Journal
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
Volume 11, Issue 45, Pages 10619-10632Publisher
ROYAL SOC CHEMISTRY
DOI: 10.1039/b910794k
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Funding
- National Science Foundation and National Institutes of Health [RO1-GM081520-01]
- Krell Institute
- US Department of Energy (DoE) [DE-FG02-97ER25308]
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM081520] Funding Source: NIH RePORTER
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Of special interest in molecular biology is the study of structural and conformational changes which are free of the additional effects of the environment. In the present contribution, we report on the ultrafast unfolding dynamics of a large DNA macromolecular ensemble in vacuo for a number of temperature jumps, and make a comparison with the unfolding dynamics of the DNA in aqueous solution. A number of coarse-graining approaches, such as kinetic intermediate structure (KIS) model and ensemble-averaged radial distribution functions, are used to account for the transitional dynamics of the DNA without sacrificing the structural resolution. The studied ensembles of DNA macromolecules were generated using distributed molecular dynamics (MD) simulations, and the ensemble convergence was ensured by monitoring the ensemble-averaged radial distribution functions and KIS unfolding trajectories. Because the order-disorder transition in free DNA implies unzipping, coiling, and strand-separation processes which occur consecutively or competitively depending on the initial and final temperature of the ensemble, DNA order-disorder transition in vacuo cannot be described as a two-state (un)folding process.
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