Fast atom bombardment combined with tandem mass spectrometry for determining structures of small oligonucleotides

A study of small (n = 3 to 6) oligonucleotide and the metastable and collisionally activated decompositions of their (M-H)- species desorbed by using fast atom bombardment (FAB) is reported. Data were obtained for both ribo- and 2'-deoxyribotrinucleotides and for 2'-deoxyribotetra-, penta-, and hexanucleotides. The favored metastable decompositions of all of the oligonucleotides studied are eliminations of neutral CONH and loss of BH, where B is the base moiety. The BH elimination, however, provides little sequence information in the higher oligonucleotides and the process is more indicative of the different bases present in the oligomer. The chemistry observed upon collisional activation changes as one goes from trinucleotides to hexanucleotides. The formation of sequence ions is more facile for processes involving the 3' terminus, allowing the sequence to be determined. As one goes to the higher oligonucleotides, however, several different competitive fragmentation processes become as facile as or more facile than the reactions giving the sequence ions. This hinders proper ion assignments and makes sequence determination difficult.