ArticleNature methods2015
Continuously tunable nucleic acid hybridization probes.
Article in Nature methods, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Machine learning-directed massively parallel programmable nucleic acid amplification.Science advances · 2026Article
- Methods Established forPlants (Basel, Switzerland) · 2025Article
- Design of mismatch closure for enhanced specificity in DNA strand displacement reactions.Nucleic acids research · 2025Article
- Massively parallel homogeneous amplification of chip-scale DNA for DNA information storage (MPHAC-DIS).Nature communications · 2025Article
- Multiplexed Biomarker Detection Using DNA Payloads: Design, Assembly, and Analysis.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Bidirectional linkage of DNA barcodes for the multiplexed mapping of higher-order protein interactions in cells.Nature biomedical engineering · 2024Article
- RT-IVT method allows multiplex real-time quantification of in vitro transcriptional mRNA production.Communications biology · 2023Article
- High-Throughput Variant Detection Using a Color-Mixing Strategy.The Journal of molecular diagnostics : JMD · 2022Article
- Article
- Ultrasensitive DNA-Biomacromolecule Sensor for the Detection Application of Clinical Cancer Samples.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2022Article
- Programmable High-Speed and Hyper-Efficiency DNA Signal Magnifier.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2022Article
- Expanding detection windows for discriminating single nucleotide variants using rationally designed DNA equalizer probes.Nature communications · 2020Article
- Critical Review: digital resolution biomolecular sensing for diagnostics and life science research.Lab on a chip · 2020Review
- Article
- Encoding multiple digital DNA signals in a single analog channel.Nucleic acids research · 2020Article
- Elucidation of leak-resistance DNA hybridization chain reaction with universality and extensibility.Nucleic acids research · 2020Article
- Enhanced nucleotide chemistry and toehold nanotechnology reveals lncRNA spreading on chromatin.Nature structural & molecular biology · 2020Article
- Enhanced Hybridization Selectivity Using Structured GammaPNA Probes.Molecules (Basel, Switzerland) · 2020Article
- Programmable mismatch-fueled high-efficiency DNA signal converter.Chemical science · 2020Article
- In situ readout of DNA barcodes and single base edits facilitated by in vitro transcription.Nature biotechnology · 2020Article
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
In silico-designed nucleic acid probes and primers often do not achieve favorable specificity and sensitivity tradeoffs on the first try, and iterative empirical sequence-based optimization is needed, particularly in multiplexed assays. We present a novel, on-the-fly method of tuning probe affinity and selectivity by adjusting the stoichiometry of auxiliary species, which allows for independent and decoupled adjustment of the hybridization yield for different probes in multiplexed assays. Using this method, we achieved near-continuous tuning of probe effective free energy. To demonstrate our approach, we enforced uniform capture efficiency of 31 DNA molecules (GC content, 0-100%), maximized the signal difference for 11 pairs of single-nucleotide variants and performed tunable hybrid capture of mRNA from total RNA. Using the Nanostring nCounter platform, we applied stoichiometric tuning to simultaneously adjust yields for a 24-plex assay, and we show multiplexed quantitation of RNA sequences and variants from formalin-fixed, paraffin-embedded samples.
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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.