Monn ST Schürch S 2007 A set of pentanucleotides was investigated by electrospray tandem mass spectrometry with the focus on the fragmentation mechanism. Results reveal new aspects of the fragmentation mechanism of modified and unmodified oligonucleotides and demonstrate the influence of the nucleobases on the decomposition of oligonucleotides. Adenine-rich oligonucleotides fragment easily resulting in abundant peaks corresponding to the DNA-typical a-B- and w-ions. On the other hand, thymine was found to have a stabilizing effect, which is reflected by the preferred formation of the w(4)-ions and the relatively low abundance of shorter w-ions upon dissociation of pentanucleotides. Data from investigation of the formation of w(4)-ions support a beta-elimination mechanism. Results obtained by investigation of oligonucleotides with an abasic site confirm this mechanism, which is independent of nucleobase loss. Experiments with methylphosphonate oligonucleotides show a remarkable change in the fragmentation pattern due to the modification. It was found that charges are located on the nucleobases and initiate the fragmentation mechanism. The stability of the oligonucleotide is reduced and no a-B-fragment ions are formed wherever there is a methylphosphonate group within the backbone. This fact also demonstrates that fragmentation is locally controlled. application/pdf https://sonar.rero.ch/global/documents/286105 eng info:eu-repo/semantics/altIdentifier/doi/10.1016/j.jasms.2007.02.006 info:eu-repo/semantics/altIdentifier/pmid/17383194 info:eu-repo/semantics/openAccess Journal of the American Society for Mass Spectrometry. - 2007 Base Sequence DNA Fingerprinting Molecular Sequence Data Oligonucleotides Organophosphorus Compounds Sequence Analysis, DNA Spectrometry, Mass, Electrospray Ionization New aspects of the fragmentation mechanisms of unmodified and methylphosphonate-modified oligonucleotides. http://purl.org/coar/resource_type/c_6501