ArticleProceedings of the National Academy of Sciences of the United States of America2001
Non-Arrhenius kinetics for the loop closure of a DNA hairpin.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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60 citing papers in PubMed.
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- Heterogeneity and multi-scale dynamics in the molecular bearing of the bacterial flagellum.Nature communications · 2026Article
- RNA adapts its flexibility to efficiently fold and resist unfolding.Nucleic acids research · 2025Article
- Evidence of a Three-State Mechanism in DNA Hairpin Folding.Journal of the American Chemical Society · 2025Article
- DNA Hybridization Kinetics Observed at the Single-Molecule Level Using Graphene Near-Field Effects.The journal of physical chemistry. A · 2024Article
- Quantifying Microsecond Solution-Phase Conformational Dynamics of a DNA Hairpin at the Single-Molecule Level.ACS physical chemistry Au · 2024Article
- Macromolecular Crowding and DNA: Bridging the Gap between In Vitro and In Vivo.International journal of molecular sciences · 2023Review
- Generation of DNA oligomers with similar chemical kinetics via in-silico optimization.Communications chemistry · 2023Article
- Sequence-Dependent Melting and Refolding Dynamics of RNA UNCG Tetraloops Using Temperature-Jump/Drop Infrared Spectroscopy.The journal of physical chemistry. B · 2023Article
- Regulating DNA-Hybridization Using a Chemically Fueled Reaction Cycle.Journal of the American Chemical Society · 2022Article
- Measuring RNA UNCG Tetraloop Refolding Dynamics Using Temperature-Jump/Drop Infrared Spectroscopy.The journal of physical chemistry letters · 2022Article
- A quantitative model predicts how mNature communications · 2021Article
- Dengue virus strain 2 capsid protein switches the annealing pathway and reduces intrinsic dynamics of the conserved 5' untranslated region.RNA biology · 2021Article
- Combinatorial Fusion Rules to Describe Codon Assignment in the Standard Genetic Code.Life (Basel, Switzerland) · 2020Article
- Validation of DBFOLD: An efficient algorithm for computing folding pathways of complex proteins.PLoS computational biology · 2020Article
- Temperature Dependence of Rate Processes Beyond Arrhenius and Eyring: Activation and Transitivity.Frontiers in chemistry · 2019Article
- Single-strand annealing between inverted DNA repeats: Pathway choice, participating proteins, and genome destabilizing consequences.PLoS genetics · 2018Article
- Probing Position-Dependent Diffusion in Folding Reactions Using Single-Molecule Force Spectroscopy.Biophysical journal · 2018Article
- Understanding the kinetic mechanism of RNA single base pair formation.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Dynamic Release of Bending Stress in Short dsDNA by Formation of a Kink and Forks.Angewandte Chemie (International ed. in English) · 2015Article
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4 authors.
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Abstract
Intramolecular chain diffusion is an elementary process in the conformational fluctuations of the DNA hairpin-loop. We have studied the temperature and viscosity dependence of a model DNA hairpin-loop by FRET (fluorescence resonance energy transfer) fluctuation spectroscopy (FRETfs). Apparent thermodynamic parameters were obtained by analyzing the correlation amplitude through a two-state model and are consistent with steady-state fluorescence measurements. The kinetics of closing the loop show non-Arrhenius behavior, in agreement with theoretical prediction and other experimental measurements on peptide folding. The fluctuation rates show a fractional power dependence (beta = 0.83) on the solution viscosity. A much slower intrachain diffusion coefficient in comparison to that of polypeptides was derived based on the first passage time theory of SSS [Szabo, A., Schulten, K. & Schulten, Z. (1980) J. Chem. Phys. 72, 4350-4357], suggesting that intrachain interactions, especially stacking interaction in the loop, might increase the roughness of the free energy surface of the DNA hairpin-loop.
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