An analysis of the different behavior of DNA and RNA through the study of the mutual relationship between stacking and hydrogen bonding.
The mutual relationship between stacking and hydrogen bonding and the possible influence of stacking in the different behavior of DNA and RNA base pairs have been studied through complete DFT optimization of different structures of A-U and A-T dimers (i.e., A-U/U-A and A-T/T-A), using some functionals developed by the group of Truhlar. The results obtained in this work clearly show that stacking and hydrogen bonding are deeply connected. The different behavior of DNA and RNA when replacing uracil by thymine can be interpreted through the formation of a stabilizing CH/pi interaction between the methyl group of thymine and the five-member ring of adenine.
Gil
Adrià
A
Departament de Quimica, Universitat Autonoma de Barcelona, Bellaterra 08193, Spain.
Branchadell
Vicenç
V
Bertran
Joan
J
Oliva
Antoni
A
D020029:Base Pairing; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D019281:Dimerization; D006860:Hydrogen Bonding; D008956:Models, Chemical; D012313:RNA / Q000737:chemistry*; D055672:Static Electricity
D012313:RNA; D004247:DNA