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

Analytical Chemistry
Julie Farand, Michael Beverly

Abstract

We report the sequencing of highly modified oligonucleotides containing a mixture of 2'-deoxy, 2'-fluoro, 2'-O-methyl, abasic, and ribonucleotides. The passenger and guide strands each containing 48% and 86% of modified nucleotides, respectively, are representative sequences of synthetic short interfering RNAs (siRNAs). We describe herein the sequence confirmation of both strands using a series of robust chemical reactions, followed by analysis via ESI-TOF and ion trap mass spectrometry (ITMS). The following method enables the rapid sequence confirmation of highly modified oligonucleotides.

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Citations

Apr 8, 2011·Journal of the American Society for Mass Spectrometry·Adrien NyakasStefan Schürch
Feb 9, 2012·Journal of the American Society for Mass Spectrometry·Nathan A HaganPlamen A Demirev
Oct 27, 2009·Journal of the American Society for Mass Spectrometry·Teng-yi HuangScott A McLuckey
Sep 29, 2011·Nucleic Acids Research·John J TurnerSven Klussmann
Mar 5, 2010·Mass Spectrometry Reviews·Michael B Beverly
Jul 22, 2014·Bioanalysis·Babak Basiri, Michael G Bartlett
Sep 5, 2017·Biomedical Chromatography : BMC·N M El ZaharMichael G Bartlett
Nov 29, 2013·Mass Spectrometry Reviews·Ed Dudley, Liz Bond
Feb 23, 2020·Nucleic Acids Research·Felix HagelskampStefanie Kellner
May 15, 2009·Analytical Chemistry·Julie Farand, Francis Gosselin
Aug 7, 2019·Analytical Chemistry·Soheil Pourshahian, Sergei M Gryaznov

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