Non-Arrhenius kinetics for the loop closure of a DNA hairpin.
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 thermo...
| Main Authors: | , , , |
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| Format: | Journal article |
| Language: | English |
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2001
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| _version_ | 1797095032567627776 |
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| author | Wallace, M Ying, L Balasubramanian, S Klenerman, D |
| author_facet | Wallace, M Ying, L Balasubramanian, S Klenerman, D |
| author_sort | Wallace, M |
| collection | OXFORD |
| description | 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. and 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. |
| first_indexed | 2024-03-07T04:22:13Z |
| format | Journal article |
| id | oxford-uuid:cb67410d-56d6-47a9-b8b7-cca2820672e3 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T04:22:13Z |
| publishDate | 2001 |
| record_format | dspace |
| spelling | oxford-uuid:cb67410d-56d6-47a9-b8b7-cca2820672e32022-03-27T07:14:36ZNon-Arrhenius kinetics for the loop closure of a DNA hairpin.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:cb67410d-56d6-47a9-b8b7-cca2820672e3EnglishSymplectic Elements at Oxford2001Wallace, MYing, LBalasubramanian, SKlenerman, DIntramolecular 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. and 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. |
| spellingShingle | Wallace, M Ying, L Balasubramanian, S Klenerman, D Non-Arrhenius kinetics for the loop closure of a DNA hairpin. |
| title | Non-Arrhenius kinetics for the loop closure of a DNA hairpin. |
| title_full | Non-Arrhenius kinetics for the loop closure of a DNA hairpin. |
| title_fullStr | Non-Arrhenius kinetics for the loop closure of a DNA hairpin. |
| title_full_unstemmed | Non-Arrhenius kinetics for the loop closure of a DNA hairpin. |
| title_short | Non-Arrhenius kinetics for the loop closure of a DNA hairpin. |
| title_sort | non arrhenius kinetics for the loop closure of a dna hairpin |
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