Gas-phase conformational and energetic properties of deprotonated dinucleotides

Ion mobility experiments and molecular modeling calculations were used to investigate the gas-phase conformations and folding energetics of 16 deprotonated dinucleotides. [M-H]- ions were formed by MALDI and their collision cross-sections measured in helium using ion mobility based techniques. Cross-sections of theoretical structures, generated by molecular mechanics/dynamics calculations, were compared to the experimental values for conformational identification of the dinucleotides. Temperature dependent measurements and kinetic theory were also used to obtain energetic and dynamic data concerning the folding properties of the dinucleotides. Three distinct families of conformations, with significantly different collision cross-sections, were identified: a “stacked” family in which the two nucleobases stack; an “H-bonded” family in which the two nucleobases stay in the same plane and are hydrogen-bonded to each other; and an “open” family in which the two nucleobases are separated from each other. At temperatures ≥ 300 K these conformers rapidly interconvert in most systems, but they can be separated and individually observed in the lower temperature (80-200 K) experiments. The types and relative amounts of each conformer observed, and the temperature at which they can be separated, are base and sequence dependent. Theoretical modeling of the temperature-dependent data was used to determine isomerization barrier heights between the various conformers and yielded values between 0.8-12.9 kcal/mol, depending on the dinucleotide.