Theoretical studies on interactions between low energy electrons and protein-DNA fragments: valence anions of AT-amino acids side chain complexes

Abstract

Electron attachment to trimeric complexes that mimic most frequent hydrogen bonding interactions between an amino acid side chain (AASC) and the Watson-Crick (WC) 9-methyladenine-1-methylthymine (MAMT) base pair has been studied at the B3LYP/6-31++G(d,p) level of theory. Although the neutral trimers will not occur in the gas phase due to unfavorable free energy of stabilization (G(stab)) they should form a protein-DNA complex where entropy changes related to formation of such a complex will more than balance its disadvantageous G(stab). The most stable neutrals possess an identical pattern of hydrogen bonds (HBs). In addition, the proton-acceptor (N7) and proton-donor (N10) atoms of adenine involved in those HBs are located in the main groove of DNA. All neutral structures support the adiabatically stable valence anions in which the excess electron is localized on a π* orbital of thymine. The vertical detachment energies (VDEs) of anions corresponding to the most stable neutrals are substantially smaller than that of the isolated WC MAMT base pair. Hence, electron transfer from the anionic thymine to the phosphate group and as a consequence formation of a single strand break (SSB) should proceed more efficiently in a protein-dsDNA complex than in the naked dsDNA as far as electron attachment to thymine is concerned.