Methods for L-ribooligonucleotide sequence determination using LCMS

Nucleic Acids Research

Volumn 39, Issue 21, 2011, Pages

  Turner, John J ^a   Hoos, Johannes S ^a   Vonhoff, Stefan ^a   Klussmann, Sven ^a  

^a NOXXON PHARMA AG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

HAPTEN; NOX A 12; NOX E 36; OLIGONUCLEOTIDE; RIBOOLIGONUCLEOTIDE; RNA DERIVATIVE; SPIEGELMER; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; ENANTIOMER; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL;

CHROMATOGRAPHY, LIQUID; OLIGORIBONUCLEOTIDES; SEQUENCE ANALYSIS, RNA; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; STEREOISOMERISM;

EID: 82255185566     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr776     Document Type: Article

References (23)

1. Eckstein, F., Krieg, A.M., Stein, C.A., Agrawal, S., Beaucage, S., Cook, P.D., Crooke, S., Gait, M.J., Gewirtz, A., Helene, C. et al. (1996) On the quality control of antisense oligonucleotides [editorial]. Antisense Nucleic Acid Drug Dev., 6, 149. (Pubitemid 26394872)
2. Srivasta, G.S. (2011) In Bonilla, J.V. and Srivasta, G.S. (eds), Handbook of Analysis of Oligonucleotides and Related Products. CRC Press, Boca Raton, FL, pp. 465-486.
3. Timar, Z. (2011) In Bonilla, J.V. and Srivasta, G.S. (eds), Handbook of Analysis of Oligonucleotides and Related Products. CRC Press, Boca Raton, FL, pp. 167-218.
4. Morrissey, D.V., Lockridge, J.A., Shaw, L., Blanchard, K., Jensen, K., Breen, W., Hartsough, K., Machemer, L., Radka, S., Jadhav, V. et al. (2005) Potent and persistent in vivo anti-HBV activity of chemically modified siRNAs. Nat. Biotechnol., 23, 1002-1007. (Pubitemid 41114035)
5. Heidenreich, O., Pieken, W. and Eckstein, F. (1993) Chemically modified RNA: approaches and applications. FASEB J., 7, 90-96. (Pubitemid 23034018)
6. Kawasaki, A.M., Casper, M.D., Freier, S.M., Lesnik, E.A., Zounes, M.C., Cummins, L.L., Gonzalez, C. and Cook, P.D. (1993) Uniformly modified 20-deoxy-20-fluoro phosphorothioate oligonucleotides as nuclease-resistant antisense compounds with high affinity and specificity for RNA targets. J. Med. Chem., 36, 831-841. (Pubitemid 23118776)
7. Shaw, J.P., Kent, K., Bird, J., Fishback, J. and Froehler, B. (1991) Modified deoxyoligonucleotides stable to exonuclease degradation in serum. Nucleic Acids Res., 19, 747-75.
8. Frank, R. and Koster, H. (1979) DNA chain length markers and the influence of base composition on electrophoretic mobility of oligodeoxyribonucleotides in polyacrylamide-gels. Nucleic Acids Res., 6, 2069-2087.
9. Kirpekar, F., Nordhoff, E., Larsen, L.K., Kristiansen, K., Roepstorff, P. and Hillenkamp, F. (1998) DNA sequence analysis by MALDI mass spectrometry. Nucleic Acids Res., 26, 2554-2559. (Pubitemid 28297364)
10. Kramer, F.R. and Mills, D.R. (1978) RNA sequencing with radioactive chain-terminating ribonucleotides. Proc. Natl Acad. Sci. USA, 75, 5334-5338. (Pubitemid 9079788)
11. Li, S., Haces, A., Stupar, L., Gebeyehu, G. and Pless, R.C. (1993) Elimination of band compression in sequencing gels by the use of N4-methyl-20-deoxycytidine 5′-triphosphate. Nucleic Acids Res., 21, 2709-2714. (Pubitemid 23209171)
12. Taucher, M., Rieder, U. and Breuker, K. (2010) Minimizing base loss and internal fragmentation in collisionally activated dissociation of multiply deprotonated RNA. J. Am. Soc. Mass Spectrom., 21, 278-285.
13. Eulberg, D., Jarosch, F., Vonhoff, S. and Klussmann, S. (2006) In Klussmann, S. (ed.), The Aptamer Handbook, Functional Oligonucleotides and Their Applications. Wiley-VCH, Weinheim, pp. 417-439.
14. Eulberg, D. and Klussmann, S. (2003) Spiegelmers: biostable aptamers. Chembiochem, 4, 979-983. (Pubitemid 37267585)
15. Klussmann, S., Nolte, A., Bald, R., Erdmann, V.A. and Furste, J.P. (1996) Mirror-image RNA that binds D-adenosine. Nat. Biotechnol., 14, 1112-1115. (Pubitemid 26299110)
16. Damha, M.J. and Ogilvie, K.K. (1993) Oligoribonucleotide synthesis. The silyl-phosphoramidite method. Methods Mol. Biol., 20, 81-114.
17. Wincott, F., DiRenzo, A., Shaffer, C., Grimm, S., Tracz, D., Workman, C., Sweedler, D., Gonzalez, C., Scaringe, S. and Usman, N. (1995) Synthesis, deprotection, analysis and purification of RNA and ribozymes. Nucleic Acids Res., 23, 2677-2684.
18. Moyroud, E., Biala, E. and Strazewski, P. (2000) Synthesis and Enzymatic Digestion of an RNA nonamer in both enantiomeric forms. Tetrahedron, 56, 1475-1484. (Pubitemid 30143592)
19. Tolson, D.A. and Nicholson, N.H. (1998) Sequencing RNA by a combination of exonuclease digestion and uridine specific chemical cleavage using MALDI-TOF. Nucleic Acids Res., 26, 446-451. (Pubitemid 28291567)
20. Peattie, D.A. (1979) Direct chemical method for sequencing RNA. Proc. Natl Acad. Sci. USA, 76, 1760-1764.
21. Farand, J. and Beverly, M. (2008) Sequence confirmation of modified oligonucleotides using chemical degradation, electrospray ionization, time-of-flight, and tandem mass spectrometry. Anal. Chem., 80, 7414-7421.
22. Farand, J. and Gosselin, F. (2009) De novo sequence determination of modified oligonucleotides. Anal. Chem., 81, 3723-3730.
23. Proudnikov, D. and Mirzabekov, A. (1996) Chemical methods of DNA and RNA fluorescent labeling. Nucleic Acids Res., 24, 4535-4542. (Pubitemid 26388642)