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Investigation of the Effect of a Single-Stranded Break on the Mechanical Parameters of DNA by Molecular Dynamics Method

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Abstract

Early detection and repair of damaged DNA is important for cell functioning and survival. The recently proposed mechanism of intranucleosomal loop formation suggests the relaxation of DNA supercoiling accumulated during transcription through damaged chromatin. The degree of DNA relaxation is affected by the mechanical properties and structure of the double helix. In this work, the consequences from the introduction of a single-stranded break on the mechanical properties of a DNA fragment are studied using molecular dynamics. It is concluded that the introduction of a single-stranded break leads to decreased stiffness and higher elasticity of the damaged DNA molecule as compared to the intact one. This, in turn, may lead to relief in the supercoiling of the defective DNA and to the enzyme arrest.

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Funding

This work was supported by the Russian Science Foundation (project no. 19-74-30003).

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Authors and Affiliations

  1. Department of Bioengineering, Faculty of Biology, Moscow State University, 119234, Moscow, Russia

    O. I. Volokh, G. A. Armeev, E. S. Trifonova & O. S. Sokolova

Authors
  1. O. I. Volokh
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  2. G. A. Armeev
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  3. E. S. Trifonova
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  4. O. S. Sokolova
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Corresponding author

Correspondence to O. S. Sokolova.

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COMPLIANCE WITH ETHICAL STANDARDS

The studies were performed without the use of animals and without the involvement of human subjects.

CONFLICT OF INTEREST

The authors declare that they have no conflict of interest.

Additional information

Translated by A. A. Lisenkova

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Volokh, O.I., Armeev, G.A., Trifonova, E.S. et al. Investigation of the Effect of a Single-Stranded Break on the Mechanical Parameters of DNA by Molecular Dynamics Method. Moscow Univ. Biol.Sci. Bull. 75, 136–141 (2020). https://doi.org/10.3103/S0096392520030098

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  • DOI: https://doi.org/10.3103/S0096392520030098

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