ArticleProceedings of the National Academy of Sciences of the United States of America2018
Tethered multifluorophore motion reveals equilibrium transition kinetics of single DNA double helices.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2018. 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 19 papers.
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Who cites it
19 citing papers in PubMed, 42 citations in OpenAlex.
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- Modular DNA origami-based electrochemical detection of DNA and proteins.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Disruption of energetic and dynamic base pairing cooperativity in DNA duplexes by an abasic site.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Hybridization kinetics of out-of-equilibrium mixtures of short RNA oligonucleotides.Nucleic acids research · 2022Article
- The stability and number of nucleating interactions determine DNA hybridization rates in the absence of secondary structure.Nucleic acids research · 2022Article
- Bleaching-Resistant Super-Resolution Fluorescence Microscopy.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2022Review
- Design Features to Accelerate the Higher-Order Assembly of DNA Origami on Membranes.The journal of physical chemistry. B · 2021Article
- Calibration-free counting of low molecular copy numbers in single DNA-PAINT localization clusters.Biophysical reports · 2021Article
- Determining Sequence-Dependent DNA Oligonucleotide Hybridization and Dehybridization Mechanisms Using Coarse-Grained Molecular Simulation, Markov State Models, and Infrared Spectroscopy.Journal of the American Chemical Society · 2021Article
- Tracking single particles for hours via continuous DNA-mediated fluorophore exchange.Nature communications · 2021Article
- A synthetic tubular molecular transport system.Nature communications · 2021Article
- DNA hybridisation kinetics using single-molecule fluorescence imaging.Essays in biochemistry · 2021Review
- Improved resolution in single-molecule localization microscopy using QD-PAINT.Experimental & molecular medicine · 2021Article
- Stable DNA Sequence Over Close-Ending and Pairing Sequences Constraint.Frontiers in genetics · 2021Article
- Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and molecular simulation.Nucleic acids research · 2020Article
- A mechanistic examination of salting out in protein-polymer membrane interactions.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- An order of magnitude faster DNA-PAINT imaging by optimized sequence design and buffer conditions.Nature methods · 2019Article
- Measuring DNA Hybridization Kinetics in Live Cells Using a Time-Resolved 3D Single-Molecule Tracking Method.Journal of the American Chemical Society · 2019Article
- Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
We describe a tethered multifluorophore motion assay based on DNA origami for revealing bimolecular reaction kinetics on the single-molecule level. Molecular binding partners may be placed at user-defined positions and in user-defined stoichiometry; and binding states are read out by tracking the motion of quickly diffusing fluorescent reporter units. Multiple dyes per reporter unit enable singe-particle observation for more than 1 hour. We applied the system to study in equilibrium reversible hybridization and dissociation of complementary DNA single strands as a function of tether length, cation concentration, and sequence. We observed up to hundreds of hybridization and dissociation events per single reactant pair and could produce cumulative statistics with tens of thousands of binding and unbinding events. Because the binding partners per particle do not exchange, we could also detect subtle heterogeneity from molecule to molecule, which enabled separating data reflecting the actual target strand pair binding kinetics from falsifying influences stemming from chemically truncated oligonucleotides. Our data reflected that mainly DNA strand hybridization, but not strand dissociation, is affected by cation concentration, in agreement with previous results from different assays. We studied 8-bp-long DNA duplexes with virtually identical thermodynamic stability, but different sequences, and observed strongly differing hybridization kinetics. Complementary full-atom molecular-dynamics simulations indicated two opposing sequence-dependent phenomena: helical templating in purine-rich single strands and secondary structures. These two effects can increase or decrease, respectively, the fraction of strand collisions leading to successful nucleation events for duplex formation.
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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.