Issue 45, 2009

Structural ultrafast dynamics of macromolecules: diffraction of free DNA and effect of hydration

Abstract

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.

Graphical abstract: Structural ultrafast dynamics of macromolecules: diffraction of free DNA and effect of hydration

Article information

Article type
Paper
Submitted
01 Jun 2009
Accepted
10 Aug 2009
First published
15 Sep 2009

Phys. Chem. Chem. Phys., 2009,11, 10619-10632

Structural ultrafast dynamics of macromolecules: diffraction of free DNA and effect of hydration

M. M. Lin, D. Shorokhov and A. H. Zewail, Phys. Chem. Chem. Phys., 2009, 11, 10619 DOI: 10.1039/B910794K

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