ArticleNucleic acids research2011
Predicting translational diffusion of evolutionary conserved RNA structures by the nucleotide number.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
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- Intersegmental transfers drive target search in an RNA-targeting CRISPR system.bioRxiv : the preprint server for biology · 2026Article
- Functional characterization of dynamic nascent RNA folding ensembles in real time.Science advances · 2026Article
- DynaRNA: accurate dynamic RNA conformation ensemble generation with diffusion model.Communications biology · 2025Article
- Digital and Absolute Assays for Low Abundance Molecular Biomarkers.Accounts of chemical research · 2023Article
- The Effect of Environment on the Evolution and Proliferation of Protocells of Increasing Complexity.Life (Basel, Switzerland) · 2022Article
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- Integrating programmable DNAzymes with electrical readout for rapid and culture-free bacterial detection using a handheld platform.Nature chemistry · 2021Article
- NMR analysis of nucleotide π-stacking in prebiotically relevant crowded environment.Communications chemistry · 2020Article
- Compartmentalised RNA catalysis in membrane-free coacervate protocells.Nature communications · 2018Article
- In vivo single-RNA tracking shows that most tRNA diffuses freely in live bacteria.Nucleic acids research · 2017Article
- Sizes of Long RNA Molecules Are Determined by the Branching Patterns of Their Secondary Structures.Biophysical journal · 2016Article
- Article
- Biologistics--diffusion coefficients for complete proteome of Escherichia coli.Bioinformatics (Oxford, England) · 2012Article
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Abstract
Ribonucleic acids are highly conserved essential parts of cellular life. RNA function is determined to a large extent by its hydrodynamic behaviour. The presented study proposes a strategy to predict the hydrodynamic behaviour of RNA single strands on the basis of the polymer size. By atom-level shell-modelling of high-resolution structures, hydrodynamic radius and diffusion coefficient of evolutionary conserved RNA single strands (ssRNA) were calculated. The diffusion coefficients D of 17-174 nucleotides (nt) containing ssRNA depended on the number of nucleotides N with D = 4.56 × 10(-10) N(-0.39) m(2) s(-1). The hydrodynamic radius R(H) depended on N with R(H) = 5.00 × 10(-10) N(0.38) m. An average ratio of the radius of gyration and the hydrodynamic radius of 0.98 ± 0.08 was calculated in solution. The empirical law was tested by in solution measured hydrodynamic radii and radii of gyration and was found to be highly consistent with experimental data of evolutionary conserved ssRNA. Furthermore, the hydrodynamic behaviour of several evolutionary unevolved ribonucleic acids could be predicted. Based on atom-level shell-modelling of high-resolution structures and experimental hydrodynamic data, empirical models are proposed, which enable to predict the translational diffusion coefficient and molecular size of short RNA single strands solely on the basis of the polymer size.
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