Department of Chemistry, Faculty of Science, Kanagawa University, 2946, Tsuchiya, Hiratsuka, Kanagawa 259-1293, Japan
DNA is highly reactive substance and is routinely damaged by the ultraviolet rays, the chemical substances, and so on. The various types of the DNA lesions have been known and the dimerized adjacent thymines, which is classified as a single-strand damage, is also one of such DNA lesions. However, the damaged DNA is immediately recovered through a repair process in order to maintain the normal genetic information. For example, the formed thymine dimer of the (6-4) photoproduct is repaired by the photolyase under the photoirradiation in plants and bacteria. The photolyase is a flavoprotein that has a chromophore cofactor flavin adenine dinucleotide (FAD) (Fig. 1) playing an important role as a coenzyme. We examined the mechanism of this electron-transfer induced repair reaction of the (6-4) T-T photolesion of DNA by the photolyase by the density functional theory (B3LYP) .
Fig. 1. A crystal structure (PDB ID : 3CVU) of a (6-4) T-T photolesion of DNA combined with a photolyase.
The repair reaction is generally thought to take place by the oxetane (Fig. 2) or the non-oxetane mechanism after an electron transfer between the cofactor FAD of the photolyase and the (6-4) T-T photolesion. Although a lot of calculations have been conducted for the radical anion pathway of both mechanisms, the relatively large energy barriers have been found in any case. We therefore calculated for the radical cation pathway in addition to the radical anion and the neutral pathways for both mechanisms to assess the possibility of the radical cation pathway. Our calculations showed that the radical anion pathway has a large energy barrier in both the oxetane and the non-oxetane mechanisms in agreement with the previous calculations. However, it was found that the radical cation pathway of the oxetane mechanism has a realistic low energy barrier. So, the further detail studies on the state of the FADH in the amino acid environment and under photoirradiation are expected, since it is general consensus that the electron transfer from the (6- 4) photoproduct to the FADH is unfavorable. The advantage of the radical cation pathway was ascribed to the following two things, (1) the unpaired electron exists on the reactive oxygen to form the oxetane (Fig. 3) and (2) the formed oxetane is stable in energy due to the strong interaction between two thymines. The dissociation of the C-C and the C-O bonds of the oxetane in the course of the repair reaction was also found to take place stepwise in the case of the radical cation, as known for the case of the radical anion. However, the order of the bonds dissociation was reversed, the unpaired electron playing a key role to determine this order.
Fig. 2. Unpaired electron and charge on the basis of the spin density and the Mulliken charge of the equilibrium and the transition state structures involved in the oxetane mechanism in the cases of the radical anion and the radical cation.
Fig. 3. Changes in the spin densities on the atoms during the repair reaction by the oxetane mechanism in the cases of the radical anion and the radical cation.
 Matsubara, T; Araida, N.; Hayashi, D.; Yamada, H. Bull. Chem. Soc. Jpn. 2014, 87, 390-399.