Electron Donor–Acceptor Interactions with Flanking Purines Influence the Efficiency of Thymine Photodimerization

Abstract

Quantum yields for thymine photodimerization (ΦTT) have been determined for a series of short DNA single-strand and base-paired hairpin structures possessing a single thymine–thymine step with flanking purines. Values of ΦTT are strongly dependent upon the oxidation potential of the flanking purine, decreasing in the order: inosine > adenine > guanine > deazaguanine. The dependence of ΦTT on the ionization potential of the flanking purine is more pronounced when the purine of lower oxidation potential is located at the 5′- versus 3′-position in either a single strand or a hairpin. Molecular dynamics simulations for hairpin structures indicate that the TT step is π-stacked with both the 5′ and 3′ purine, but that there is little π-stacking with either purine in single-strand structures. The observation of moderately intense long-wavelength UV absorption features for hairpins having 5′-Z or G flanking purines suggests that excitation of ground state donor–acceptor complexes may account for more extensive quenching of dimerization by 5′- versus 3′-purines. The “purine effect” on ΦTT is attributed to a combination of ground state conformation, ground state electron donor–acceptor interactions, and excited state exciplex formation.