Decompositions of multiply charged oligonucleotide anions

Multiply charged single-strand deoxyoligonucleotide anions fragment first 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 proceed via 1,2-elimination involving hydrogens from the sugar and to yield a stable substituted furan as one of the products. There is a strong preference for loss of charged adenine followed by loss of charged thymine. This tendency is strongly dependent, however, upon the internal 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 present in the sequence is at the 3' terminus. Relatively small oligomers can be fully or nearly fully sequenced via several stages of mass spectrometry. Sequencing adjacent deoxyguanylate and deoxycytidylate residues tends to be difficult due to the much lower abundances of product ions formed via reaction channels beginning with losses of cytidine and guanine. Multiple stages of mass spectrometry are facilitated by highly charged parent ions.