Nymirum (United States)

Abstract Replicative errors contribute to the genetic diversity needed for evolution but in high frequency can lead to genomic instability. The mechanisms determining the frequency of DNA copying errors are not fully understood. Here, we show DNA dynamics determines the frequency of misincorporating the A-G mismatch and altered dynamics explains the high frequency of 8-oxoguanine (8OG) A-8OG misincorporation. NMR measurements revealed Aanti-Ganti (pop. >91%) transiently forms sparsely-populated and short-lived Aanti+-Gsyn (pop. ~ 2% and kex=kforward + kreverse ~ 137 s− 1) and Asyn-Ganti (pop. ~ 6% and kex ~ 2200 s− 1) Hoogsteen conformations. 8OG redistributed the ensemble rendering Aanti-8OGsyn the dominant state. A kinetic model in which Aanti+-Gsyn is misincorporated quantitatively predicted the kinetics of dA-dGTP misincorporation by human polymerase b, the pH dependence of misincorporation, and the impact of the 8OG lesion. Thus, 8OG increases replicative errors by increasing the abundance of a pre-existing, sparsely-populated, short-lived, and mutagenic Aanti+-Gsyn Hoogsteen state.

The use of NMR-derived chemical shifts in protein structure determination and prediction has received much attention, and, as such, many methods have been developed to predict protein chemical shifts from three-dimensional (3D) coordinates. In contrast, little attention has been paid to predicting chemical shifts from RNA coordinates. Using the random forest machine learning approach, we developed RAMSEY, which is capable of predicting both (1)H and protonated (13)C chemical shifts from RNA coordinates. In this report, we introduce RAMSEY, assess its accuracy, and demonstrate the sensitivity of RAMSEY-predicted chemical shifts to RNA 3D structure.