Ribose Sugar Alters Conformational Sampling of G•T Mismatched Duplex DNA.

Abstract

Polymerases erroneously incorporate Guanine-Thymine (dG•dT) mismatches in genomic DNA that further evades repair by transient sampling of tautomeric/ionic states compromising fidelity of repairing dG•dT mismatches. In conjunction, significant frequency of ribose (mis)incorporation in duplex DNA permits for misincorporated-mismatch in the genome. Ribose incorporated G(rG) mismatched with T(rG•dT) is the most stable across all misincorporated-mismatch calling into question the conformational consequences of the ribose sugar in addition to the mismatch. In this work, the effects of single rG•dT is investigated within a dodecamer DNA duplex employing solution-state NMR spectroscopy, partial anisotropic measurements in conjunction with molecular dynamics simulations to evaluate the impact on base pairs and the overall duplex structure. It is observed that rG•dT pairs exhibit enhanced flexibility in both base-pair and sugar dynamics compared to dG•dT, and the perturbations are enhanced in comparison to a ribose incorporated adenine-thymine (rA•dT) pair. The structural perturbations compared between rG•dT and dG•dT provides clues on plausible recognition modes of ribonucleotide excision repair (RER) pathway that looks for misincorporated ribose and mismatch repair (MMR) enzymes that scout for a mismatch.