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Review of Mathematical Models Describing the Mechanical Motion in a DNA Molecule

  • MOLECULAR BIOPHYSICS
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Abstract

Several mechanical models that reproduce the DNA structure were considered. Evolution was described in more detail for the mechanical model proposed for a DNA molecule by Englander, who suggested that nonlinear effects can play an important role in DNA dynamics. The paper discusses the mechanical model of a DNA molecule that takes into account the rotational motion of nitrogenous bases around the sugar-phosphate backbone and the influence of external periodic action on the dynamics of the molecule. When the model is numerically solved without simplifications, the DNA molecule starts oscillating under periodic external influence, and the specifics of its oscillations depend on its nucleotide sequence. Importantly, this mathematical model makes it possible to calculate the frequency and amplitude of vibrations for a particular DNA site. Calculations show that zones of open states appear more often at gene boundaries and in regions with a predominance of A–T base pairs.

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Funding

This work was supported by the Kuban Science Foundation (project no. N-21.1/11), a state grant to support young Russian researchers, candidates of sciences from the President of the Russian Federation (project no. MK-2366.2022.1.4), the Russian Foundation for Basic Research (project no. 19- 44-230026), and a state agreement with the Southern Research Center (no. 122020100351-9).

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Authors and Affiliations

  1. Southern Research Center, Russian Academy of Sciences, 344006, Rostov-on-Don, Russia

    M. V. Bezhenar, A. A. Elkina, M. G. Baryshev & S. S. Dzhimak

  2. Kuban State University, 350040, Krasnodar, Russia

    M. V. Bezhenar, A. A. Elkina, M. G. Baryshev, A. O. Sulima, S. S. Dzhimak & V. A. Isaev

  3. Cuban Center for Neurosciences, Playa, La Habana, Cuba

    J. L. Hernandez Caceres

Authors
  1. M. V. Bezhenar
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  2. A. A. Elkina
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  3. J. L. Hernandez Caceres
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  4. M. G. Baryshev
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  5. A. O. Sulima
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  6. S. S. Dzhimak
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  7. V. A. Isaev
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Correspondence to M. V. Bezhenar.

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Translated by T. Tkacheva

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Bezhenar, M.V., Elkina, A.A., Caceres, J.L. et al. Review of Mathematical Models Describing the Mechanical Motion in a DNA Molecule. BIOPHYSICS 67, 867–875 (2022). https://doi.org/10.1134/S0006350922060021

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  • DOI: https://doi.org/10.1134/S0006350922060021

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