Noncanonical Stacking Geometries of Nucleobases as a Preferred Target for Solar Radiation

Direct DNA absorption of UVB photons in a spectral range of 290–320 nm of terrestrial solar radiation is responsible for formation of cyclobutane pyrimidine dimers causing skin cancer. Formation of UVB-induced lesions is not random, and conformational features of their hot spots remain poorly understood. We calculated the electronic excitation spectra of thymine, cytosine, and adenine stacked dimers with ab initio methods in a wide range of conformations derived from PDB database and molecular dynamics trajectory of thymine-containing oligomer. The stacked dimers with reduced interbase distances in curved, hairpin-like, and highly distorted DNA and RNA structures exhibit excitonic transitions red-shifted up to 0.6 eV compared to the B-form of stacked bases, which makes them the preferred target for terrestrial solar radiation. These results might have important implications for predicting the hot spots of UVB-induced lesions in nucleic acids.