified dNTPs is to further extend the DNA strand to continue the determination of the DNA sequence.
  • the polymerase reaction Upon removing the 3′-OH capping group from the DNA products generated by incorporating the 3′-O-modified dNTPs and the fluorophore from the DNA products terminated with the ddNTPs, the polymerase reaction reinitiates to continue the sequence determination ( FIG. 26 ).
  • the second stage of SBS is conducted using mixture of nucleotide reversible terminators and fluorescently labeled dideoxynucleotides as incorporation substrates same as described above. Another cluster of bases on the template can be continuously revealed, leading to the doubling of the original read length.
  • the SBS-walking-SBS process is repeated to generate maximum read length.
  • 3′-O-azidomethyl-modified NRTs (3′-O—N 3 -dNTPs) were synthesized and evaluated ( FIG. 32 ) for use in the hybrid SBS approach.
  • the 3′-O-modified NRTs containing an azidomethyl group to cap the 3′-OH on the sugar ring were synthesized based on similar method to that reported by Zavgorodny et al.
  • the 3′-O-azidomethyl group on the DNA extension product generated by incorporating each of the NRTs is efficiently removed by the Staudinger reaction using aqueous Tris(2-carboxy-ethyl) phosphine (TCEP) solution followed by hydrolysis to yield a free 3′-OH group for elongating the DNA chain in subsequent cycles of the hybrid SBS ( FIG. 34A ).
  • TCEP Tris(2-carboxy-ethyl) phosphine
  • ddNTP-N 3 -Fluorophores ddCTP-N 3 -Bodipy-FL-510, ddUTP-N 3 -R6G, ddATP-N 3 -ROX and ddGTP-N 3 -Cy5 ( FIG. 33 ).
  • the ddNTP-N 3 -Fluorophore were used in combination with the four NRTs ( FIG. 32 ) to perform the hybrid SBS.
  • Modified DNA polymerases have been shown to be highly tolerant to nucleotide modifications with bulky groups at the 5-position of pyrimidines (C and U) and the 7-position of purines (A and G). Thus, a each unique fluorophore was attached to the 5 position of C/U and the 7 position of A/G through a cleavable linker.
  • the cleavable linker is also based on an azido modified moiety as a trigger for cleavage, a mechanism that is similar to the removal of the 3′-O-azidomethyl group ( FIG. 34B ).
  • Hybrid SBS was performed on a chip-immobilized DNA template using the 3′-O—N 3 -dNTP/ddNTP-N 3 -fluorophore combination and the results are shown in FIG. 35 .
  • the general four-color sequencing reaction scheme on a chip is shown in FIG. 35A .
  • the de novo sequencing reaction on the chip was initiated by extending the self-priming DNA using a solution containing the combination of the four 3′-O—N 3 -dNTPs and the four ddNTP-N 3 -fluorophores, and 9°N DNA polymerase.
  • the four-color images from a fluorescence scanner for each step of the hybrid SBS on a chip is shown in FIG. 35B .
  • the entire process of incorporation, synchronization, detection and cleavage was performed multiple times to identify 32 successive bases in the DNA template.
  • the plot of the fluorescence intensity vs. the progress of sequencing extension (raw 4-color sequencing data) is shown in FIG. 35C .
  • the DNA sequences were unambiguously identified with no errors from the 4-color raw fluorescence data without any processing.
  • the same self-priming DNA was immobilized on surface as template.
  • the primer was reset for the second round SBS by elongating the original primer over the sequenced region via enzymatic incorporations.
  • 9°N DNA polymerase incorporates 3′ unblocked nucleotides more efficiently, leading to certain percentage of primers not fully extended by 3′-O—N 3 -dGTP. To minimize this effect, a synchronization step was added to reduce the amount of out-of-phase primers after the initial extension reaction.
  • a synchronization reaction mixture consisting of just 3′-O—N 3 -dGTP in relative high concentration was used along with the 9°N DNA polymerase.
