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

Articles

Abstract

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 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.

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© American Society for Mass Spectrometry 2003

Authors and Affiliations

  1. 1.Department of Chemistry and BiochemistryUniversity of CaliforniaSanta BarbaraUSA

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