ArticleNucleic acids research2020
Improved nearest-neighbor parameters for the stability of RNA/DNA hybrids under a physiological condition.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 26 papers.
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26 citing papers in PubMed, 59 citations in OpenAlex.
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- Label-free milk biopsy using nanochannel-based biosensors for early-stage bovine mastitis screening.Mikrochimica acta · 2026Article
- Stability of non-canonical nucleic acid structure as a potential modulator of cell fate.Nucleic acids research · 2026Review
- Controlling DNA-RNA strand displacement kinetics with base distribution.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Predictability of environment-dependent formation of G-quadruplex DNAs in human mitochondria.Communications chemistry · 2025Article
- Hybrid RNA/DNA Concatemers and Self-Limited Complexes: Structure and Prospects for Therapeutic Applications.Molecules (Basel, Switzerland) · 2024Article
- Sequence-Specific Free Energy Changes in DNA/RNA Induced by a Single LNA-T Modification in Antisense Oligonucleotides.International journal of molecular sciences · 2024Article
- The Thermodynamic and Kinetic Properties of the dA-rU DNA-RNA Hybrid Base Pair Investigated via Molecular Dynamics Simulations.Molecules (Basel, Switzerland) · 2024Article
- A mechanistic study on the tolerance of PAM distal end mismatch by SpCas9.The Journal of biological chemistry · 2024Article
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- NMR characterization of RNA binding property of the DEAD-box RNA helicase DDX3X and its implications for helicase activity.Nature communications · 2024Article
- A FRET-Based Assay and Computational Tools to Quantify Enzymatic Rates and Explore the Mechanisms of RNA Deadenylases in Heterogeneous Environments.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Unmodificated stepless regulation of CRISPR/Cas12a multi-performance.Nucleic acids research · 2023Article
- CRISPR-Cas9 Activities with Truncated 16-Nucleotide RNA Guides Are Tuned by Target Duplex Stability Beyond the RNA/DNA Hybrid.Biochemistry · 2023Article
- Defining an optimal control for RNAi experiments with adult Schistosoma mansoni.Scientific reports · 2023Article
- Nearest-neighbor parameters for the prediction of RNA duplex stability in diverse in vitro and cellular-like crowding conditions.Nucleic acids research · 2023Article
- Substrate Specificity and Kinetics of RNA Hydrolysis by SARS-CoV-2 NSP10/14 Exonuclease.ACS bio & med chem Au · 2022Article
Corrections and comments
- Erratum issued
Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The stability of Watson-Crick paired RNA/DNA hybrids is important for designing optimal oligonucleotides for ASO (Antisense Oligonucleotide) and CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas9 techniques. Previous nearest-neighbour (NN) parameters for predicting hybrid stability in a 1 M NaCl solution, however, may not be applicable for predicting stability at salt concentrations closer to physiological condition (e.g. ∼100 mM Na+ or K+ in the presence or absence of Mg2+). Herein, we report measured thermodynamic parameters of 38 RNA/DNA hybrids at 100 mM NaCl and derive new NN parameters to predict duplex stability. Predicted ΔG°37 and Tm values based on the established NN parameters agreed well with the measured values with 2.9% and 1.1°C deviations, respectively. The new results can also be used to make precise predictions for duplexes formed in 100 mM KCl or 100 mM NaCl in the presence of 1 mM Mg2+, which can mimic an intracellular and extracellular salt condition, respectively. Comparisons of the predicted thermodynamic parameters with published data using ASO and CRISPR-Cas9 may allow designing shorter oligonucleotides for these techniques that will diminish the probability of non-specific binding and also improve the efficiency of target gene regulation.
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