ArticleNucleic acids research2013
Mesoscopic model parametrization of hydrogen bonds and stacking interactions of RNA from melting temperatures.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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9 citing papers in PubMed.
- Mesoscopic Calculation of Single Mismatches in RNA/DNA Hybrids: Strong Hydrogen Bonds of dTrG Affect CRISPR Off-Target Binding.The journal of physical chemistry. B · 2026Article
- Article
- Weak-cooperative binding of a long single-stranded DNA chain on a surface.Nucleic acids research · 2024Article
- Twist-stretch relations in nucleic acids.European biophysics journal : EBJ · 2023Article
- DNA-Based Biosensors for the Biochemical Analysis: A Review.Biosensors · 2022Review
- Article
- Optical and theoretical study of strand recognition by nucleic acid probes.Communications chemistry · 2020Article
- Melting temperature measurement and mesoscopic evaluation of single, double and triple DNA mismatches.Chemical science · 2020Article
- Mesoscopic model and free energy landscape for protein-DNA binding sites: analysis of cyanobacterial promoters.PLoS computational biology · 2014Article
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Abstract
Information about molecular interactions in DNA can be obtained from experimental melting temperature data by using mesoscopic statistical physics models. Here, we extend the technique to RNA and show that the new parameters correctly reproduce known properties such as the stronger hydrogen bonds of AU base pairs. We also were able to calculate a complete set of elastic constants for all 10 irreducible combinations of nearest neighbours (NNs). We believe that this is particularly useful as experimentally derived information about RNA elasticity is relatively scarce. The melting temperature prediction using the present model improves over those from traditional NN model, providing thus an alternative way to calculate these temperatures for RNA. Additionally, we calculated the site-dependent base pair oscillation to explain why RNA shows larger oscillation amplitudes despite having stronger AU hydrogen bonds.
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