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

AbstractThe 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 Å2, 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 Å2, 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