Direct Measurement of 8OG syn-anti Flips in Mutagenic 8OG·A and Long-Range Damage-Dependent Hoogsteen Breathing Dynamics Using 1H CEST NMR

Abstract

Elucidating how damage impacts DNA dynamics is essential for understanding the mechanisms of damage recognition and repair. Many DNA lesions alter the propensities to form lowly-populated and short-lived conformational states. However, NMR methods to measure these dynamics require isotopic enrichment, which is difficult for damaged nucleotides. Here, we demonstrate the utility of the 1H chemical exchange saturation transfer (CEST) NMR experiment in measuring the dynamics of oxidatively damaged 8-oxoguanine (8OG) in the mutagenic 8OGsyn*Aanti mismatch. Using 8OG-H7 as an NMR probe of the damaged base, we directly measured 8OG syn-anti flips to form a lowly-populated (pop. [~] 5%) and short-lived (lifetime [~] 50 ms) non-mutagenic 8OGanti*Aanti. These exchange parameters were in quantitative agreement with values from 13C off-resonance R1{rho} and CEST on a labeled partner adenine. The Watson-Crick-like 8OGsyn*Aanti mismatch also rescued the kinetics of Hoogsteen motions at distance A-T base pairs, which the G*A mismatch had slowed down. The results lend further support for 8OGanti*Aanti as a minor conformational state of 8OG*A, reveal that 8OG damage can impact Hoogsteen dynamics at a distance, and demonstrate the utility of 1H CEST for measuring damage-dependent dynamics in unlabeled DNA.