Sequence dependent proton‐transfer reaction in stacked GC pair I: The possibility of proton‐transfer reactions

Abstract

AbstractWe explored the possibilities of proton‐transfer reactions between guanines (G) and cytosines (C) in stacking two GC pairs by means of density functional methods. There are two combinations of sequences, GC/GC (5′‐dGpG‐3′) and CG/GC (5′‐dCpG‐3′). We found that the simultaneous single proton transfer (SPT) in two base pairs, two independent double proton transfer (DPT), and continuous double SPT reactions strongly depend on the sequence of the DNA, because the SPT reaction occurs in specific sequences including CG/GC and the latter DPTs occur in those including GC/GC. The properties of the DPT products, such as effective charges, are almost the same as the original GC/GC, whereas the effective charges on G and C in the simultaneous SPT product become negative and positive in comparison with those in the original GC/GC. Coulomb attraction caused by the charge separation mainly contributes to the stability of the SPT product. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009