ArticleProceedings of the National Academy of Sciences of the United States of America2023
Universality in RNA and DNA deformations induced by salt, temperature change, stretching force, and protein binding.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 29 citations in OpenAlex.
- DNA twist at high alkali ion concentrations: evidence against C-form DNA in solution.Nucleic acids research · 2026Article
- Local cation-clamping distorts and softens RNA duplex.Communications biology · 2026Article
- A universal entropic pulling force caused by binding.Nature communications · 2025Article
- The effects of DMSO on DNA conformations and mechanics.Biophysical journal · 2025Article
- Counterintuitive DNA destabilization by monovalent salt at high concentrations due to overcharging.Nature communications · 2025Article
- Predicting the effect of binding molecules on the shape and mechanical properties of structured DNA assemblies.Nature communications · 2024Article
- Article
- Effect of temperature on anisotropic bending elasticity of dsRNA: an all-atom molecular dynamics simulation.RSC advances · 2024Article
- Biocontrol Potential of Sodin 5, Type 1 Ribosome-Inactivating Protein fromBiomolecules · 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
- Article
- On the common pathways of deformation: RNA vs DNA under interrogation.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nucleic acid deformations play important roles in many biological processes. The physical understanding of nucleic acid deformation by environmental stimuli is limited due to the challenge in the precise measurement of RNA and DNA deformations and the complexity of interactions in RNA and DNA. Magnetic tweezers experiments provide an excellent opportunity to precisely measure DNA and RNA twist changes induced by environmental stimuli. In this work, we applied magnetic tweezers to measure double-stranded RNA twist changes induced by salt and temperature changes. We observed RNA unwinds when lowering salt concentration, or increasing temperature. Our molecular dynamics simulations revealed the mechanism: lowering salt concentration or increasing temperature enlarges RNA major groove width, which causes twist decrease through twist-groove coupling. Combining these results with previous results, we found some universality in RNA and DNA deformations induced by three different stimuli: salt change, temperature, and stretching force. For RNA, these stimuli first modify the major groove width, which is transduced into twist change through twist-groove coupling. For DNA, these stimuli first modify diameter, which is transduced into twist change through twist-diameter coupling. Twist-groove coupling and twist-diameter coupling appear to be utilized by protein binding to reduce DNA and RNA deformation energy cost upon protein binding.
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