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Nucleic Acids Research 2005 33(22):7029-7038; doi:10.1093/nar/gki1010
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Published online 14 December 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

Structure and energy of a DNA dodecamer under tensile load

Stefano Piana

Department of Applied Chemistry, Nanochemistry Research Institute, Curtin University of Technology GPO Box U1987, Perth 6845, Western Australia

Email: piana{at}power.curtin.edu.au

Received November 9, 2005. Revised November 28, 2005. Accepted November 28, 2005.

In the last decade, methods to study single DNA molecules under tensile load have been developed. These experiments measure the force required to stretch and melt the double helix and provide insights into the structural stability of DNA. However, it is not easy to directly relate the shape of the force curve to the structural changes that occur in the double helix under tensile load. Here, state-of-the-art computer simulations of short DNA sequences are preformed to provide an atomistic description of the stretching of the DNA double helix. These calculations show that for extensions larger that ~25% the DNA undergoes a structural transformation and a few base pairs are lost from both the terminal and central part of the helix. This locally melted DNA duplex is stable and can be extended up to ~50–60% of the equilibrium length at a constant force. It is concluded that melting under tension cannot be modeled as a simple two-state process. Finally, the important role of the cantilever stiffness in determining the shape of the force–extension curve and the most probable rupture force is discussed.


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