  • the 3′-O-azidomethyl group on the DNA extension product generated by incorporating 3′-O—N 3 -dGTP was efficiently removed by using aqueous Tris(2-carboxy-ethyl) phosphine (TCEP) solution to yield a free 3′-OH group for elongating the DNA chain in subsequent cycles of enzymatic incorporation.
  • TCEP Tris(2-carboxy-ethyl) phosphine
  • the second stage of SBS was conducted using mixture of nucleotide reversible terminators and fluorescently labeled dideoxynucleotides as incorporation substrates same as described above. Another 13 bases were successfully identified after template “walking” ( FIG. 14 ).
  • DNA sequencing by synthesis offers a paradigm to efficiently decipher multiple DNA sequences in parallel.
  • SBS DNA sequencing by synthesis
  • C—F-NRTs modified cleavable fluorescent nucleotide reversible terminators
  • C-NRTs 3′-O—R 1 -dNTPs-R 2 -fluorophore
  • a set of four C—F-NRTs is produced via dual modifications by capping the 3′-OH group with a small chemical moiety and tethering a fluorophore through a cleavable linker to either the 7-position of the purines (A, G) or the 5-position of the pyrimidines (C, T) so that they are still recognized as substrates by DNA polymerase.
  • Another set of four C-NRTs is modified similarly as the C—F-NRTs except no fluorophore is attached, which results in a reduction of the size of C-NRTs and the increment of DNA polymerase incorporation efficiency.
  • an extension mixture composed of the C-NRTs with a small percentage of the C—F-NRTs is used to perform SBS. Sequences are determined by the unique fluorescence emission of each fluorophore on the DNA products terminated by the C—F-NRTs. Immediately following the detection step, a synchronization reaction is performed using only the C-NRTs to extend the un-extended DNA strands. A dideoxynucleotides (ddNTPs) capping step is carried out afterwards to completely rid of the remaining un-extended DNA.
  • ddNTPs dideoxynucleotides
  • the polymerase reaction Upon removing the 3′-OH capping group from the DNA products generated by incorporating both C—F-NRTs and C-NRTs and the fluorophore from the C—F-NRTs, the polymerase reaction reinitiates to continue the sequence determination.
  • the following scheme ( FIG. 37 ) illustrates the general process for SBS with C—F-NRTs.
  • the azidomethyl capping moiety on the 3′-OH and the fluorophore attached to the DNA extension product via the azido-based cleavable linker are efficiently removed using tris(2-carboxyethyl)phosphine (TCEP) in aqueous solution compatible with DNA.
  • TCEP tris(2-carboxyethyl)phosphine
  • DNA templates are denatured by heat or mild alkali conditions to rid of the extended primer.
  • the same original primer is re-hybridized to the template chain, and one of the five “walking” methods described in the previous section can be applied to reset the start point for the next round of SBS at the end of the first sequencing run ( FIGS. 40 , 41 , 42 , 43 , and 44 ).
  • the primer is extended to the end of the previous round of SBS.
  • hybrid SBS is carried out to identify the subsequent bases. If the process can be repeated more times, it should be theoretically possible to achieve long and significant read length.
  • the reset is achieved not with nucleotide walking, but with the use of a longer primer partially consisting of universal nucleotides for the second round. Attachment of the template DNA to the surface and the first few steps of the procedure are identical to the first method. However, after stripping the first extended primer for the initial 20 base readout, a long primer with the following features will be hybridized to the template: (a) the first half is identical to the initial primer; (b) the second half is composed almost entirely of universal bases.
  • the universal base is inosine, which, in its deoxynucleoside form, can base pair with all four nucleotides, though its affinity for C and A is significantly higher than for G and T; a second possibility is 5-nitroindole; (c) the last one or two anchoring bases of the long primers are degenerate with each of the four possible bases being represented. Because the universal bases can form hydrogen bonds with any of the other four bases with some efficiency, they have the capacity to bind to the first 20 or so bases of the sequence. However, the melting temperature of the ensuing hybridization is reduced substantially by the run of inosines, a few of the bases in the first half and the two 3′-anchoring bases can be substituted with locked nucleotides.
