Interaction energies in non watson-crick pairs: An ab initio study of g·u and u·u pairs

• SANDRA T MADARIAGA ^[1] ; J.GUILLERMO CONTRERAS ^[2] ; C.GLORIA SEGUEL ^[3]
  1. [1] Universidad Austral de Chile

     Universidad Austral de Chile

     Valdivia, Chile

     
  2. [2] Universidad de Concepción

     Universidad de Concepción

     Comuna de Concepción, Chile

     
  3. [3] Universidad de Tarapacá

     Universidad de Tarapacá

     Arica, Chile

     

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• Localización: Journal of the Chilean Chemical Society (Boletín de la Sociedad Chilena de Química), ISSN-e 0717-6309, ISSN 0366-1644, Vol. 50, Nº. 1, 2005, págs. 435-438
• Idioma: inglés
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  • Ab initio calculations at the MP2/6-31G** level have been carried out on the non-Watson-Crick nucleic acids pairs to obtain the interaction energies and to see whether the derived values are comparable or not with the canonical G-C, A-T and A-U pairs. Optimized geometries of the pairs show that the structural parameters of the isolated bases differ very little on pairing. The guanine -NH2 group does not participate in the hydrogen bonding formation and possesses a pyramidal structure; its intrinsic nonplanarity plays an important role in the out-of-plane intermolecular interactions. Thus, the pair projects three hydrogen bonding acceptor sites, namely, N7(G), O6(G) and O4(U) to the RNA major groove. The interaction energy (DHºint) calculated for the (-13.6 kcal/mol) is comparable to that determined for A-T (-13.0 kcal/mol), but considerable smaller than the experimental value reported for G-C (-21.0 kcal/mol). The pair follows the trend that pairing between pyrimidines bases should have lower interacting energies than purine-pyrimidine pairs