Theoretical Study on the Repair Mechanism of the (6−4) Photolesion by the (6−4) Photolyase

Abstract

UV irradiation of DNA can lead to the formation of mutagenic (6-4) pyrimidine-pyrimidone photolesions. The (6-4) photolyases are the enzymes responsible for the photoinduced repair of such lesions. On the basis of the recently published crystal structure of the (6-4) photolyase bound to DNA [Maul et al. 2008] and employing quantum mechanics/molecular mechanics techniques, a repair mechanism is proposed, which involves two photoexcitations. The flavin chromophore, initially being in its reduced anionic form, is photoexcited and donates an electron to the (6-4) form of the photolesion. The photolesion is then protonated by the neighboring histidine residue and forms a radical intermediate. The latter undergoes a series of energy stabilizing hydrogen-bonding rearrangements before the electron back transfer to the flavin semiquinone. The resulting structure corresponds to the oxetane intermediate, long thought to be formed upon DNA-enzyme binding. A second photoexcitation of the flavin promotes another electron transfer to the oxetane. Proton donation from the same histidine residue allows for the splitting of the four-membered ring, hence opening an efficient pathway to the final repaired form. The repair of the lesion by a single photoexcitation was shown not to be feasible.

Repair of the (6–4) Photoproduct by DNA Photolyase Requires Two Photons

“…[8] This and other experimental or theoretical studies generally assumed that the (6-4)PPs, like CPDs, are repaired upon absorption of a single photon by the enzyme. [8][9][10][11] The possibility of a two-photon process has been ignored, except for one computational study by Sadeghian et al [12] They suggested that a first photo-induced electron transfer (ET) from FADH À converts T(6-4)T to the oxetane-linked dimer, denoted T(ox)T, also involved in photodamage (see Scheme 1); after return of the excess electron to the flavin, a second photo-induced ET from FADH À splits the oxetane ring with restoration of two intact thymines and return of the electron. Of note, it was long believed [2,6,10] that the (6-4)PP is converted to the oxetane (or azetidine for the T(6-4)C lesion) upon binding to the enzyme in the dark.…”

Hetero-cycloreversions Mediated by Photoinduced Electron Transfer

“…22,23,24,25,26,27 The idea that (6-4) photoproducts are converted to oxetanes (or azetidines) upon binding to the enzyme in the dark has been questioned based on the crystal structure of a model (6-4) photoproduct in the binding pocket. 28,29 In general, experimental and theoretical studies assume that (6-4) photoproducts are repaired upon absorption of a single photon by the enzyme.…”

Computational Study on the Mechanism of the Electron-Transfer-Induced Repair of the (6–4) T–T Photoproduct of DNA by Photolyase: Possibility of a Radical Cation Pathway

“…In contrast, the energy barrier for the splitting is only about 2 kcal mol ¹1 in the case of CPD. 7,8 The calculated large energy barrier for the (64) 9 where the electron transfer between the cofactor FAD and the TT lesion at the active site occurs two times. However, the large energy barrier at the oxetane itself basically remains as it is.…”

“…The repair reaction was followed by a model system of (64) TT photoproduct and its surrounding amino acids were approximated by the polarized-continuum-model (PCM), because the surrounding amino acids are not essential in the discussion of the energy profile of the repair reaction. 9 …”