Relationship between conformational changes in pol λ's active site upon binding incorrect nucleotides and mismatch incorporation rates

The correct replication and repair of DNA is critical for a cell's survival. Here, we investigate the fidelity of mammalian DNA polymerase λ (pol λ) utilizing dynamics simulation of the enzyme bound to incorrect incoming nucleotides including A:C, A:G, A(syn):G, A:A, A(syn):A, and T:G, all of which exhibit differing incorporation rates for pol λ as compared to A:T bound to pol λ. The wide range of DNA motion and protein residue side-chain motions observed in the mismatched systems demonstrates distinct differences when compared to the reference (correct base pair) system. Notably, Arg517's interactions with the DNA template strand bases in the active site are more limited, and Arg517 displays increased interactions with the incorrect dNTPs. This effect suggests that Arg517 helps provide a base-checking mechanism to discriminate correct from incorrect dNTPs. In addition, we find Tyr505 and Phe506 also play key roles in this base checking. A survey of the electrostatic potential landscape of the active sites and concomitant changes in electrostatic interaction energy between Arg517 and the dNTPs reveals that pol λ binds incorrect dNTPs less tightly than the correct dNTP. These trends lead us to propose the following order for mismatch insertion by pol λ: A:C > A:G > A(syn):G > T:G > A(syn):A > A:A. This sequence agrees with available kinetic data for incorrect nucleotide insertion opposite template adenine, with the exception of T: G, which may be more sensitive to the insertion context.