ArticleNature chemistry2015
Simulation-guided DNA probe design for consistently ultraspecific hybridization.
Article in Nature chemistry, 2015. 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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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.
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Who cites it
57 citing papers in PubMed.
- Machine learning-directed massively parallel programmable nucleic acid amplification.Science advances · 2026Article
- Erasable and regenerated multicomponent patterned polymer brushes.Chemical science · 2026Article
- Design of mismatch closure for enhanced specificity in DNA strand displacement reactions.Nucleic acids research · 2025Article
- Rapid Amplification and Detection of Single-Stranded Nucleic Acids for Point-of-Care Diagnosis.Small methods · 2025Review
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- Massively parallel homogeneous amplification of chip-scale DNA for DNA information storage (MPHAC-DIS).Nature communications · 2025Article
- Virtual Screening and Validation of Affinity DNA Functional Ligands for IgG Fc Segment.International journal of molecular sciences · 2024Article
- Kinetic Proofreading Can Enhance Specificity in a Nonenzymatic DNA Strand Displacement Network.Journal of the American Chemical Society · 2024Article
- Erasable and Field Programmable DNA Circuits Based on Configurable Logic Blocks.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Recent advances in enzyme-free and enzyme-mediated single-nucleotide variation assayNational science review · 2024Review
- Heteromultivalency enables enhanced detection of nucleic acid mutations.Nature chemistry · 2024Article
- Article
- Speed and Correctness Guarantees for Programmable Enthalpy-Neutral DNA Reactions†.ACS synthetic biology · 2023Article
- Improving the Accuracy of Single-Nucleotide Variant Diagnosis Using On-Off Discriminating Primers.Biosensors · 2023Article
- Nucleic Acid Molecular Systems for In Vitro Detection of Biomolecules.ACS materials Au · 2023Review
- PAM-independent ultra-specific activation of CRISPR-Cas12a via sticky-end dsDNA.Nucleic acids research · 2022Article
- Programmable mismatch-fueled high-efficiency DNA signal amplifier.Chemical science · 2022Article
- A paper-based assay for the colorimetric detection of SARS-CoV-2 variants at single-nucleotide resolution.Nature biomedical engineering · 2022Article
- Competitive SNP-LAMP probes for rapid and robust single-nucleotide polymorphism detection.Cell reports methods · 2022Article
- Unified-amplifier based primer exchange reaction (UniAmPER) enabled detection of SARS-CoV-2 from clinical samples.Sensors and actuators. B, Chemical · 2022Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Hybridization of complementary sequences is one of the central tenets of nucleic acid chemistry; however, the unintended binding of closely related sequences limits the accuracy of hybridization-based approaches to analysing nucleic acids. Thermodynamics-guided probe design and empirical optimization of the reaction conditions have been used to enable the discrimination of single-nucleotide variants, but typically these approaches provide only an approximately 25-fold difference in binding affinity. Here we show that simulations of the binding kinetics are both necessary and sufficient to design nucleic acid probe systems with consistently high specificity as they enable the discovery of an optimal combination of thermodynamic parameters. Simulation-guided probe systems designed against 44 sequences of different target single-nucleotide variants showed between a 200- and 3,000-fold (median 890) higher binding affinity than their corresponding wild-type sequences. As a demonstration of the usefulness of this simulation-guided design approach, we developed probes that, in combination with PCR amplification, detect low concentrations of variant alleles (1%) in human genomic DNA.
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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.