Theoretical Studies of GG-Specific Photocleavage of DNA via Electron Transfer: Significant Lowering of Ionization Potential and 5‘-Localization of HOMO of Stacked GG Bases in B-Form DNA

Abstract

Ab initio molecular orbital calculations of stacked DNA bases were performed at the 3-21G(*) and 6-31G* levels to elucidate the origin of the 5‘-GG-3‘ sequence specificity for the photocleavage of DNA in the presence of electron-accepting photosensitizers. Ionization potentials (IP) were estimated as Koopman's theorem values for 16 sets of two stacked nucleobases and seven sets of stacked nucleobase pair systems in a B-form geometry. It was found that the GG/CC system is the lowest among the 10 possible stacked nucleobase pairs and that approximately 70% of the HOMO is localized on the 5‘-G of 5‘-GG-3‘. These calculations indicate that the 5‘-G of 5‘-GG-3‘ is the most electron donating site in B DNA and suggest that one-electron transfer from DNA to an electron acceptor occurs most effectively at 5‘-GG-3‘ sites which are fully consistent with the experimental data. In order to know the fate of the cation radical, the vertical IPs were estimated for seven stacked nucleobase pairs. It was found that the GG/CC system possesses the smallest vertical IP and that the cation radical is localized on the 5‘-G of 5‘-GG-3‘. These results imply that the 5‘-G of 5‘-GG-3‘ is a sink in “hole” migration through DNA, i . e ., an electron-loss center created in a B-form DNA will end up predominantly on the 5‘-G of 5‘-GG-3‘, and suggest that not only the base specificity for initial photoionization but also subsequent energetically favored hole migration to the lowest 5‘-GG-3‘ site are the origin of the 5‘-GG-3‘ specific cleavage. Calculations of stacked GGs with various geometries including orientations of A- and Z-form DNA were also examined.