title: Gas-phase dissociation of homo-DNA oligonucleotides.
abstract: 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.
authors.affiliation: Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland.
authors.forename: Silvan R
authors.initials: SR
authors.lastname: Stucki
authors.forename: Camille
authors.initials: C
authors.lastname: Désiron
authors.forename: Adrien
authors.initials: A
authors.lastname: Nyakas
authors.forename: Simon
authors.initials: S
authors.lastname: Marti
authors.forename: Christian J
authors.initials: CJ
authors.lastname: Leumann
authors.forename: Stefan
authors.initials: S
authors.lastname: Schürch
mesh_terms: D000838:Anions / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D005740:Gases / Q000737:chemistry; D006601:Hexoses / Q000737:chemistry; D008958:Models, Molecular; D009841:Oligonucleotides / Q000737:chemistry*; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods; D053719:Tandem Mass Spectrometry / Q000379:methods
chemical_list: D000838:Anions; D005740:Gases; D006601:Hexoses; D009841:Oligonucleotides; D004247:DNA
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