Metal ions and sugar puckering balance single-molecule kinetic heterogeneity in RNA and DNA tertiary contacts.

ABSTRACT: The fidelity of group II intron self-splicing and retrohoming relies on long-range tertiary interactions between the intron and its flanking exons. By single-molecule FRET, we explore the binding kinetics of the most important, structurally conserved contact, the exon and intron binding site 1 (EBS1/IBS1). A comparison of RNA-RNA and RNA-DNA hybrid contacts identifies transient metal ion binding as a major source of kinetic heterogeneity which typically appears in the form of degenerate FRET states. Molecular dynamics simulations suggest a structural link between heterogeneity and the sugar conformation at the exon-intron binding interface. While Mg²⁺ ions lock the exon in place and give rise to long dwell times in the exon bound FRET state, sugar puckering alleviates this struc

SUBMITTER: Steffen FD 

PROVIDER: S-EPMC6949254 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature