ArticleThe EMBO journal2008
Specific recognition of RNA/DNA hybrid and enhancement of human RNase H1 activity by HBD.
Article in The EMBO journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.
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Who cites it
75 citing papers in PubMed.
- The MODNAP benchmark set for modeling ribose-based modified nucleic acid and nucleic acid-protein complexes: a case study with AlphaFold 3.Nucleic acids research · 2026Article
- An RNase domain-dependent microRNA detection with DNA-spiked nanocage for accurate cancer diagnosis.Nature communications · 2026Article
- Sequence and structural alignments reveal insights into ANKLE2 evolution and function.Protein science : a publication of the Protein Society · 2026Article
- R-loop homeostasis at transposable elements safeguards transcriptional silencing in replication-quiescent oocytes.Nature communications · 2026Article
- RPA hyperphosphorylation hinders the resolution of R-loops and G-quadruplex-associated R-loops during RAS-driven senescence.Nucleic acids research · 2026Article
- Advancement in the Methods for Isolating High Quality RNA From Mouse and Rat Intervertebral Disc.JOR spine · 2026Article
- Regulation of transcription by R loop-nucleated transcription condensate assembly.Cell & bioscience · 2026Review
- Biochemical Characterization of R-Loop Degradation by Chloroplast-Localized RNase H1 fromInternational journal of molecular sciences · 2025Article
- RNA-DNA hybrid binding domain broadens the editing window of base editors.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Article
- Endogenous Ribonucleases: Therapeutic Targeting of the Transcriptome Through Oligonucleotide-Triggered RNA Inactivation.Biomolecules · 2025Review
- An improved cytological assay for R-loop detection in Saccharomyces cerevisiae utilizing a catalytically inactive RNase H.G3 (Bethesda, Md.) · 2025Article
- Interferon-dependent R-loop induction by Zika virus contributes to growth attenuation.PNAS nexus · 2025Article
- Selectively expressed RNA molecules as a versatile tool for functionalized cell targeting.Nature communications · 2025Article
- Global coupling of R-loop dynamics with RNA polymerase II modulates gene expression and early development of Drosophila.Nucleic acids research · 2024Article
- Article
- RPA transforms RNase H1 to a bidirectional exoribonuclease for processive RNA-DNA hybrid cleavage.Nature communications · 2024Article
- AFM Imaging Reveals MicroRNA-132 to be a Positive Regulator of Synaptic Functions.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- TERRA-LSD1 phase separation promotes R-loop formation for telomere maintenance in ALT cancer cells.Nature communications · 2024Article
- Live-cell imaging unveils distinct R-loop populations with heterogeneous dynamics.Nucleic acids research · 2023Article
- Genome-wide map of R-loops reveals its interplay with transcription and genome integrity during germ cell meiosis.Journal of advanced research · 2023Article
15 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
Abstract
Human RNase H1 contains an N-terminal domain known as dsRHbd for binding both dsRNA and RNA/DNA hybrid. We find that dsRHbd binds preferentially to RNA/DNA hybrids by over 25-fold and rename it as hybrid binding domain (HBD). The crystal structure of HBD complexed with a 12 bp RNA/DNA hybrid reveals that the RNA strand is recognized by a protein loop, which forms hydrogen bonds with the 2'-OH groups. The DNA interface is highly specific and contains polar residues that interact with the phosphate groups and an aromatic patch that appears selective for binding deoxyriboses. HBD is unique relative to non-sequence-specific dsDNA- and dsRNA-binding domains because it does not use positive dipoles of alpha-helices for nucleic acid binding. Characterization of full-length enzymes with defective HBDs indicates that this domain dramatically enhances both the specific activity and processivity of RNase H1. Similar activity enhancement by small substrate-binding domains linked to the catalytic domain likely occurs in other nucleic acid enzymes.
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