Dynamics of DNA Repair by Class-II Photolyases via a Unified Electron-Transfer Bifurcating Mechanism

The class-II photolyases (PLs) are distantly related to the microbial class-I photolyases with low sequence similarity, yet they maintain a similar structural topology and repair the same UV-induced cyclobutane pyrimidine dimer (CPD). The class-I photolyases have been well characterized through a direct electron-transfer (ET) tunneling mechanism with high repair quantum yield, but such a mechanism seemingly does not apply to all of the members in the diversified photolyase family. Here, using femtosecond spectroscopy, we show our systematic characterization of CPD repair by the class-II photolyases from <i>Methanosarcina mazei</i> and <i>Drosophila melanogaster</i> and reveal their complete photocycles with determination of reaction times of all ten elementary steps, including seven electron-transfer processes. We found that the initial electron injection bifurcates along two parallel routes, direct tunneling and two-step hopping. Unlike the class-I photolyases, the direct tunneling process here is significantly slower, occurring in several nanoseconds. This slow tunneling route leads to shifting of the branching yield toward the intrinsic two-step hopping pathway through the adenine intermediate. Throughout the photolyase family, the enzymes have adopted a unified bifurcating electron-transfer strategy as a universal repair mechanism through evolution.