Gas-phase Dissociation of homo-DNA Oligonucleotides

Stucki, Silvan R.; Désiron, Camille; Nyakas, Adrien; Marti, Simon; Leumann, Christian J.; Schürch, Stefan (2013). Gas-phase Dissociation of homo-DNA Oligonucleotides. Journal of the American Society for Mass Spectrometry, 24(12), pp. 1997-2006. Springer US; 10.1007/s13361-013-0729-3

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Synthetic modified oligonucleotides are of interest for diagnostic and therapeutic applications, as their biological stability, pairing selectivity, and binding strength can be considerably increased by the incorporation of unnatural structural elements. Homo-DNA is an oligonucleotide homologue based on dideoxy-hexopyranosyl sugar moieties, which follows the Watson-Crick A-T and G-C base pairing system, but does not hybridize with complementary natural DNA and RNA. Homo-DNA has found application as a bioorthogonal element in templated chemistry applications. The gas-phase dissociation of homo-DNA has been investigated by ESI-MS/MS and MALDI-MS/MS, and mechanistic aspects of its gas-phase dissociation are discussed. Experiments revealed a charge state dependent preference for the loss of nucleobases, which are released either as neutrals or as anions. In contrast to DNA, nucleobase loss from homo-DNA was found to be decoupled from backbone cleavage, thus resulting in stable products. This renders an additional stage of ion activation necessary in order to generate sequence-defining fragment ions. Upon MS(3) of the primary base-loss ion, homo-DNA was found to exhibit unspecific backbone dissociation resulting in a balanced distribution of all fragment ion series.

Item Type:

Journal Article (Original Article)


08 Faculty of Science > Departement of Chemistry and Biochemistry

UniBE Contributor:

Stucki, Silvan; Désiron, Camille; Nyakas, Adrien; Marti, Simon; Leumann, Christian and Schürch, Stefan


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




Springer US;




Christian Leumann

Date Deposited:

08 Jan 2014 16:04

Last Modified:

25 Oct 2019 00:42

Publisher DOI:


PubMed ID:


Uncontrolled Keywords:

Gas-phase fragmentation, Modified nucleic acids, homo-DNA, Nucleobase loss, Sugar-modification, ESI-MS, MALDI-MS, Bioorthogonality




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