Role of Substrate Binding Interactions on DNA Repair by Photolyase

The repair of the cyclobutane pyrimidinedimer (CPD) lesion inDNA by photolyase is determined by its initial recognition, and thecatalytic efficiency depends on a series of intermolecular electron-transfer(ET) processes. Here, we investigated the repair of a CPD structuralisomer, replacing the deoxyribose with a pyranose sugar on the 5 & PRIME;site, and found a loss in binding efficiency and repair quantum yield.Using femtosecond spectroscopy, we characterized all elementary repairsteps and observed a systemic slowdown of the four intermolecularET reactions and the second bond splitting. Our observations and moleculardynamics simulations suggest that the sugar replacement disrupts thelesion binding configuration, weakening the electronic coupling betweenthe cofactor and lesion and altering the stability of lesion intermediates.These findings highlight how the CPD photolyases have utilized thestructural features of the CPD lesion and optimized its interactionswith the cofactor and key active-site residues to maximize repairyields.