Gas-phase conformations of deprotonated trinucleotides (dGTT-, dTGT-, and dTTG-): the question of zwitterion formation.

The gas-phase conformations of a series of trinucleotides containing thymine (T) and guanine (G) bases were investigated for the possibility of zwitterion formation. Deprotonated dGTT-, dTGT-, and dTTG- ions were formed by MALDI and their collision cross-sections in helium measured by ion mobility based methods. dTGT- was theoretically modeled assuming a zwitterionic and non-zwitterionic structure while dGTT- and dTTG- were considered "control groups" and modeled only as non-zwitterions. In the zwitterion, G is protonated at the N7 site and the two neighboring phosphates are deprotonated. In the non-zwitterion, G is not protonated and only one phosphate group is deprotonated. Two conformers, whose cross-sections differ by 17 +/- 2 A2, are observed for dTGT- in the 80 K experiments. Multiple conformers are also observed for dGTT- and dTTG- at 80 K, though relative cross-section differences between the conformers could not be accurately obtained. At higher temperatures (>200 K), the conformers rapidly interconvert on the experimental time scale and a single "time-averaged" conformer is observed in the ion mobility data. Theory predicts only one low-energy conformation for the zwitterionic form of dTGT- with a cross-section 8% smaller than experimental values. Additionally, the extra H+ on G does not bridge both phosphates. Thus, dTGT- does not appear to be a stable zwitterion in the gas-phase. Theory does, however, predict two low-energy conformers for the non-zwitterionic form of dTGT- that differ in cross-section by 18 +/- 3 A2, in good agreement with the experiment. In the smaller cross-section form (folded conformer), G and one of the T bases are stacked while the other T folds towards the stacked pair and hydrogen bonds to G. In the larger cross-section form (open conformer), the unstacked T extends away from the T/G stacked pair. Similar folded and open conformers are predicted for all three trinucleotides, regardless of which phosphate is deprotonated.