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Possible scenarios of DNA double-helix unzipping process in single-molecule manipulation experiments

Original Article
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Abstract

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.

Keywords

DNA base pairs Unzipping 

Notes

Funding

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.

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Copyright information

© European Biophysical Societies' Association 2018

Authors and Affiliations

  1. 1.Bogolyubov Institute for Theoretical PhysicsKievUkraine

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