Unlocking the chemistry facilitated by enzymes that process nucleic acids using quantum mechanical and combined...

The diverse cellular functions of nucleic acids are made possible by enzymes that catalyze cleavage of glycosidic (nucleobase-sugar) and phosphodiester bonds. Despite advancements in experimental biochemical methods, critical information about such enzyme-catalyzed reactions is difficult to obtain from traditional experiments. However, computational quantum mechanical (QM) methods can provide atomic level details of catalytic pathways that are complementary to experimental data. This perspective highlights various QM techniques used to advance our understanding of enzymes that process nucleic acids. First, select DNA glycosylases are discussed to showcase how QM calculations on nucleoside/tide and small molecule complexes uncover roles of active site interactions and the preferred order of reaction steps along DNA repair pathways. Furthermore, the ability of calculations on nucleic acid-enzyme complexes that combine QM methods with molecular mechanics (MM) force fields to challenge traditional views of enzyme function and lead to consensus for mechanistic pathways is illustrated. Subsequently, QM-based studies of select nucleases are discussed to highlight how this methodology can discern the various strategies enzymes use to cleave nucleic acid backbones. Overall, this contribution underscores the value in combining QM-based computational work with experimental studies to uncover enzyme-facilitated nucleic acid chemistry to be harnessed in future medicinal, biotechnological and materials applications.