DECOMPOSITIONS OF MULTIPLY-CHARGED OLIGONUCLEOTIDE ANIONS

Multiply charged single-strand deoxyoligonucleotide anions fragment fi rst by loss of a nucleobase followed by cleavage at the 3; C-O bond of the sugar from which the base is lost. Both steps are proposed to pro ceed via 1,2-elimination involving hydrogens from the sugar and to yie ld a stable substituted furan as one of the products. There is a stron g preference for loss of charged adenine followed by loss of charged t hymine. This tendency is strongly dependent, however, upon the interna l Coulombic repulsion experienced by the ion. The position of the base in the chain is not a major factor in determining which base is lost first, except in the case of the base at the 3' terminus. The loss of the base at the 3' terminus tends to be disfavored, and this tendency may result in the more abundant loss of a charged thymine, for example , than the loss of charged adenine when the only deoxyadenylate presen t in the sequence is at the 3' terminus. Relatively small oligomers ca n be fully or nearly fully sequenced via several stages of mass spectr ometry. Sequencing adjacent deoxyguanylate and deoxycytidylate residue s tends to be difficult due to the much lower abundances of product io ns formed via reaction channels beginning with losses of cytidine and guanine. Multiple stages of mass spectrometry are facilitated by highl y charged parent ions.