ArticleNature chemistry2018
Predicting DNA hybridization kinetics from sequence.
Article in Nature chemistry, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
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Who cites it
67 citing papers in PubMed.
- Deep Learning Predicts Dissimilar DNA-DNA Binding and Engineers Hyperconnected Networks.Nature communications · 2026Article
- Accurate prediction of oligonucleotide probe hybridization efficiency via a transformer-based model.BMC genomics · 2026Article
- Machine learning-directed massively parallel programmable nucleic acid amplification.Science advances · 2026Article
- Kinetics and Activation Strategies in Toehold-Mediated and Toehold-Free DNA Strand Displacement.Biosensors · 2025Review
- Overcoming the Speed Limit of Four-Way DNA Branch Migration with Bulges in Toeholds.Nano letters · 2025Article
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- A Generalizable Screening Platform for Developing Functional Aptasensors.Analytical chemistry · 2025Article
- All-in-one Biocomputing Nanoagents with Multilayered Transformable Architecture based on DNA Interfaces.Theranostics · 2025Article
- Interpreting CRISPR-Cas12a enzyme kinetics through free energy change of nucleic acids.Nucleic acids research · 2024Article
- Parental Reconstruction from a Half-Sib Population of Stoneless JujubePlants (Basel, Switzerland) · 2024Article
- Predicting DNA Reactions with a Quantum Chemistry-Based Deep Learning Model.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Hopping and crawling DNA-coated colloids.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Understanding the relationship between sequences and kinetics of DNA strand displacements.Nucleic acids research · 2024Article
- Weak-cooperative binding of a long single-stranded DNA chain on a surface.Nucleic acids research · 2024Article
- Erasable and Field Programmable DNA Circuits Based on Configurable Logic Blocks.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Molecular insight into how the position of an abasic site modifies DNA duplex stability and dynamics.Biophysical journal · 2024Article
- Generation of DNA oligomers with similar chemical kinetics via in-silico optimization.Communications chemistry · 2023Article
- Unlocking Genetic Profiles with a Programmable DNA-Powered Decoding Circuit.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- Bleaching-resistant, Near-continuous Single-molecule Fluorescence and FRET Based on Fluorogenic and Transient DNA Binding.Chemphyschem : a European journal of chemical physics and physical chemistry · 2023Article
- A molecular assessment of the practical potential of DNA-based computation.Current opinion in biotechnology · 2023Review
7 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Hybridization is a key molecular process in biology and biotechnology, but so far there is no predictive model for accurately determining hybridization rate constants based on sequence information. Here, we report a weighted neighbour voting (WNV) prediction algorithm, in which the hybridization rate constant of an unknown sequence is predicted based on similarity reactions with known rate constants. To construct this algorithm we first performed 210 fluorescence kinetics experiments to observe the hybridization kinetics of 100 different DNA target and probe pairs (36 nt sub-sequences of the CYCS and VEGF genes) at temperatures ranging from 28 to 55 °C. Automated feature selection and weighting optimization resulted in a final six-feature WNV model, which can predict hybridization rate constants of new sequences to within a factor of 3 with ∼91% accuracy, based on leave-one-out cross-validation. Accurate prediction of hybridization kinetics allows the design of efficient probe sequences for genomics research.
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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.