Sequence confirmation of modified oligonucleotides using chemical degradation, electrospray ionization, time-of-flight, and tandem mass spectrometry

Analytical Chemistry

Volumn 80, Issue 19, 2008, Pages 7414-7421

  Farand, Julie ^a   Beverly, Michael ^a  

^a MERCK RESEARCH LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL REACTIONS; ELECTROSPRAY IONIZATION; GRAFTING (CHEMICAL); MASS SPECTROMETERS; MASS SPECTROMETRY; NUCLEIC ACIDS; NUCLEOTIDES; OLIGONUCLEOTIDES; SPECTROMETERS; SPECTROMETRY; SPECTRUM ANALYSIS; SYNTHESIS (CHEMICAL);

CHEMICAL DEGRADATION; ELECTRO SPRAYING; ION TRAP-MASS SPECTROMETRY; MODIFIED NUCLEOTIDES; MODIFIED OLIGONUCLEOTIDES; RIBONUCLEOTIDES; SHORT INTERFERING; TANDEM MASS SPECTROMETRY; TIME -OF-FLIGHT;

HIGH PERFORMANCE LIQUID CHROMATOGRAPHY;

OLIGONUCLEOTIDE; SMALL INTERFERING RNA;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ACCURACY; ANALYTIC METHOD; ARTICLE; CHEMICAL REACTION; DEGRADATION; ELECTROSPRAY MASS SPECTROMETRY; MASS; NUCLEOTIDE SEQUENCE; TANDEM MASS SPECTROMETRY; TIME OF FLIGHT MASS SPECTROMETRY;

BASE SEQUENCE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDES; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; TANDEM MASS SPECTROMETRY;

EID: 54749151857     PISSN: 00032700     EISSN: None     Source Type: Journal    
DOI: 10.1021/ac8011158     Document Type: Article

References (35)

1. Opalinska, J. B.; Gewirtz, A. M. Nat. Rev. Drug Discovery 2002, 1, 503-514.
2. Goodchild, J. Curr. Opin. Mol. Ther. 2004, 6, 120-128.
3. Morrissey, D. V.; Zinnen, S. P.; Dickinson, B. A.; Jensen, K.; McSwiggen, J. A.; Vargeese, C.; Polisky, B. Pharm. Discovery 2005, 5, 16-20.
4. Verma, S.; Eckstein, F. Annu. Rev. Biochem. 1998, 67, 99-134.
5. Manoharan, M. Curr. Opin. Chem. Biol. 2004, 8, 570-579.
6. Limbach, P. A. Mass Spectrom. Rev. 1996, 15, 297-336.
7. Maxam, A. M.;.; Gilbert, W. Proc. Natl. Acad. Sci. U.S.A. 1977, 74, 560-564.
8. Peattie, D. A. Proc. Natl. Acad. Sci. U.S.A. 1979, 76, 1760-1764.
9. Frank, R.; Köster, H. Nucleic Acids Res. 1979, 6, 2069-2087.
10. Li, S.; Haces, A.; Stupar, L.; Gebeyehu, G.; Pless, R. C. Nucleic Acids Res. 1993, 21, 2709-2714.
11. Sanger, F.; Nicklen, S.; Coulson, A. R. Proc. Natl. Acad. U.S.A. 1977, 74, 5463-5467.
12. Shahn, C.; Strauss, E. G.; Strauss, J. H. Methods Enzymol. 1989, 180, 121-130.
13. Tang, J.; Roskey, A. M.; Agrawal, S. Anal. Biochem. 1993, 212, 134-137.
14. Shaw, J.-P.; Kent, K.; Bird, J.; Fishback, J.; Froehler, B. Nucleic Acids Res. 1991, 19, 747-750.
15. Kawasaki, A.; Casper, M. D.; Freier, S. M.; Lesnik, E. A.; Zounes, M. C.; Cummins, L. L.; Gonzalez, C.; Cook, P. D. J. Med. Chem. 1993, 36, 831-841.
16. Egli, M.; Minasov, G.; Tereshko, V.; Pallan, P. S.; Teplova, M.; Inamati, G. B.; Lesnik, E. A.; Owens, S. R.; Ross, B. S.; Prakash, T. P.; Manoharan, M. Biochemistry 2005, 44, 9045-9057.
17. Nordhoff, E.; Kirpekar, F.; Roepstorff, P. Mass Spectrom. Rev. 1996, 15, 67-138.
18. Tang, W.; Zhu, L.; Smith, L. M. Anal. Chem. 1997, 69, 302-312.
19. Barry, J. P.; Vouros, P.; Schepdael, A. V.; Law, S.-J. J. Mass Spectrom, 1995, 30, 993-1006.
20. McLuckey, S. A.; Habibi-Goudarzi, S. J. Am. Soc. Mass Spectrom. 1994, 5, 740-747.
21. Monn, S. T. M.; Tromp, J. M.; Schüren, S. Chimia 2005, 59, 822-825.
22. McLuckey, S. A.; Van Berkel, G. J.; Glish, G. L. J. Am. Soc. Mass Spectrom. 1992, 3, 60-70.
23. Wu, J.; McLuckey, S. A. Int. J. Mass Spectrom. 2004, 237, 197-241.
24. Hölzl, G.; Oberacher, H.; Pitsch, S.; Stutz, A.; Huber, C. G. Anal. Chem. 2005, 77, 673-680.
25. Fenn, J. B.; Mann, M.; Meng, C. K.; Wong, S. F.; Whitehouse, C. M. Science 1989, 246, 64-71.
26. Mann, M.; Hendrickson, R. C.; Pandey, A. Annu. Rev. Biochem. 2001, 70, 437-473.
27. Thomas, B.; Akoulitchev, A. V. Trends Biochem. Sci. 2006, 31, 173-181.
28. For seminal work, see Caruthers, M. H.; Barone, A. D.; Beaucage, S. L.; Dodds, D. R.; Fisher, E. F.; McBride, L. J.; Matteucci, M.; Stabinsky, Z.; Tang, J.-Y. Methods Enzymol. 1985, 154, 287-313.
29. Toison, D. A.; Nicholson, N. H. Nucleic Acids Res. 1998, 26, 446-451.
30. Apffel, A.; Chakel, J. A.; Fischer, S.; Lichtenwalter, K.; Hancock, W. S. Anal. Chem. 1997, 69, 1320-1325.
31. Greig, M.; Griffey, R. Rapid Commun. Mass Spectrom. 1995, 9, 97-102.
32. The presence of electronegative groups at C2 presumably enhances the electrophilic character of the aldehyde carbonyl in acyclic sugar 4 and favors the cyclic form 3 (see Figure 3). This likely affects the rate of strand scission via β-elimination.
33. Rubin, C. M.; Schmid, C. W. Nucleic Acids Res. 1980, 8, 4613-4619.
34. Ehresmann, C.; Baudin, F.; Mougel, M.; Romby, P.; Ebel, J.-P.; Ehresmann, B. Nucleic Acids Res. 1997, 15, 9109-9128.
35. This methodology has been successfully applied toward de novo sequencing of highly modified oligonucleotides and will be reported in due course.