  • Locked nucleic acids have a chemical bond between the 2′ and 4′ carbons of the ribose. While slower to associate with their complementary base, once hybridized, they tend not to dissociate. Thus, they provide a nice solution to ensure that the long primer remains attached appropriately to the template. In addition, the percentage of locked nucleosides in the primer can be manipulated to achieve higher hybridization strength. After hybridization of the above long primer, a second round of either Hybrid SBS or SBS with C—F—NRTs can be performed ( FIG. 45 ).
  • an alternative approach to Strategy 2 is the use of a detachable loop primer, possibly with a labile sugar and glycosylase treatment.
  • the loop is removed by enzymatic cleavage and denaturation, and then a new identical loop is attached.
  • the new loop primer can be composed of an initial portion identical to the first loop primer, a “loop out” region that bypasses the first set of sequenced nucleotides, and a degenerate anchoring nucleotide to initiate the second round of sequencing.
  • one or two additional primer annealing sites are introduced into the DNA to be sequenced at a distance just about equal to the number of bases that can be sequenced from the first primer.
  • template preparation for SBS will utilize the cloning of genomic DNA into a specially designed vector containing type IIS or III restriction sites (MmeI and EcoP15 I) flanking the genomic DNA cloning site.
  • size fractionated DNA minimum length 100 bp
  • the resulting recombinant plasmids will be re-cut at one of the type IIS/III sites and the sticky ends will be filled in with Klenow enzyme.
  • specific sequencing primers will be introduced via ligation inside the genomic DNA inserts, 22 bases distant from the first primer in the case of MmeI or 27 bases away in the case of EcoP15 I.
  • the constructs After insertion of the internal priming sites, the constructs will be re-cloned in E. coli , the recombinant plasmids isolated and the inserts re-amplified by PCR at vector-insert junctions and attached to the beads for sequencing.
  • emulsion or polony PCR strategies can be used to accomplish attachment of single molecules to individual beads or slide locations and their subsequent amplification at a much lower cost than cloning.
  • the first round of Hybrid SBS or SBS with C—F-NRTs will be primed from the flanking primer, then after stripping these extended primers, the second set of sequencing reactions will be initiated at the internal primer. It should be noted that with this scheme, the two sequenced portions come from opposite ends of the initial DNA, and are in essence paired end reads.
  • the extra cycles would enable some of the sequence reads to run into the next primer, which would help to confirm the direction (e.g., the last sequence might end with the MmeI or EcoP15I site.
  • Other tricks would include modifying the ends of the primers to allow looping and reverse direction sequencing, incorporation of one or two decoding bases in the internal primers to confirm directions, and deconvoluting the results after all the data is generated.
  • the four NRTs (3′-O—N 3 -dATP, 3′-O—N 3 -dCTP, 3′-O—N 3 -dGTP and 3′-O—N 3 -dTTP) have been characterized, by performing four continuous DNA-extension reactions sequentially using a self-priming DNA template (5′-ATCGGCGCCGCGCCTTGGCGCGGCGC-3′ (SEQ ID No:1).
  • the four nucleotides in the template immediately adjacent to the annealing site of the primer are 3′-GCTA-5′, which allows the evaluation of the incorporation and cleavage efficiency of the 4 NRTs.
  • a polymerase extension reaction using a pool of all four NRTs along with the self-priming DNA template was performed producing a single base extension product.
  • the reaction mixture for this, and all subsequent extension reactions consisted of 80 pmol of self-priming DNA template, 160 pmol of 3′-O—N 3 -dNTPs, 1 ⁇ Thermopol II reaction buffer (New England Biolabs), 40 nmol of MnCl 2 and 1 unit of 9°N DNA polymerase (exo-) A485L/Y409V (New England Biolabs) in a total reaction volume of 20 ⁇ l.
  • the reaction consisted of incubation at 94° C. for 5 min, 4° C. for 5 min, and 65° C. for 20 min.
