ArticleBiochemistry2012
Testing the nearest neighbor model for canonical RNA base pairs: revision of GU parameters.
Article in Biochemistry, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed.
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- Nearest Neighbor Parameters for Estimating the Folding Stability of RNA Including Pseudouridine.bioRxiv : the preprint server for biology · 2026Article
- RNA Folding Nearest Neighbor Parameters Including the Modification 1-Methyl-Pseudouridine.bioRxiv : the preprint server for biology · 2026Article
- Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers.Chemical reviews · 2024Review
- The Impact of Second-Shell Nucleotides on Ligand Specificity in Cyclic Dinucleotide Riboswitches.Biochemistry · 2024Article
- DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters.ACS synthetic biology · 2023Article
- Position-dependent sequence motif preferences of SpCas9 are largely determined by scaffold-complementary spacer motifs.Nucleic acids research · 2023Article
- DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters.bioRxiv : the preprint server for biology · 2023Article
- A Test and Refinement of Folding Free Energy Nearest Neighbor Parameters for RNA Including NJournal of molecular biology · 2022Article
- Thermodynamic characterization of naturally occurring RNA pentaloops.RNA (New York, N.Y.) · 2022Article
- Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects.Nucleic acids research · 2022Article
- Nuclear magnetic resonance reveals a two hairpin equilibrium near the 3'-splice site of influenza A segment 7 mRNA that can be shifted by oligonucleotides.RNA (New York, N.Y.) · 2022Article
- Cotranscriptionally encoded RNA strand displacement circuits.Science advances · 2022Article
- Secondary structure prediction for RNA sequences including NNature communications · 2022Article
- Developing an Updated Strategy for Estimating the Free-Energy Parameters in RNA Duplexes.International journal of molecular sciences · 2021Article
- Development of antisense RNA-mediated quantifiable inhibition for metabolic regulation.Metabolic engineering communications · 2021Article
- Making ends meet: New functions of mRNA secondary structure.Wiley interdisciplinary reviews. RNA · 2021Review
- Predictions and analyses of RNA nearest neighbor parameters for modified nucleotides.Nucleic acids research · 2020Article
- The nature of the purine at position 34 in tRNAs of 4-codon boxes is correlated with nucleotides at positions 32 and 38 to maintain decoding fidelity.Nucleic acids research · 2020Article
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7 authors.
Funding
Abstract
Thermodynamic parameters for GU pairs are important for predicting the secondary structures of RNA and for finding genomic sequences that code for structured RNA. Optical melting curves were measured for 29 RNA duplexes with GU pairs to improve nearest neighbor parameters for predicting stabilities of helixes. The updated model eliminates a prior penalty assumed for terminal GU pairs. Six additional duplexes with the 5'GG/3'UU motif were added to the single representation in the previous database. This revises the ΔG°(37) for the 5'GG/3'UU motif from an unfavorable 0.5 kcal/mol to a favorable -0.2 kcal/mol. Similarly, the ΔG°(37) for the 5'UG/3'GU motif changes from 0.3 to -0.6 kcal/mol. The correlation coefficients between predicted and experimental ΔG°(37), ΔH°, and ΔS° for the expanded database are 0.95, 0.89, and 0.87, respectively. The results should improve predictions of RNA secondary structure.
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