ArticleNucleic acids research2011
Thermodynamic contributions of single internal rA·dA, rC·dC, rG·dG and rU·dT mismatches in RNA/DNA duplexes.
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 24 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
24 citing papers in PubMed.
- Molecular Interpretation of Temperature-Induced DNA Melting Monitored through Base Dipole Moment Changes as a Surrogate of the Hypochromic Shift.The journal of physical chemistry letters · 2026Article
- Rho (bioRxiv : the preprint server for biology · 2026Article
- 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
- NUPACK: Computational Nucleic Acid Analysis and Design.ACS synthetic biology · 2026Article
- Single-cell characterization of the gastrointestinal HIV reservoir reveals heterogeneous cellular phenotypes.The Journal of clinical investigation · 2026Article
- Nonequilibrium hybridization-driven CRISPR/Cas adapter with extended energetic penalty for discrimination of single-nucleotide variants.Nucleic acids research · 2025Article
- Cas12a domain flexibility guides R-loop formation and forces RuvC resetting.Molecular cell · 2024Article
- CRISPR/Cas9 gRNA activity depends on free energy changes and on the target PAM context.Nature communications · 2022Article
- Guide-target mismatch effects on dCas9-sgRNA binding activity in living bacterial cells.Nucleic acids research · 2021Article
- Optical and theoretical study of strand recognition by nucleic acid probes.Communications chemistry · 2020Article
- A Polymer Physics Framework for the Entropy of Arbitrary Pseudoknots.Biophysical journal · 2019Article
- Role of nucleotide identity in effective CRISPR target escape mutations.Nucleic acids research · 2018Article
- CRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters.Genome biology · 2018Article
- Kinetic Basis for DNA Target Specificity of CRISPR-Cas12a.Molecular cell · 2018Article
- Transcriptional accuracy modeling suggests two-step proofreading by RNA polymerase.Nucleic acids research · 2017Article
- Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast.PloS one · 2017Article
- Revealing Nucleic Acid Mutations Using Förster Resonance Energy Transfer-Based Probes.Sensors (Basel, Switzerland) · 2016Review
- Rapid generation of CRISPR/dCas9-regulated, orthogonally repressible hybrid T7-lac promoters for modular, tuneable control of metabolic pathway fluxes in Escherichia coli.Nucleic acids research · 2016Article
- A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation.PLoS computational biology · 2016Article
- Structure and specificity of the RNA-guided endonuclease Cas9 during DNA interrogation, target binding and cleavage.Nucleic acids research · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
Abstract
The thermodynamic contributions of rA·dA, rC·dC, rG·dG and rU·dT single internal mismatches were measured for 54 RNA/DNA duplexes in a 1 M NaCl buffer using UV absorbance thermal denaturation. Thermodynamic parameters were obtained by fitting absorbance versus temperature profiles using the curve-fitting program Meltwin. The weighted average thermodynamic data were fit using singular value decomposition to determine the eight non-unique nearest-neighbor parameters for each internal mismatch. The new parameters predict the ΔG°(37), ΔH° and melting temperature (T(m)) of duplexes containing these single mismatches within an average of 0.33 kcal/mol, 4.5 kcal/mol and 1.4°C, respectively. The general trend in decreasing stability for the single internal mismatches is rG·dG > rU·dT > rA·dA > rC·dC. The stability trend for the base pairs 5' of the single internal mismatch is rG·dC > rC·dG > rA·dT > rU·dA. The stability trend for the base pairs 3' of the single internal mismatch is rC·dG > rG·dC >> rA·dT > rU·dA. These nearest-neighbor values are now a part of a complete set of single internal mismatch thermodynamic parameters for RNA/DNA duplexes that are incorporated into the nucleic acid assay development software programs Visual oligonucleotide modeling platform (OMP) and ThermoBLAST.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.