Free Energy Landscape and Conformational Kinetics of Hoogsteen Base Pairing in DNA vs. RNA.

ABSTRACT: Genetic information is encoded in the DNA double helix, which, in its physiological milieu, is characterized by the iconical Watson-Crick nucleo-base pairing. Recent NMR relaxation experiments revealed the transient presence of an alternative, Hoogsteen (HG) base pairing pattern in naked DNA duplexes, and estimated its relative stability and lifetime. In contrast with DNA, such structures were not observed in RNA duplexes. Understanding HG base pairing is important because the underlying "breathing" motion between the two conformations can significantly modulate protein binding. However, a detailed mechanistic insight into the transition pathways and kinetics is still missing. We performed enhanced sampling simulation (with combined metadynamics and adaptive force-bias method) and Markov s

SUBMITTER: Ray D 

PROVIDER: S-EPMC7642241 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature