Ultrafast dynamics of energy and electron transfer in DNA-photolyase

One of the detrimental effects of UV radiation on the biosphere is the formation of cyclobutane pyrimidine dimers (Pyr<>Pyr) between two adjacent thymine bases in DNA. Pyr<>Pyr dimers can not be repaired by normal DNA repair machinery and may result in gene mutation or cell death. Photolyase, a photoenzyme harnesses blue or near-UV light energy to cleave the cyclobutane ring of the Pyr<>Pyr and thus protects against the harmful effects of UV radiation. In the proposed hypothesis for the catalysis, the enzyme binds a Pyr<>Pyr in DNA, independent of light. The photoantenna, a photolyase cofactor methenyltetrahydrofolate (MTHF) harvests a UV/blue-light photon, and transfers the excitation energy (dipole-dipole interaction) to another photolyase cofactor, a fully reduced flavin (FADH-). Excited FADH-* then transfers an electron to the Pyr<>Pyr, which consequently splits the Pyr<>Pyr into two pyrimidine moieties and hence repairs the damaged DNA. As proposed, the repair cycle ends when the excess electron from the repaired pyrimidine moieties is transferred back to the nascent-formed neutral FADH· species and regenerates the active FADH- form. The complex mechanism of energy and electron transfer in photolyase enzyme involved in performing its DNA repair function was investigated using femtosecond-resolved fluorescence up-conversion and transient absorption methods. Under physiological conditions, the excitation energy transfer from the antenna molecule MTHF to the FADH- occurs in 292 ps, but it takes 19 ps to the in vitro oxidized neutral cofactor FADH·. The orientation factors were found to be 0.11 for the MTHF-FADH- pair and 0.28 for MTHF-FADH ·, unfavorable for energy transfer, indicating the existing structural constraints probably placed by three functional binding sites. The photoreduction of the neutral FADH· to the catalytically active cofactor FADH- was revealed to evolve along two electron-transfer pathways: one is along a tryptophan triad with the initial electron hop in 10 ps; the other route starts with an initial electron separation in 40 ps through the neighboring phenylalanine followed by either tunneling along an alpha-helix or hopping through the tryptophan triad again. Ultrafast libration/rotation motions of local protein residues and trapped water molecules at the active site were observed to initially occur in ∼2 ps. These ultrafast ordered-water motions are critical to stabilizing the photoreduction product FADH- instantaneously to prevent fast charge recombination.; Monitoring the catalytic processes we observed direct electron transfer from the FADH-* to the Pyr<>Pyr in 170 ps and back electron transfer from the repaired thymines in 560 ps. Both reactions are strongly modulated by active-site solvation to achieve maximum repair efficiency. These results show that the photocycle of DNA repair by photolyase is through a radical mechanism and completed on subnanosecond time scale at the dynamic active site, with no net change in the redox state of the flavin cofactor.; The photophysics of FADH- cofactor was studied in aqueous solution. Dramatic shortening of the excited state lifetime of FADH - in aqueous solution compare to its lifetime in protein environment compelled us to propose that enzyme photolyase also modulates photophysical properties of the flavin cofactor to perform the essential biological function of electron transfer to repair damaged DNA.