Collision-induced dissociation of 16-mer DNA duplexes with various sequences: evidence for conservation of the double helix conformation in the gas phase

The MS/MS of 11 different 16-mer non-self-complementary DNA duplexes with various sequences has been under-taken with a quadrupole-TOF hybrid instrument, The comparison of the dissociation yields for complexes having different amounts of GC base pairs, though complicated by side-reactions like single-strand fragmentation, confirms the effect of the number of GC base pairs. More importantly, for complexes containing the same fraction of GC and different base sequences, the fragmentation yield remarkably parallels the DeltaH(diss) in solution calculated by a nearest-neighbor model for B-DNA. In addition to specific hydrogen bonding interactions, base stacking interactions also seem to survive in the gas phase and the conformation is conserved in the gas phase. Moreover, we have studied the uneven partition of the negative charges between the single strands, which was found to be directed by the nature of the terminal bases exclusively, and correlated with the gas-phase acidities of the (sugar-phosphate-sugar-base) species.