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Proton transfer induced SOMO-to-HOMO level switching in one-electron oxidized A-T and G-C base pairs: a density functional theory study.

ABSTRACT: In the present study, we show that for one-electron oxidized A-T or G-C base pairs the singly occupied molecular orbital (SOMO) is located on A or G and is lower in energy than the doubly occupied highest-occupied molecular orbital (HOMO) localized to the pyrimidines, T or C. This directs second ionizations to the pyrimidine bases resulting in triplet state diradical dications, (A(•+)-T(•+)) and (G(•+)-C(•+)). On interbase proton transfer, the SOMO and HOMO levels switch and the second oxidation is redirected to G and A. For G-C, the doubly oxidized singlet G(-H)(+)-C(H(+)) is more stable than its triplet (G(•+)-C(•+)); however, for A-T, the triplet (A(•+)-T(•+)) lies lowest in energy. The study demonstrates that double ionization of the A-T base pair results in a triplet dication diradical, which is more stable than the proton-transferred triplet or singlet species; whereas, double ionization of the G-C base pair, the proton transferred doubly oxidized singlet, G(-H)(+)-C(H(+)), is more stable and has both oxidations on guanine. In DNA, with both A-T and G-C, multiple oxidations would transfer to the guanine base alone.

SUBMITTER: Kumar A

PROVIDER: S-EPMC4032191 | biostudies-literature | 2014 May

REPOSITORIES: biostudies-literature

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Proton transfer induced SOMO-to-HOMO level switching in one-electron oxidized A-T and G-C base pairs: a density functional theory study.

Kumar Anil A Sevilla Michael D MD

The journal of physical chemistry. B 20140513 20

In the present study, we show that for one-electron oxidized A-T or G-C base pairs the singly occupied molecular orbital (SOMO) is located on A or G and is lower in energy than the doubly occupied highest-occupied molecular orbital (HOMO) localized to the pyrimidines, T or C. This directs second ionizations to the pyrimidine bases resulting in triplet state diradical dications, (A(•+)-T(•+)) and (G(•+)-C(•+)). On interbase proton transfer, the SOMO and HOMO levels switch and the second oxidation ...[more]

PMID: 24798145

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Project description:We address the recent debate surrounding the ability of 2,4-difluorotoluene (F), a low-polarity mimic of thymine (T), to form a hydrogen-bonded complex with adenine in DNA. The hydrogen bonding ability of F has been characterized as small to zero in various experimental studies, and moderate to small in computational studies. However, recent X-ray crystallographic studies of difluorotoluene in DNA/RNA have indicated, based on interatomic distances, possible hydrogen bonding interactions between F and natural bases in nucleic acid duplexes and in a DNA polymerase active site. Since F is widely used to measure electrostatic contributions to pairing and replication, it is important to quantify the impact of this isostere on DNA stability. Here, we studied the pairing stability and selectivity of this compound and a closely related variant, dichlorotoluene deoxyriboside (L), in DNA, using both experimental and computational approaches. We measured the thermodynamics of duplex formation in three sequence contexts and with all possible pairing partners by thermal melting studies using the van't Hoff approach, and for selected cases by isothermal titration calorimetry (ITC). Experimental results showed that internal F-A pairing in DNA is destabilizing by 3.8 kcal/mol (van't Hoff, 37 °C) as compared with T-A pairing. At the end of a duplex, base-base interactions are considerably smaller; however, the net F-A interaction remains repulsive while T-A pairing is attractive. As for selectivity, F is found to be slightly selective for adenine over C, G, T by 0.5 kcal mol, as compared with thymine's selectivity of 2.4 kcal/mol. Interestingly, dichlorotoluene in DNA is slightly less destabilizing and slightly more selective than F, despite the lack of strongly electronegative fluorine atoms. Experimental data were complemented by computational results, evaluated at the M06-2X/6-31+G(d) and MP2/cc-pVTZ levels of theory. These computations suggest that the pairing energy of F to A is ~28% of that of T-A, and most of this interaction does not arise from the F···HN interaction, but rather from the CH···N interaction. The nucleobase analogue shows no inherent selectivity for adenine over other bases, and L-A pairing energies are slightly weaker than for F-A. Overall, the results are consistent with a small favorable noncovalent interaction of F with A offset by a large desolvation cost for the polar partner. We discuss the findings in light of recent structural studies and of DNA replication experiments involving these analogues.

Dataset Information

Proton transfer induced SOMO-to-HOMO level switching in one-electron oxidized A-T and G-C base pairs: a density functional theory study.

Publications

Proton transfer induced SOMO-to-HOMO level switching in one-electron oxidized A-T and G-C base pairs: a density functional theory study.

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