ArticleBiophysical journal2019
The Mechanical Properties of RNA-DNA Hybrid Duplex Stretched by Magnetic Tweezers.
Article in Biophysical journal, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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34 citing papers in PubMed, 69 citations in OpenAlex.
- Measuring cellular force using DNA-based tension probes: from ensemble to single-molecule studies.Nature protocols · 2026Review
- Hepatitis B virus ribonuclease H inhibitors: Coming of age?Antiviral research · 2026Review
- A tunable autonomous RNA-fueled micro-engine.Nature communications · 2026Article
- Local cation-clamping distorts and softens RNA duplex.Communications biology · 2026Article
- Programmable electric tweezers.Science advances · 2026Article
- LbuCas13a directly targets DNA and elicits strong trans-cleavage activity.Nature biomedical engineering · 2025Article
- Supramolecular Interactions Modulate RNA:DNA Folding Observed via Nanopore Sensing.Angewandte Chemie (International ed. in English) · 2025Article
- RNA polymerase II is a polar roadblock to a progressing DNA fork.Nature communications · 2025Article
- High Bendability of Short RNA-DNA Hybrid Duplex Revealed by Single-Molecule Cyclization and Molecular Dynamics Simulations.Biomolecules · 2025Article
- Identifying the interactions conferring functional mechanical rigidity on RNase-resistant RNA from Zika virus.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Discovery of bimodal hepatitis B virus ribonuclease H and capsid assembly inhibitors.PLoS pathogens · 2025Article
- Force-enhanced sensitive and specific detection of DNA-intercalative agents directly from microorganisms at single-molecule level.Nucleic acids research · 2024Article
- Nanopore Translocation Reveals Electrophoretic Force on Noncanonical RNA:DNA Double Helix.ACS nano · 2024Article
- Effect of temperature on anisotropic bending elasticity of dsRNA: an all-atom molecular dynamics simulation.RSC advances · 2024Article
- Vibration spectra of DNA and RNA segments.European biophysics journal : EBJ · 2024Article
- The origin of different bending stiffness between double-stranded RNA and DNA revealed by magnetic tweezers and simulations.Nucleic acids research · 2024Article
- Temperature-dependent elasticity of DNA, RNA, and hybrid double helices.Biophysical journal · 2024Article
- Temperature-Dependent Twist of Double-Stranded RNA Probed by Magnetic Tweezer Experiments and Molecular Dynamics Simulations.The journal of physical chemistry. B · 2024Article
- Optical Tweezers to Study Viruses.Sub-cellular biochemistry · 2024Review
- A novel design for magnetic tweezers with wide-range temperature control.Biophysical journal · 2023Article
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA can anneal to its DNA template to generate an RNA-DNA hybrid (RDH) duplex and a displaced DNA strand, termed R-loop. RDH duplex occupies up to 5% of the mammalian genome and plays important roles in many biological processes. The functions of RDH duplex are affected by its mechanical properties, including the elasticity and the conformation transitions. The mechanical properties of RDH duplex, however, are still unclear. In this work, we studied the mechanical properties of RDH duplex using magnetic tweezers in comparison with those of DNA and RNA duplexes with the same sequences. We report that the contour length of RDH duplex is ∼0.30 nm/bp, and the stretching modulus of RDH duplex is ∼660 pN, neither of which is sensitive to NaCl concentration. The persistence length of RDH duplex depends on NaCl concentration, decreasing from ∼63 nm at 1 mM NaCl to ∼49 nm at 500 mM NaCl. Under high tension of ∼60 pN, the end-opened RDH duplex undergoes two distinct overstretching transitions; at high salt in which the basepairs are stable, it undergoes the nonhysteretic transition, leading to a basepaired elongated structure, whereas at low salt, it undergoes a hysteretic peeling transition, leading to the single-stranded DNA strand under force and the single-stranded RNA strand coils. The peeled RDH is difficult to reanneal back to the duplex conformation, which may be due to the secondary structures formed in the coiled single-stranded RNA strand. These results help us understand the full picture of the structures and mechanical properties of nucleic acid duplexes in solution and provide a baseline for studying the interaction of RDH with proteins at the single-molecule level.
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