Structural ultrafast dynamics of macromolecules: diffraction of free DNA and effect of hydration
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.
Additional Information© 2009 Royal Society of Chemistry. Received 1st June 2009, Accepted 10th August 2009; first published on the web 15th September 2009. This article is part of themed collection: Nucleic acid simulations. We are grateful to the National Science Foundation and National Institutes of Health (NIH grant # RO1-GM081520-01) for funding of this research. We wish to thank the referees for their thorough reviews of the paper. MML acknowledges financial support from the Krell Institute and the US Department of Energy (DoE grant # DE-FG02-97ER25308) for a graduate fellowship at Caltech.