The Effect of Pyrimidine Bases on the Hole-Transfer Coupling in DNA†

Abstract

Electron hole migration along the π-stack of DNA is mediated by the electronic coupling between the purines (guanine, adenine) of adjacent Watson-Crick pairs (WCPs). We have investigated the effect of the complementary pyrimidines (cytosine, thymine) on this coupling using the two-state model of electron transfer where, at the Hartree-Fock level, the hole-transfer coupling can be described by the energy splitting of the HOMO and HOMO-1 molecular orbitals of WCP dimers. Using the constrained space orbital variation method, we considered the effects of exchange, polarization, and electrostatic interactions (including hydrogen bonds of a WCP) of pyrimidines on the purine-purine electronic couplings. We also performed a detailed analysis of HOMO and HOMO-1 of the duplexes. We conclude that the effect of pyrimidines on the electronic coupling of neighboring purines cannot be described via perturbation theory nor simply reduced to an electrostatic polarization of the purines. However, the combination of exchange (frozen core) and electrostatic effects reproduces the coupling matrix elements between adjacent WCPs rather well. Analysis of the spatial overlap between orbital fragments of HOMO and HOMO-1 suggests that hydrogen bonds between complementary bases play a crucial role in the electronic coupling of neighboring WCPs.