DNA polymerases must quickly and accurately distinguish between similar nucleic acids to form Watson-Crick base pairs and avoid DNA replication errors. Deoxynucleoside triphosphate (dNTP) binding to the DNA polymerase active site induces a large conformational change that is difficult to characterize experimentally on an atomic level. We have previously simulated DNA polymerase I bound to DNA with a dNTP present in the active site that forms a WC base pair, causing the polymerase to close. Here we describe the interactions between DNA polymerase bound to DNA in the presence of non-Watson-Crick base pairs. Our simulations allowed us to characterize the key steps involved in dNTP discrimination, which is a crucial biochemical process for DNA replication in organisms. Additionally, we further elucidated the role of active site residues in dNTP binding and discriminating between correct and incorrect nucleotides. Specifically, we describe the structural role of Tyr714 in destabilizing the dTTP-dG mismatch, while contrastingly stabilizing a dTTP-dA base pair.

Understanding the fidelity and specificity of DNA polymerase I

251st National Meeting (2016)

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