Sequence dependence of transient Hoogsteen base pairing in DNA.

ABSTRACT: Hoogsteen (HG) base pairing is characterized by a 180° rotation of the purine base with respect to the Watson-Crick-Franklin (WCF) motif. Recently, it has been found that both conformations coexist in a dynamical equilibrium and that several biological functions require HG pairs. This relevance has motivated experimental and computational investigations of the base-pairing transition. However, a systematic simulation of sequence variations has remained out of reach. Here, we employ advanced path-based methods to perform unprecedented free-energy calculations. Our methodology enables us to study the different mechanisms of purine rotation, either remaining inside or after flipping outside of the double helix. We study seven different sequences, which are neighbor variations of a well-studie

SUBMITTER: Perez de Alba Ortiz A 

PROVIDER: S-EPMC9177043 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature