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.