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More Than Charged Base Loss — Revisiting the Fragmentation of Highly Charged Oligonucleotides

Nyakas, Adrien ; Eberle, Rahel ; Stucki, Silvan ; Schürch, Stefan

In: Journal of The American Society for Mass Spectrometry, 2014, vol. 25, no. 7, p. 1155-1166

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    Titre
    • More Than Charged Base Loss — Revisiting the Fragmentation of Highly Charged Oligonucleotides
    Auteur
    • Nyakas, Adrien. Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
    • Eberle, Rahel. Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
    • Stucki, Silvan. Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
    • Schürch, Stefan. Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
    Type de document
    • Postprint
    Langue
    • Anglais
    Publié dans
    • Journal of The American Society for Mass Spectrometry, 2014, vol. 25, no. 7, p. 1155-1166. Springer US; http://www.springer-ny.com
    Autre version électronique
    Identifiant OAI-PMH
    • oai:doc.rero.ch:324993
    Summary
    Tandem mass spectrometry is a well-established analytical tool for rapid and reliable characterization of oligonucleotides (ONs) and their gas-phase dissociation channels. The fragmentation mechanisms of native and modified nucleic acids upon different mass spectrometric activation techniques have been studied extensively, resulting in a comprehensive catalogue of backbone fragments. In this study, the fragmentation behavior of highly charged oligodeoxynucleotides (ODNs) comprising up to 15 nucleobases was investigated. It was found that ODNs exhibiting a charge level (ratio of the actual to the total possible charge) of 100% follow significantly altered dissociation pathways compared with low or medium charge levels if a terminal pyrimidine base (3' or 5') is present. The corresponding product ion spectra gave evidence for the extensive loss of a cyanate anion (NCO-), which frequently coincided with the abstraction of water from the 3'- and 5'-end in the presence of a 3'- and 5'-terminal pyrimidine nucleobase, respectively. Subsequent fragmentation of the M-NCO- ion by MS3 revealed a so far unreported consecutive excision of a metaphosphate (PO3 -)-ion for the investigated sequences. Introduction of a phosphorothioate group allowed pinpointing of PO3 - loss to the ultimate phosphate group. Several dissociation mechanisms for the release of NCO- and a metaphosphate ion were proposed and the validity of each mechanism was evaluated by the analysis of backbone- or sugar-modified ONs. Graphical abstract ᅟ