Oxidative damage to DNA: Theoretical determination of ionization potential of deoxyriboguanosine (dG)–deoxyribocytidine (dC) and proton transfer in its cation

Abstract

The geometries of the DNA nucleoside pairs between 2′-deoxyriboguanosine (dG) and 2′-deoxyribocytidine (dC) and its cation (dGdC +) were fully optimized using density functional methods. The ionization of an electron from dGdC results in remarkable changes to the three hydrogen bonding distances, the O⋯H4–N4 distance increasing by 0.160 Å and the N1–H1⋯N3 distance and the N2–H2⋯O2 distance decreasing by 0.116 Å and 1.234 Å, respectively. The ionization potential of the dGdC pair was studied to reveal the correct trends of adiabatic ionization potential (AIP) under the influence of the additional components to the individual bases. The result of a positive charge in terms of structural variations, energetic changes, and charge distribution were explored. The AIP of dGdC is predicted to be positive (6.48 eV), and exhibits a substantial increase compared with those of the corresponding bases G and C and the nucleic acid base pair GC. The effects of pairing and the addition of the sugar moiety on the AIP are well described as the summation of the individual influences. The influence of the pairing on the G is comparable to that of the addition of 2′-deoxyribose. The singlet charge is mainly located on the deoxyriboguanosine moiety in the cationic dGdC pair. The negative vertical electron attachment energy (−5.98 eV) for dGdC + suggests the cationic state is unstable with respect to electron attachment vertically. A large vertical ionization potential (VIP 7.05 eV) has been determined for the neutral dGdC nucleoside pair. The proton-transfer process between N1 of the guanine and N3 of the cytosine can occur in the GC cation and dGdC cation, and this process becomes easier when the sugar moiety linked on the base pair. Therefore, one may expect that the cationic dGdC nucleoside pair before and after proton transfer should be exist simultaneously.