Chapter 4: Intrinsic Motions of DNA Polymerases Underlie Their Remarkable Specificity and Selectivity and Suggest a Hybrid Substrate Binding Mechanism

DNA polymerases have essential roles in DNA replication and repair. Deciphering the subtle details of the dynamical motion of different polymerases may help in identifying common features of polymerase mechanisms. Here, we analyze by principal component and covariance analyses the essential motions of several X-family DNA polymerases (β, λ, X, and µ) bound to correct and incorrect nucleotides as well as mutant and misaligned DNA complexes bound to the correct nucleotide. Results reveal distinct trends in subdomain/active-site residue motions before correct and incorrect nucleotide insertion that correlate with misinsertion efficiency. For example, correct/incorrect nucleotides enhance/reduce certain correlated motions that impact proper assembly of the active site for catalysis. In like manner, pol λ aligned and misaligned DNA complexes show nearly identical correlated motions, which agrees with pol λ's efficient correct nucleotide insertion within both substrates. Moreover, mutations in pol β's regions of correlated motions have been shown to affect substrate binding, function, and fidelity. Such correlated motion of DNA polymerases can be useful in identifying potential mutations that impair polymerase function and fidelity. It also suggests a ligand-binding mechanism that merges induced-fit with conformational sampling and could assist in the development of therapeutic agents for DNA repair-related diseases.