ArticleProceedings of the National Academy of Sciences of the United States of America2017
Understanding the mechanical response of double-stranded DNA and RNA under constant stretching forces using all-atom molecular dynamics.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Molecular architecture of heterochromatin at the nuclear periphery of primary human cells.Nature communications · 2026Article
- TAV2b Peptide Derivatives Underwind and Stabilize Double-Stranded RNA upon Binding.Journal of the American Chemical Society · 2026Article
- Sequence-Dependent Shape and Stiffness of DNA and RNA Double Helices: Hexanucleotide Scale and Beyond.Journal of chemical information and modeling · 2025Article
- Engineering tunable catch bonds with DNA.Nature communications · 2024Article
- Effect of temperature on anisotropic bending elasticity of dsRNA: an all-atom molecular dynamics simulation.RSC 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
- Assembly mechanism of the inflammasome sensor AIM2 revealed by single molecule analysis.Nature communications · 2023Article
- Asymmetric Periodic Boundary Conditions for All-Atom Molecular Dynamics and Coarse-Grained Simulations of Nucleic Acids.The journal of physical chemistry. B · 2023Article
- 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
- Twisting DNA by salt.Nucleic acids research · 2022Article
- Accurate Sequence-Dependent Coarse-Grained Model for Conformational and Elastic Properties of Double-Stranded DNA.Journal of chemical theory and computation · 2022Article
- Twist-diameter coupling drives DNA twist changes with salt and temperature.Science advances · 2022Article
- Molecular dynamics analysis of biomolecular systems including nucleic acids.Biophysics and physicobiology · 2022Article
- Double-stranded RNA bending by AU-tract sequences.Nucleic acids research · 2020Article
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4 authors.
Funding
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Abstract
Multiple biological processes involve the stretching of nucleic acids (NAs). Stretching forces induce local changes in the molecule structure, inhibiting or promoting the binding of proteins, which ultimately affects their functionality. Understanding how a force induces changes in the structure of NAs at the atomic level is a challenge. Here, we use all-atom, microsecond-long molecular dynamics to simulate the structure of dsDNA and dsRNA subjected to stretching forces up to 20 pN. We determine all of the elastic constants of dsDNA and dsRNA and provide an explanation for three striking differences in the mechanical response of these two molecules: the threefold softer stretching constant obtained for dsRNA, the opposite twist-stretch coupling, and its nontrivial force dependence. The lower dsRNA stretching resistance is linked to its more open structure, whereas the opposite twist-stretch coupling of both molecules is due to the very different evolution of molecules' interstrand distance with the stretching force. A reduction of this distance leads to overwinding in dsDNA. In contrast, dsRNA is not able to reduce its interstrand distance and can only elongate by unwinding. Interstrand distance is directly correlated with the slide base-pair parameter and its different behavior in dsDNA and dsRNA traced down to changes in the sugar pucker angle of these NAs.
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