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.
Torsional Energy Barriers of Biaryls Could Be Predicted by Electron Richness/Deficiency of Aromatic Rings; Advancement of Molecular Mechanics toward Atom-Type Independence