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Issue 45, 2009
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Structural ultrafast dynamics of macromolecules: diffraction of free DNA and effect of hydration

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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

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Publication details

The article was received on 01 Jun 2009, accepted on 10 Aug 2009 and first published on 15 Sep 2009


Article type: Paper
DOI: 10.1039/B910794K
Citation: Phys. Chem. Chem. Phys., 2009,11, 10619-10632
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    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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