Possible scenarios of DNA double-helix unzipping process in single-molecule manipulation experiments
Single-molecule experiments on DNA unzipping are analyzed on the basis of the mobility of nucleic bases in complementary pairs. Two possible scenarios of DNA double-helix unzipping are proposed and studied, using the atom–atom potential function method. According to the first scenario, the base pairs transit into a ‘preopened’ metastable state and then fully open along the ‘stretch’ pathway. In this case, the DNA unzipping takes place slowly and as an equilibrium process, with the opening energies being similar to the energies obtained in thermodynamic experiments on DNA melting. The second scenario is characterized by higher opening forces. In this case, the DNA base pairs open directly along the ‘stretch’ pathway. It follows from our calculations that, in this scenario, the enthalpy difference between the A\(\cdot \)T and G\(\cdot \)C base pairs is much higher than in the first case. The features of the first unzipping scenario show that it can play a key role during the process of DNA genetic information transfer in vivo. It follows from our study that a peculiarity of the second scenario is that it can be used for the development of faster methods for reading genetic information in vitro.
KeywordsDNA base pairs Unzipping
The present work was partially supported by the Program of Fundamental Research of the Division of Physics and Astronomy of the National Academy of Sciences of Ukraine.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
- Volkov SN (1995) Pre-opened state of the DNA duplex. Mol Biol 29(5):1086–1094Google Scholar
- Volkov SN, Kosevich AM (1987) About the conformational vibrations of DNA. Mol Biol 21:797–806Google Scholar
- Zefirov UV, Zorkyi PM (1974) Van der Waals radii of atoms in crystal chemistry and structure chemistry. Zh Strukt Khimii 15:118–122Google Scholar
- Zhurkin VB, Poltev VI, Florent’ev VL (1980) Atom-atom potential functions for conformational calculations of nucleic acids. Mol Biol (USSR) 14:1116–1130Google Scholar