Four-color DNA sequencing with 3′-O-modified nucleotide reversible terminators and chemically cleavable fluorescent dideoxynucleotides

Proceedings of the National Academy of Sciences of the United States of America

Volumn 105, Issue 27, 2008, Pages 9145-9150

  Guo, Jia ^a,b,c   Xu, Ning ^a   Li, Zengmin ^a,b   Zhang, Shenglong ^a,b,c   Wu, Jian ^a,b,c   Dae, Hyun Kim ^a   Mong, Sano Marma ^a,b   Meng, Qinglin ^a,b,c   Cao, Huanyan ^a   Li, Xiaoxu ^a,b   Shi, Shundi ^a   Yu, Lin ^a   Kalachikov, Sergey ^a   Russo, James J ^a   Turro, Nicholas J ^b,c   Ju, Jingyue ^a,b  

^a Columbia University College of Physicians and Surgeons ^*  (United States)

^b Columbia University ^*  (United States)

^c Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

DNA chip; Sequencing by synthesis

Indexed keywords

AZIDE; DEOXYRIBONUCLEOTIDE; DIDEOXYNUCLEOTIDE; DNA POLYMERASE; TRIS(2 CARBOXYETHYL)PHOSPHINE;

ARTICLE; DNA SEQUENCE; DNA STRUCTURE; DNA SYNTHESIS; FLUORESCENCE; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; PRIORITY JOURNAL;

BASE SEQUENCE; COLOR; DIDEOXYNUCLEOTIDES; DNA-DIRECTED DNA POLYMERASE; FLUORESCENT DYES; MOLECULAR SEQUENCE DATA; SEQUENCE ANALYSIS, DNA; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 48249132489     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0804023105     Document Type: Article

References (34)

1. Lander ES, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409:860-921.
2. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:5463-5467.
3. Smith LM, et al. (1986) Fluorescence detection in automated DNA sequence analysis. Nature 321:674-679.
4. Prober JM, et al. (1987) A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides. Science 238:336-341.
5. Ju J, Ruan C, Fuller CW, Glazer AN, Mathies RA (1995)Fluorescence energy transfer dye-labeled primers for DNA sequencing and analysis. Proc Natl Acad Sci USA 92:4347-4351.
6. Blazej RG, Kumaresan P, Mathies RA (2006) Microfabricated bioprocessor for integrated nanoliter-scale Sanger DNA sequencing. Proc Natl Acad Sci USA 103:7240-7245.
7. Drmanac S, et al. (1998) Accurate sequencing by hybridization for DNA diagnostics and individual genomics. Nat Biotechnol 16:54-58.
8. Fu DJ, et al. (1998) Sequencing exons 5 to 8 of the p53 gene by MALDI-TOF mass spectrometry. Nat Biotechnol 16:381-384.
9. Edwards JR, Itagaki Y, Ju J (2001) DNA sequencing using biotinylated dideoxynucleotides and mass spectrometry. Nucleic Acids Res 29:E104.
10. Kasianowicz JJ, Brandin E, Branton D, Deamer DW (1996) Characterization of individual polynucleotide molecules using a membrane channel. Proc Natl Acad Sci USA 93:13770-13773.
11. Shendure J, et al. (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309:1728-1732.
12. Ronaghi M, Uhlen M, Nyrén P (1998) A sequencing method based on real-time pyrophosphate. Science 281:363-365.
13. Harris TD, et al. (2008) Single-molecule DNA sequencing of a viral genome. Science 320:106-109.
14. Greenleaf WJ, Block SM (2006) Single-molecule, motion-based DNA sequencing using RNA polymerase. Science 313:801.
15. Mitra RD, Shendure J, Olejnik J, Olejnik EK, Church GM (2003) Fluorescent in situ sequencing on polymerase colonies. Anal Biochem 320:55-65.
16. Ju J, Li Z, Edwards J, Itagaki Y (2003) Massive parallel method for decoding DNA and RNA. US Patent 6,664,079.
17. Li Z, et al. (2003) A photocleavable fluorescent nucleotide for DNA sequencing and analysis. Proc Natl Acad Sci USA 100:414-419.
18. Ruparel H, et al. (2005) Design and synthesis of a 3′-O-allyl photocleavable fluorescent nucleotide as a reversible terminator for DNA sequencing by synthesis. Proc Natl Acad Sci USA 102:5932-5937.
19. Seo TS, et al. (2005) Four-color DNA sequencing by synthesis on a chip using photocleavable fluorescent nucleotides. Proc Natl Acad Sci USA 102:5926-5931.
20. Ju J, et al. (2006) Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators. Proc Natl Acad Sci USA 103:19635-19640.
21. Mikkelsen TS, et al. (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448:553-560.
22. Johnson DS, Mortazavi A, Myers RM, Wold B (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316:1497-1502.
23. Barski A, et al. (2007) High-resolution profiling of histone methylations in the human genome. Cell 129:823-837.
24. Wu J, et al. (2007) 3′-O-modified nucleotides as reversible terminators for pyrosequencing. Proc Natl Acad Sci USA 104:16462-16467.
25. Zavgorodny S, et al. (1991) 1-Alkylthioalkylation of nucleoside hydroxyl functions and its synthetic applications: A new versatile method in nucleoside chemistry. Tetrahedron Lett 32:7593-7596.
26. Zavgorodny S, Pechenov AE, Shvets VI, Miroshnikov AI (2000) S,X-acetals in nucleoside chemistry. III. Synthesis of 2′-and 3′-O- azidomethyl derivatives of ribonucleosides. Nucleosides, Nucleotides Nucleic Acids 19:1977-1991.
27. Barnes C, Balasubramanian S, Liu X, Swerdlow H, Milton J (2006) Labelled nucleotides. US Patent 7,057,026.
28. Saxon E, Bertozzi CR (2000) Cell surface engineering by a modified Staudinger reaction. Science 287:2007-2010.
29. Milton J, Ruediger S, Liu X (2006) Nucleosides/nucleotides conjugated to labels via cleavable linkages and their use in nucleic acid sequencing. US Patent Appl US20060160081A1.
30. Rosenblum BB, et al. (1997) New dye-labeled terminators for improved DNA sequencing patterns. Nucleic Acids Res 25:4500-4504.
31. Wu W, et al. (2007) Termination of DNA synthesis by N6-alkylated, not 3′-O-alkylated, photocleavable 2′-deoxyadenosine triphosphates. Nucleic Acids Res 35:6339-6349.
32. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW (1995) Serial analysis of gene expression. Science 270:484-487.
33. Kim JB, et al. (2007) Polony multiplex analysis of gene expression (PMAGE) in mouse hypertrophic cardiomyopathy. Science 316:1481-1484.
34. Margulies M, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376-380.