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

Nyakas, Adrien; Eberle, Rahel Patricia; Stucki, Silvan; Schürch, Stefan (2014). More Than Charged Base Loss — Revisiting the Fragmentation of Highly Charged Oligonucleotides. Journal of the American Society for Mass Spectrometry, 25(7), pp. 1155-1166. Springer 10.1007/s13361-014-0873-4

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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 MNCO– 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

Item Type:

Journal Article (Original Article)


08 Faculty of Science > Department of Chemistry, Biochemistry and Pharmaceutical Sciences (DCBP)

UniBE Contributor:

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


500 Science > 570 Life sciences; biology
500 Science > 540 Chemistry








Stefan Schürch

Date Deposited:

27 Jan 2015 13:07

Last Modified:

02 Mar 2023 23:25

Publisher DOI:





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