title: Stability of the valence anion of cytosine is governed by nucleobases sequence in the double stranded DNA pi-stack: A computational study.
abstract: The stabilities of the valence anion of cytosine (C(-)) in model trimers of complementary base pairs that possess the B-DNA geometry but differ in base sequence are reported. In order to estimate the energetics of electron attachment to the middle cytosine incorporated in the trimer, a thermodynamic cycle employing all possible two-body interaction energies in the neutral and anionic duplex as well as the adiabatic electron affinity of isolated cytosine were developed. All calculations were carried out at the MP2 level of theory with the aug-cc-pVDZ basis set. We have demonstrated that contrary to the literature reports, concerning single stranded DNA, the sequence of nucleic bases has a profound effect on the stability of the cytosine valence anion. The anionic 3(')-CCC-5(') complex is the most stable configuration (EA=0.399 eV) and the 3(')-GCG-5(') trimer anion is the most unstable species (EA=-0.193 eV). Moreover, with the energetic correction for the presence of sugar-phosphate backbone all possible double stranded DNA sequences lead to the stable C(-). The predicted electron affinities of the cytosine anion have been compared to the results of analogous studies on the thymine anion published recently [M. Kobyłecka et al., J. Am. Chem. Soc. 130, 15683 (2008)]. The consequences of low-energy barrier proton transfer in the GC anion have been discussed in the context of induced by electrons DNA single strand breaks. The DNA sequences that should dramatically differ in their vulnerability to be damaged by low energy electrons have been proposed.
authors.affiliation: Faculty of Chemistry, University of Gdańsk, 80-952 Gdansk, Poland.
authors.forename: Monika
authors.initials: M
authors.lastname: Kobyłecka
authors.forename: Jerzy
authors.initials: J
authors.lastname: Leszczynski
authors.forename: Janusz
authors.initials: J
authors.lastname: Rak
mesh_terms: D020029:Base Pairing; D003198:Computer Simulation; D003596:Cytosine / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D003854:Deoxyribonucleotides / Q000737:chemistry*; D004583:Electrons; D008958:Models, Molecular; D011522:Protons; D013941:Thymine / Q000737:chemistry
chemical_list: D003854:Deoxyribonucleotides; D011522:Protons; D003596:Cytosine; D004247:DNA; D013941:Thymine