ArticleNucleic acids research2018
Improving RNA nearest neighbor parameters for helices by going beyond the two-state model.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Hierarchical analysis of RNA secondary structures with pseudoknots based on sections.PLoS computational biology · 2026Article
- 40S ribosomal subunits scan mRNA for the start codon by one-dimensional diffusion.RNA (New York, N.Y.) · 2025Article
- High-throughput DNA melt measurements enable improved models of DNA folding thermodynamics.Nature communications · 2025Article
- Hybrid RNA/DNA Concatemers and Self-Limited Complexes: Structure and Prospects for Therapeutic Applications.Molecules (Basel, Switzerland) · 2024Article
- Causes, functions, and therapeutic possibilities of RNA secondary structure ensembles and alternative states.Cell chemical biology · 2024Review
- Competitive Influence of Alkali Metals in the Ion Atmosphere on Nucleic Acid Duplex Stability.ACS omega · 2024Article
- Diversity of Self-Assembled RNA Complexes: From Nanoarchitecture to Nanomachines.Molecules (Basel, Switzerland) · 2023Article
- Thermodynamics and kinetics of DNA and RNA dinucleotide hybridization to gaps and overhangs.Biophysical journal · 2023Article
- Direct monitoring of the thermodynamics and kinetics of DNA and RNA dinucleotide dehybridization from gaps and overhangs.bioRxiv : the preprint server for biology · 2023Article
- Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects.Nucleic acids research · 2022Article
- Predicting the Structure of a Viroid : Structure, Structure Distribution, Consensus Structure, and Structure Drawing.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Vfold2D-MC: A Physics-Based Hybrid Model for Predicting RNA Secondary Structure Folding.The journal of physical chemistry. B · 2021Article
- Developing an Updated Strategy for Estimating the Free-Energy Parameters in RNA Duplexes.International journal of molecular sciences · 2021Article
- Salt-Dependent RNA Pseudoknot Stability: Effect of Spatial Confinement.Frontiers in molecular biosciences · 2021Article
- 5-Carboxylcytosine and Cytosine Protonation Distinctly Alter the Stability and Dehybridization Dynamics of the DNA Duplex.The journal of physical chemistry. B · 2020Article
- Stability of an RNA•DNA-DNA triple helix depends on base triplet composition and length of the RNA third strand.Nucleic acids research · 2019Article
- Estimating uncertainty in predicted folding free energy changes of RNA secondary structures.RNA (New York, N.Y.) · 2019Article
- Validation of the nearest-neighbor model for Watson-Crick self-complementary DNA duplexes in molecular crowding condition.Nucleic acids research · 2019Article
- The shaping of a molecular linguist: How a career studying DNA energetics revealed the language of molecular communication.The Journal of biological chemistryArticle
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
RNA folding free energy change nearest neighbor parameters are widely used to predict folding stabilities of secondary structures. They were determined by linear regression to datasets of optical melting experiments on small model systems. Traditionally, the optical melting experiments are analyzed assuming a two-state model, i.e. a structure is either complete or denatured. Experimental evidence, however, shows that structures exist in an ensemble of conformations. Partition functions calculated with existing nearest neighbor parameters predict that secondary structures can be partially denatured, which also directly conflicts with the two-state model. Here, a new approach for determining RNA nearest neighbor parameters is presented. Available optical melting data for 34 Watson-Crick helices were fit directly to a partition function model that allows an ensemble of conformations. Fitting parameters were the enthalpy and entropy changes for helix initiation, terminal AU pairs, stacks of Watson-Crick pairs and disordered internal loops. The resulting set of nearest neighbor parameters shows a 38.5% improvement in the sum of residuals in fitting the experimental melting curves compared to the current literature set.
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