SGMS Meeting 2001

Gas-phase Dissociation of Mixed-Sequence RNA/DNA Oligonucleotides

Stefan Schürch, Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern

The fragmentation of mixed ribo- and deoxyribo-oligonucleotides upon low-energy collision-induced dissociation in a hybrid quadrupole time-of-flight mass spectrometer was investigated. The preferences for base loss and backbone fragmentation of a number of mixed-sequence pentanucleotides were studied. Product ion spectra revealed a site- and base-specific dissociation behavior, which is strongly influenced by the presence of the ribose 2'-substituent. Mechanistic aspects of base loss and backbone cleavage of oligoribonucleotides and mixed RNA/DNA sequences are discussed. Additional results obtained from CID of dodecanucleotides demonstrate the potential of tandem mass spectrometry for sequence elucidation of unnatural oligonucleotides.