What happens when a dideoxynucleotide gets added to a DNA molecule during a DNA sequencing reaction?

1. Smith L.M., Sanders,J.Z., Kaiser,R.J., Hughes,P., Dodd,C., Connell,C.R., Heiner,C., Kent,S.B.H. and Hood,L.E. (1986) Fluorescence detection in automated DNA sequencing analysis. Nature, 321, 674–679. [PubMed] [Google Scholar]

2. Ju J., Ruan,C., Fuller,C.W., Glazer,A.N. and Mathies,R.A. (1995) Energy transfer fluorescent dye-labeled primers for DNA sequencing and analysis. Proc. Natl Acad. Sci. USA, 92, 4347–4351. [PMC free article] [PubMed] [Google Scholar]

3. Ju J., Glazer,A.N. and Mathies,R.A. (1996) Cassette labeling for facile construction of energy transfer fluorescent primers. Nucleic Acids Res., 24, 1144–1148. [PMC free article] [PubMed] [Google Scholar]

4. Kheterpal I., Scherer,J., Clark,S.M., Radhakrishnan,A., Ju,J., Ginther,C.L., Sensabaugh,G.F. and Mathies,R.A. (1996) DNA sequencing using a four-color confocal fluorescence capillary array scanner. Electrophoresis, 17, 1852–1859. [PubMed] [Google Scholar]

5. Bowling J.M., Bruner,K.L., Cmarik,J.L. and Tibbetts,C. (1991) Neighboring nucleotide interactions during DNA sequencing gel electrophoresis. Nucleic Acids Res., 19, 3089–3097. [PMC free article] [PubMed] [Google Scholar]

6. Yamakawa H. and Ohara,O. (1997) A DNA cycle sequencing reaction that minimizes compressions on automated fluorescent sequencers. Nucleic Acids Res., 25, 1311–1312. [PMC free article] [PubMed] [Google Scholar]

7. Fitzgerald M.C., Zhu,L. and Smith,L.M. (1993) The analysis of mock DNA sequencing reactions using matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun. Mass Spectrom., 7, 895–897. [Google Scholar]

8. Roskey M.T., Juhasz,P., Smirnov,I.P., Takach,E.J., Martin,S.A. and Haff,L.A. (1996) DNA sequencing by delayed extraction-matrix-assisted laser desorption/ionization time of flight mass spectrometry. Proc. Natl Acad. Sci. USA, 93, 4724–4729. [PMC free article] [PubMed] [Google Scholar]

9. Taranenko N.I., Allman,S.L., Golovlev,V.V., Taranenko,N.V., Isola,N.R. and Chen,C.H. (1998) Sequencing DNA using mass spectrometry for ladder detection. Nucleic Acids Res., 26, 2488–2490. [PMC free article] [PubMed] [Google Scholar]

10. Kirpekar F., Norhoff,E., Larsen,L., Kristiansen,K., Roepstorff,P. and Hillenkamp,F. (1998) DNA sequence analysis by MALDI mass spectrometry. Nucleic Acids Res., 26, 2554–2559. [PMC free article] [PubMed] [Google Scholar]

11. Nordhoff E., Luebert,C., Thiele,G., Heiser,V. and Lehrach,H. (2000) Rapid determination of short DNA sequences by the use of MALDI-MS. Nucleic Acids Res., 28, e86. [PMC free article] [PubMed] [Google Scholar]

12. Monforte J. and Becker,C. (1997) High-throughput DNA analysis by time-of-flight mass spectrometry. Nature Med., 3, 360–362. [PubMed] [Google Scholar]

13. Fu D.J., Tang,K., Braun,A., Reuter,D., Darnhofer-Demar,B., Little,D.P., O’Donnell,M.J., Cantor,C.R. and Koster,H. (1998) Sequencing exons 5 to 8 of the p53 gene by MALDI-TOF mass spectrometry. Nat. Biotechnol., 16, 381–384. [PubMed] [Google Scholar]

14. Langer P.R., Waldrop,A.A. and Ward,D.C. (1981) Enzymatic synthesis of biotin-labeled polynucleotides: novel nucleic acid affinity probes. Proc. Natl Acad. Sci. USA, 78, 6633–6637. [PMC free article] [PubMed] [Google Scholar]

15. Hawkins T.L. (1992) M13 single-strand purification using a biotinylated probe and streptavidin coated magnetic beads. DNA Seq., 3, 65–69. [PubMed] [Google Scholar]

16. Hawkins T.L., O’Connor-Morin,T., Roy,A. and Santillan,C. (1994) DNA purification and isolation using a solid-phase. Nucleic Acids Res., 22, 4543–4544. [PMC free article] [PubMed] [Google Scholar]

17. Uhlen M. (1989) Magnetic separation of DNA. Nature, 340, 733–734. [PubMed] [Google Scholar]

18. Hultman T., Bergh,S., Moks,T. and Uhlen,M. (1991) Bidirectional solid-phase sequencing of in vitro-amplified plasmid DNA. Biotechniques, 10, 84–93. [PubMed] [Google Scholar]

19. Tong X. and Smith,L.M. (1992) Solid-phase method for the purification of DNA sequencing reactions. Anal. Chem., 64, 2672–2677. [PubMed] [Google Scholar]

20. Tong X. and Smith,L.M. (1993) Solid-phase purification in automated DNA sequencing, DNA Seq., 4, 151–162. [PubMed] [Google Scholar]

21. Ju J. (1999) US Patent no. 5 876 936.

22. Tang K., Fu,D., Julien,D., Braun,A., Cantor,C.R. and Koster,H. (1999) Chip-based genotyping by mass spectrometry. Proc. Natl Acad. Sci. USA, 96, 10016–10020. [PMC free article] [PubMed] [Google Scholar]

23. Roses A. (2000) Pharmacogenetics and the practice of medicine. Nature, 405, 857–865. [PubMed] [Google Scholar]

24. Prober J., Trainor,G., Dam,R., Hobbs,F., Robertson,C., Zagursky.R., Cocuzza,A., Jensen,M. and Baumeister,K. (1987) A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides. Science, 238, 336–341. [PubMed] [Google Scholar]

25. Gebeyehu G., Rao,P., SooChan,P., Simms,D.A. and Klevan,L. (1987) Novel biotinylated nucleotide—analogs for labeling and calorimetric detection of DNA. Nucleic Acids Res., 15, 4513–4534. [PMC free article] [PubMed] [Google Scholar]

26. Herman T., Lefever,E. and Shimkus,M. (1986) Affinity chromatography of DNA labeled with chemically cleavable biotinylated nucleotide analogs. Anal. Biochem., 156, 48–55. [PubMed] [Google Scholar]

27. Fei Z., Ono,T. and Smith,L.M. (1998) MALDI-TOF mass spectrometric typing of single nucleotide polymorphisms with mass-tagged ddNTPs. Nucleic Acids Res., 26, 2827–2828. [PMC free article] [PubMed] [Google Scholar]

28. Hilton G.C., Martinis,J.M., Wollman,D.A., Irwin,K.D., Dulcie,L.L., Gerber,D., Gillevet,P.M. and Twerenbold,D. (1998) Impact energy measurement in time-of-flight mass spectrometry with cryogenic microcalorimeters. Nature, 391, 672–675. [PubMed] [Google Scholar]

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The structure of the biotinylated dideoxynucleotides used to generate Sanger sequencing products for MS analysis. The biotinylated ddUTPs function the same way as ddTTP in the Sanger DNA-sequencing reaction.

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