ArticleProceedings of the National Academy of Sciences of the United States of America2017
Direct measurement of sequence-dependent transition path times and conformational diffusion in DNA duplex formation.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Cooperative Native Contact Formation Facilitates Free Energy Barrier Crossing in Protein Folding.Physical review letters · 2026Article
- Static and dynamic rough energy landscapes can lead to identical diffusivity.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- Observing the base-by-base search for native structure along transition paths during the folding of single nucleic acid hairpins.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Estimating transition path times and shapes from single-molecule photon trajectories: A simulation analysis.The Journal of chemical physics · 2021Article
- Disordered proteins follow diverse transition paths as they fold and bind to a partner.Science (New York, N.Y.) · 2020Article
- The Role of Electrostatics and Folding Kinetics on the Thermostability of Homologous Cold Shock Proteins.Journal of chemical information and modeling · 2020Article
- Slow Transition Path Times Reveal a Complex Folding Barrier in a Designed Protein.Frontiers in chemistry · 2020Article
- Measuring the average shape of transition paths during the folding of a single biological molecule.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Experimental evidence of symmetry breaking of transition-path times.Nature communications · 2019Article
- Instrumental Effects in the Dynamics of an Ultrafast Folding Protein under Mechanical Force.The journal of physical chemistry. B · 2018Article
- Probing Position-Dependent Diffusion in Folding Reactions Using Single-Molecule Force Spectroscopy.Biophysical journal · 2018Article
- Transition paths in single-molecule force spectroscopy.The Journal of chemical physics · 2018Article
- Transition Path Times Measured by Single-Molecule Spectroscopy.Journal of molecular biology · 2018Review
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The conformational diffusion coefficient, D, sets the timescale for microscopic structural changes during folding transitions in biomolecules like nucleic acids and proteins. D encodes significant information about the folding dynamics such as the roughness of the energy landscape governing the folding and the level of internal friction in the molecule, but it is challenging to measure. The most sensitive measure of D is the time required to cross the energy barrier that dominates folding kinetics, known as the transition path time. To investigate the sequence dependence of D in DNA duplex formation, we measured individual transition paths from equilibrium folding trajectories of single DNA hairpins held under tension in high-resolution optical tweezers. Studying hairpins with the same helix length but with G:C base-pair content varying from 0 to 100%, we determined both the average time to cross the transition paths, τ
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