RNADNAbinding

RNADNAbinding refers to interactions in which RNA molecules associate with DNA, either directly through base pairing with DNA to form RNA-DNA hybrids or triplex structures, or indirectly via proteins that bridge RNA and DNA. These interactions can influence transcription, replication, and chromatin organization.

Mechanisms include RNA-DNA hybrids formed when nascent transcripts reanneal to the template strand (R-loops); triplex DNA formed by Hoogsteen base pairing between RNA and duplex DNA; and protein-mediated contacts in which RNA-binding proteins recruit to specific DNA regions or modify chromatin states. Binding specificity is governed by sequence, structure, and the presence of DNA motifs.

Biological roles include regulation of transcription and epigenetic marks, participation in telomere maintenance and genome stability, and involvement in immune receptor rearrangements and CRISPR-Cas–guided DNA targeting. Misregulation of RNA-DNA interactions can promote genomic instability and is linked to cancer and neurodegenerative diseases.

Methods used to study RNADNAbinding include DNA-RNA immunoprecipitation (DRIP) and DRIP-seq to map RNA-DNA hybrids, ChIP-based approaches for RNA-binding proteins at chromatin, and crosslinking and immunoprecipitation (CLIP, RIP) to study RNA-protein complexes. Structural studies (X-ray, NMR, cryo-EM) reveal binding interfaces. Related concepts include R-loops, triplex DNA, and RNA-guided DNA targeting systems such as CRISPR.