  • extension product was desalted by using a ZipTip and analyzed by Voyager DE MALDI-TOF mass spectrometry (Applied Biosystems).
  • the desalted DNA extension product bearing the 3′-O-azidomethyl group was first resuspended with 5 ⁇ l of 50 mM EDTA solution to quench the polymerase activity.
  • This DNA solution was then mixed with 10 ⁇ l of 225 mM TCEP solution (pH 9.0) and incubated at 65° C. for 15 min to yield a cleaved DNA product which was characterized by MALDI-TOF MS.
  • the DNA product with the 3′-O-azidomethyl group removed to generate a free 3′-OH group was purified by using an Oligonucleotide Purification Cartridge (Applied Biosystems) and used as a primer for a second extension reaction using 3′-O—N 3 -dNTPs.
  • the second extended DNA product was then purified by ZipTip and cleaved as described above.
  • the third and the fourth extensions were carried out in a similar manner by using the previously extended and cleaved product as the primer.
  • ddNTP-N3-fluorophores ddCTP-N3-Bodipy-FL-510, ddUTP-N3-R6G, ddATP-N3-ROX, and ddGTP-N3-Cy5
  • ddNTP-N3-fluorophores ddCTP-N3-Bodipy-FL-510, ddUTP-N3-R6G, ddATP-N3-ROX, and ddGTP-N3-Cy5
  • Each of the extension reactions consisted of all four ddNTP-N 3 -fluorophores (e.g., 120 pmol each of ddCTP-N 3 -Bodipy-FL-510, ddUTP-N 3 -R6G, ddATP-N 3 -ROX, and ddGTP-N 3 -Cy5) along with 60 pmol of the self-priming DNA template, 1 ⁇ Thermopol II reaction buffer, 40 nmol of MnCl 2 and 1 unit of 9°N DNA polymerase (exo-) A485L/Y4Q9V in a total reaction volume of 20 ⁇ l.
  • the reaction consisted of incubations at 94° C. for 5 min, 4° C.
  • the extension product was purified by reverse-phase HPLC using established procedures (40). The fraction containing the desired product was collected and freeze-dried for analysis by MALDI-TOF MS and cleavage.
  • the purified DNA product was resuspended in 50 ml of 100 mM TCEP solution (pH 9.0) at 65° C. for 15 min and then analyzed by MALDI-TOF MS.
  • the nucleotide complementary to the DNA template was allowed to incorporate into the primer at 62° C. for 15 min.
  • an extension solution consisting of 38 pmol each of 3′-O—N 3 -dTTP, 3′-O—N 3 -dATP, 3′-O—N 3 -dGTP and 75 pmol of 3′-O—N 3 -dCTP, 1 unit of 9°N mutant DNA polymerase(exo-) A485L/Y409V, 20 nmol of MnCl 2 and 1 ⁇ Thermopol II reaction buffer was added to the same spot and incubated at 62° C. for 15 min.
  • the chip After washing with SPSC buffer containing 0.1% Tween 20 for 1 min, the chip was rinsed with dH 2 O, and then scanned with a 4-color fluorescence ScanArray Express scanner (Perkin-Elmer Life Sciences) to detect the fluorescence signal. To perform the cleavage, the DNA chip was placed inside a chamber filled with 100 mM TCEP (pH 9.0) and incubated at 65° C. for 10 min. After washing the surface with dH 2 O, the chip was scanned again to measure the background fluorescence signal.
  • TCEP pH 9.0
  • the 5′-amino-labeled self-priming DNA template 5′-NH 2 -CAC-TCA-CAT-ATG-TTT-TTT-AGC-TTT-TTT-AAT-TTC-TTA-ATG-ATG-TTG-TTG-CAT-GCG-ACT-TAA-GGC-GCT-TGC-GCC-TTA-AGT-CG-3′ (SEQ ID No:6) was purchased from IDT (Coralville, Iowa).
  • the DNA template was dissolved at 40 ⁇ M in 50 mM sodium phosphate buffer, pH 8.5 and spotted using SpotArray 72 arraying robot (Perkin Elmer) onto high density CodeLink microarray slides (GE Healthcare).
  • the slides were incubated at ambient temperature ( ⁇ 24° C.) for 20 hours in a humid chamber containing saturated sodium chloride solution ( ⁇ 75% humidity) to allow for 5′-tethering of the spotted amino-modified DNA templates to the slide surface functionalized with succinimide ester groups.
  • the slides were removed from the humid chamber and stored in vacuum desiccator at room temperature until further use.
  • the principal advantage of the hairpin structure introduced into the 3′-portion of the self-priming DNA template is its higher stability and the increased priming efficiency for DNA polymerases as compared to a separate primer/template complex, which is prone to spontaneous dissociation.
  • the SBS cycle was repeated multiple times using the combination mixture of solution A consisting of 3′-O—N 3 -dCTP (3 ⁇ M), 3′- ⁇ -N 3 -dTTP (3 ⁇ M), 3′-O—N 3 -dATP (3 ⁇ M) and 3′-O—N 3 -dGTP (0.5 ⁇ M) and solution B consisting of ddCTP-N 3 -Bodipy-FL-510 (50 nM), ddUTP-N 3 -R6G (100 nM), ddATP-N 3 -ROX (200 nM) and ddGTP-N 3 -Cy5 (100 nM) in each polymerase extension reaction.
  • solution A and B in each SBS cycle were used to achieve relatively even fluorescence signals.
  • 3′-O-modified cleavable reversible terminator nucleotides (3′-O—N 3 -dNTPs) along with four fluorescent ddNTPs have been synthesized and characterized, and used them to produce 4-color de novo DNA sequencing data on a chip by Sanger/SBS hybrid sequencing approach that has the following advantages.
  • 3′-O—N 3 -dNTPs After cleavage of the 3′OH capping group of the DNA extension product, there are no traces of modification left on the growing DNA strand. Therefore, there are no adverse effects on the DNA polymerase for incorporation of the next complementary nucleotide.
  • the cleavable fluorescent ddNTPs and 3′-O—N 3 -dNTPs permanent and reversible terminators, respectively, which allow the interrogation of each base in a serial manner, a key procedure enabling accurate determination of homopolymeric regions of DNA.
  • all of the steps of the nucleotide incorporation, fluorescence detection for sequence determination, cleavage of the fluorophore, and the 3′-O-azidomethyl group are performed on a DNA chip, there is no longer a need for electrophoretic DNA fragment separation as in the classical Sanger sequencing method.
  • the identity of the incorporated nucleotide is determined by the unique fluorescence emission from the four fluorescent dideoxynucleotides, whereas the role of the 3′-O-modified NRTs is to further extend the DNA strand. Therefore, the ratio of the ddNTP-N 3 -fluorophores and 3′-O—N 3 -dNTPs during the polymerase reaction determines how much of the ddNTP-N 3 -fluorophores incorporate and, thus, the corresponding fluorescence emission strength.
  • the majority of the priming strands should be extended with 3′-O—N 3 -dNTPs, whereas a relatively smaller amount should be extended with ddNTP-N 3 -fluorophores to produce sufficient fluorescent signals that are above the fluorescence detection system's sensitivity threshold for sequence determination.
  • the amount of the ddNTP-N 3 -fluorophores needs to be gradually increased to maintain the fluorescence emission strength for detection.
  • the signal strength at base 32 is as strong as that of the first base ( FIG. 21C ), indicating it should be possible to increase the read length of the hybrid SBS further by optimizing the extension conditions to reduce the background fluorescence in the later sequencing cycles.
  • the ultimate read length of this hybrid SBS system depends on three factors: the number of starting DNA molecules on each spot of a DNA chip, the reaction efficiency, and the detection sensitivity of the system.
  • the read length with the Sanger sequencing method commonly reaches >700 bp.
  • the hybrid SBS approach described here may have the potential to reach this read length, especially with improvements in the sensitivity of the fluorescent detection system, where single molecules can be reliably detected.
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