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Journal of Nanomaterials
Volume 2015, Article ID 546851, 7 pages
Research Article

Configuration Transitions of Free Circular DNA System Induced by Nicks

1Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
2College of Biological Science, Weifang Medical University, Shandong 261053, China

Received 27 May 2015; Accepted 7 July 2015

Academic Editor: Song Cui

Copyright © 2015 Chao Ji et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Nicks have important functions in the biological functions of DNA-mediated systems. However, the configuration transitions of DNA molecules induced by the presence of nicks have not been quantitatively investigated. This study aims to analyze the configuration transitions of free circular DNA system induced by nicks. Using atomic force microscopy, two configuration states were observed in the free circular DNA system with different nick numbers. To understand the transmission of torsional energy among DNA base pairs, we defined the effective length and nicking angle. In the free DNA system, a torsional energy of 233 bp can be completely released by nicks. Based on the experimental and quantitative results, we propose a physical mechanism to explain the configuration transitions of the free circular DNA system induced by nicks. This study and the presented method are very useful in understanding the physical mechanism of nicks in DNA-mediated systems.