ArticleBiophysical journal2010
Toward a consensus view of duplex RNA flexibility.
Article in Biophysical journal, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Effect of temperature on anisotropic bending elasticity of dsRNA: an all-atom molecular dynamics simulation.RSC advances · 2024Article
- Systematic Comparison of Atomistic Force Fields for the Mechanical Properties of Double-Stranded DNA.Journal of chemical theory and computation · 2024Article
- Twist-stretch relations in nucleic acids.European biophysics journal : EBJ · 2023Article
- Structure-mechanics statistical learning unravels the linkage between local rigidity and global flexibility in nucleic acids.Chemical science · 2020Article
- Bending of DNA duplexes with mutation motifs.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- Structural Flexibility of DNA-RNA Hybrid Duplex: Stretching and Twist-Stretch Coupling.Biophysical journal · 2019Article
- Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Regulation of the activity of the promoter of RNA-induced silencing, C3PO.Protein science : a publication of the Protein Society · 2017Article
- Martini Coarse-Grained Force Field: Extension to RNA.Biophysical journal · 2017Article
- Determination of the conformational ensemble of the TAR RNA by X-ray scattering interferometry.Nucleic acids research · 2017Article
- Understanding the Relative Flexibility of RNA and DNA Duplexes: Stretching and Twist-Stretch Coupling.Biophysical journal · 2017Article
- Specificity and nonspecificity in RNA-protein interactions.Nature reviews. Molecular cell biology · 2015Review
- Slowdown of Interhelical Motions Induces a Glass Transition in RNA.Biophysical journal · 2015Article
- All-atom crystal simulations of DNA and RNA duplexes.Biochimica et biophysica acta · 2015Article
- Isosteric and nonisosteric base pairs in RNA motifs: molecular dynamics and bioinformatics study of the sarcin-ricin internal loop.The journal of physical chemistry. B · 2013Article
- NAFlex: a web server for the study of nucleic acid flexibility.Nucleic acids research · 2013Article
- tRNA residues evolved to promote translational accuracy.RNA (New York, N.Y.) · 2013Article
- Improved nucleic acid descriptors for siRNA efficacy prediction.Nucleic acids research · 2013Article
- Mesoscopic model parametrization of hydrogen bonds and stacking interactions of RNA from melting temperatures.Nucleic acids research · 2013Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The structure and flexibility of the RNA duplex has been studied using extended molecular dynamics simulations on four diverse 18-mer oligonucleotides designed to contain many copies of the 10 unique dinucleotide steps in different sequence environments. Simulations were performed using the two most popular force fields for nucleic acids simulations (AMBER and CHARMM) in their latest versions, trying to arrive to a consensus picture of the RNA flexibility. Contrary to what was found for DNA duplex (DNA(2)), no clear convergence is found for the RNA duplex (RNA(2)), but one of the force field seems to agree better with experimental data. MD simulations performed with this force field were used to fully characterize, for the first time to our knowledge, the sequence-dependent elastic properties of RNA duplexes at different levels of resolutions. The flexibility pattern of RNA(2) shows similarities with DNA(2), but also surprising differences, which help us to understand the different biological functions of both molecules. A full mesoscopic model of RNA duplex at different resolution levels is derived to be used for genome-wide description of the flexibility of double-helical fragments of RNA.
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