PNNL

Abstract

Dissociation reactions of a series of multiply charged oligonucleotides anions were studied using an ion trap mass spectrometer. These mixed-nucleobase 12-mers fragment first by loss of a nucleobase (A, G, C and/or 5-methyl-cytosine) followed by cleavage at 3' C-O bond of the sugar from which the base is lost to produce the complementary sequence ions, i.e. a-B and w type of ions. No detectable loss of 8-oxo-guanine and/or thymine from these 12-mers is observed for the gentle collision conditions in the ion trap. The primary loss of a nucleobase and the subsequent backbone cleavage to generate sequence ions strongly depend on the charge state of the parent molecular ion. For low charge states (-2 and ?3), product ions due to the loss of a neutral guanine base and related sequence ions are dominant in the tandem mass spectra. However, preferential loss of a neutral adenine becomes the primary reaction channel from the ?5 charge state of the molecular ion. Such charge state dependent fragmentation behavior was utilized to determine the sites of 8-oxo-dG residue in a series of structural isomers. The position of 8-oxo-dG residue can be simply determined from the fragmentation pattern of ?3 charge state, but not of ?5 charge state. The strategy illustrated here for positional mapping of damaged residues in oligonucleotides is highly sensitive due to effective dynamic range enhancement in the product ion spectra by accessing the sequence informative reaction channels.