High Bendability of Short RNA-DNA Hybrid Duplex Revealed by Single-Molecule Cyclization and Molecular Dynamics Simulations.

ABSTRACT: R-loops are nucleic acid structures composed of an RNA-DNA hybrid (RDH) duplex and a displaced single-stranded DNA (ssDNA), which are fundamentally involved in key biological functions, including transcription and the preservation of genome stability. In an R-loop, the RDH duplex is bent by the folded secondary structures of the displaced ssDNA. Previous experiments and simulations indicated the high bendability of DNA below the persistence length. However, the bendability of a short RDH duplex remains unclear. Here, we report that an RDH duplex exhibits higher bendability than a DNA duplex on the short length scale using single-molecule cyclization experiments. Our molecular dynamics simulations show that an RDH duplex has larger intrinsic curvature and structural fluctuations and more ea

SUBMITTER: Wu B 

PROVIDER: S-EPMC12109412 | biostudies-literature | 2025 May

REPOSITORIES: biostudies-literature