Single-Strand Stacking Free Energy from DNA Beacon Kinetics
| Autor: | Daniel P. Aalberts, John Parman, Noel L. Goddard |
|---|---|
| Rok vydání: | 2003 |
| Předmět: |
Models
Molecular Macromolecular Substances Monte Carlo method Kinetics Biophysics Stacking DNA Single-Stranded Thermodynamics Motion Biopolymers Nucleic Acids Computer Simulation Closing (morphology) chemistry.chemical_classification Persistence length Quantitative Biology::Biomolecules Models Statistical Polymer Loop (topology) Crystallography Energy Transfer chemistry Exponent Nucleic Acid Conformation Monte Carlo Method |
| Zdroj: | Biophysical Journal. 84:3212-3217 |
| ISSN: | 0006-3495 |
| DOI: | 10.1016/s0006-3495(03)70045-9 |
| Popis: | DNA beacons are short single-stranded chains which can form closed hairpin shapes through complementary base pairing at their ends. Contrary to the common polymer theory assumption that only their loop length matters, experiments show that their closing kinetics depend on the loop composition. We have modeled the closing kinetics and in so doing have obtained stacking enthalpies and entropies for single-stranded nucleic acids. The resulting change of persistence length with temperature effects the dynamics. With a Monte Carlo study, we answer another polymer question of how the closing time scales with chain length, finding tau approximately N(2.44+/-0.02). There is a significant crossover for shorter chains, bringing the effective exponent into good agreement with experiment. |
| Databáze: | OpenAIRE |
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