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

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. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png European Biophysics Journal Springer Journals

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

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Publisher
Springer Journals
Copyright
Copyright © 2018 by European Biophysical Societies' Association
Subject
Life Sciences; Biochemistry, general; Biological and Medical Physics, Biophysics; Cell Biology; Neurobiology; Membrane Biology; Nanotechnology
ISSN
0175-7571
eISSN
1432-1017
DOI
10.1007/s00249-018-1313-3
Publisher site
See Article on Publisher Site

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.

Journal

European Biophysics Journal – Springer Journals

Published: May 31, 2018

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