ArticleNucleic acids research2015
Explaining the striking difference in twist-stretch coupling between DNA and RNA: A comparative molecular dynamics analysis.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 72 citations in OpenAlex.
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- Sequence-Dependent Shape and Stiffness of DNA and RNA Double Helices: Hexanucleotide Scale and Beyond.Journal of chemical information and modeling · 2025Article
- siRNA Interaction and Transfection Properties of Polycationic Phosphorus Dendrimers.Biomacromolecules · 2025Article
- Comparative molecular dynamics calculations of duplexation of chemically modified analogs of DNA used for antisense applications.NAR genomics and bioinformatics · 2024Article
- Effect of temperature on anisotropic bending elasticity of dsRNA: an all-atom molecular dynamics simulation.RSC advances · 2024Article
- An RNA origami robot that traps and releases a fluorescent aptamer.Science advances · 2024Article
- The origin of different bending stiffness between double-stranded RNA and DNA revealed by magnetic tweezers and simulations.Nucleic acids research · 2024Article
- Systematic Comparison of Atomistic Force Fields for the Mechanical Properties of Double-Stranded DNA.Journal of chemical theory and computation · 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
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- Computational Modeling of DNA 3D Structures: From Dynamics and Mechanics to Folding.Molecules (Basel, Switzerland) · 2023Review
- 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
- Universality in RNA and DNA deformations induced by salt, temperature change, stretching force, and protein binding.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- 3D RNA-scaffolded wireframe origami.Nature communications · 2023Article
- Twisting DNA by salt.Nucleic acids research · 2022Article
- Doxorubicin impacts chromatin binding of HMGB1, Histone H1 and retinoic acid receptor.Scientific reports · 2022Article
- Twist-diameter coupling drives DNA twist changes with salt and temperature.Science advances · 2022Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Double stranded helical DNA and RNA are flexible molecules that can undergo global conformational fluctuations. Their bending, twisting and stretching deformabilities are of similar magnitude. However, recent single-molecule experiments revealed a striking qualitative difference indicating an opposite sign for the twist-stretch couplings of dsDNA and dsRNA [Lipfert et al. 2014. Proc. Natl. Acad. Sci. U.S.A. 111, 15408] that is not explained by existing models. Employing unconstrained Molecular Dynamics (MD) simulations we are able to reproduce the qualitatively different twist-stretch coupling for dsDNA and dsRNA in semi-quantitative agreement with experiment. Similar results are also found in simulations that include an external torque to induce over- or unwinding of DNA and RNA. Detailed analysis of the helical deformations coupled to twist indicate that the interplay of helical rise, base pair inclination and displacement from the helix axis upon twist changes are responsible for the different twist-stretch correlations. Overwinding of RNA results in more compact conformations with a narrower major groove and consequently reduced helical extension. Overwinding of DNA decreases the size of the minor groove and the resulting positive base pair inclination leads to a slender and more extended helical structure.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.