High temperature unfolding simulations of a single stranded DNA i-motif

We present the results of high temperature 500 K Molecular Dynamics simulations of the DNA i-motif. The essential dynamics and the main unfolding pathways are compared to a biased metadynamics simulation at 300 K. Our results indicate a remarkable agreement of the concerted motion at both temperatur...

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Bibliographic Details
Published in:arXiv.org 2011-03
Main Authors: Smiatek, Jens, Liu, Dongsheng, Heuer, Andreas
Format: Article
Language:English
Subjects:
Deoxyribonucleic acid
DNA
Eigenvectors
High temperature
Molecular dynamics
Simulation
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Summary:We present the results of high temperature 500 K Molecular Dynamics simulations of the DNA i-motif. The essential dynamics and the main unfolding pathways are compared to a biased metadynamics simulation at 300 K. Our results indicate a remarkable agreement of the concerted motion at both temperatures. The transition can be described by a few number of eigenvectors indicating a simple unfolding process. Two main mechanisms for the unfolding pathway at 500 K can be detected which are in good agreement to the results of the biased simulation at 300 K.
ISSN:2331-8422