ArticleBiophysical journal2015
Modelling toehold-mediated RNA strand displacement.
Article in Biophysical journal, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- RNA structure modulates Cas13 activity and enables mismatch detection.Nature biotechnology · 2026Article
- Periodic Temperature Fluctuations as an Energy Source for RNA Evolution.Life (Basel, Switzerland) · 2026Article
- U2 snRNP recognizes the branch site through a loaded-spring strand-invasion mechanism.Nucleic acids research · 2026Article
- Fitting coarse-grained models to macroscopic experimental data via automatic differentiation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Coarse-Grained Modeling and Simulation of Multistranded RNA Nanostars.Chem & bio engineering · 2026Article
- Structural and Physicochemical Optimization of Next-Generation Antisense Oligonucleotide with BROTHERS for Mitigating Off-Target Effects.Methods in molecular biology (Clifton, N.J.) · 2026Article
- The human branchpoint-interacting stem loop sequence and structure regulates U2 snRNA expression, branchpoint recognition, and transcriptome.bioRxiv : the preprint server for biology · 2025Article
- Reconfigurable Nucleic Acid Nanoparticles with Therapeutic RNAi Responses to Intracellular Disease Markers.Advanced functional materials · 2025Article
- Controlling DNA-RNA strand displacement kinetics with base distribution.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- Article
- Unmodificated stepless regulation of CRISPR/Cas12a multi-performance.Nucleic acids research · 2023Article
- Direct monitoring of the thermodynamics and kinetics of DNA and RNA dinucleotide dehybridization from gaps and overhangs.bioRxiv : the preprint server for biology · 2023Article
- Nucleic acid strand displacement - from DNA nanotechnology to translational regulation.RNA biology · 2023Article
- Programming cell-free biosensors with DNA strand displacement circuits.Nature chemical biology · 2022Article
- Cotranscriptionally encoded RNA strand displacement circuits.Science advances · 2022Article
- A kinetic model predicts SpCas9 activity, improves off-target classification, and reveals the physical basis of targeting fidelity.Nature communications · 2022Article
- Molecular dynamics simulation-guided toehold mediated strand displacement probe for single-nucleotide variants detection.Exploration (Beijing, China) · 2022Article
- Toehold-mediated strand displacement to measure released product from self-cleaving ribozymes.RNA (New York, N.Y.) · 2022Article
- Biomotors, viral assembly, and RNA nanobiotechnology: Current achievements and future directions.Computational and structural biotechnology journal · 2022Review
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We study the thermodynamics and kinetics of an RNA toehold-mediated strand displacement reaction with a recently developed coarse-grained model of RNA. Strand displacement, during which a single strand displaces a different strand previously bound to a complementary substrate strand, is an essential mechanism in active nucleic acid nanotechnology and has also been hypothesized to occur in vivo. We study the rate of displacement reactions as a function of the length of the toehold and temperature and make two experimentally testable predictions: that the displacement is faster if the toehold is placed at the 5' end of the substrate; and that the displacement slows down with increasing temperature for longer toeholds.
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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.