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The Dynamic and Statistical Properties of DNA Kinks

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Abstract—Conformational mobility is one of the most important properties of the DNA molecule. A striking example of this mobility is provided by the formation of regions where the double helix is locally unwound. The resulting so-called open DNA states play an important role in transcription, replication, and denaturation. In a “nonrelativistic” approximation, the open DNA states are often modeled as quasiparticles, or kinks, with a certain mass (mk), velocity (uk), and rest energy (E0 k). When more than one open state forms in a DNA molecule, statistics can be considered for an ensemble of N DNA kinks. The statistical properties of the ensemble are still poorly understood. In this paper the properties were investigated on the basis of recent data on the dynamic characteristics of DNA kinks. It was assumed that the interaction between the kinks is weak, all kinks are identical and the number N of DNA kinks is fixed. The statistical sum Zk, the free energy Fk, the velocity distribution function ρ1(vk), the average energy εk, the heat capacity Cv, k, and the entropy Sk were calculated for the ensemble of N DNA kinks. Temperature dependence curves of these characteristics were obtained and compared for four homogeneous sequences (poly(A), poly(T), poly(G), and poly(C)) and the pBR322 plasmid sequence.

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Authors and Affiliations

  1. Siberian State Medical University, 634050, Tomsk, Russia

    L. A. Krasnobaeva

  2. Tomsk State University, 634050, Tomsk, Russia

    L. A. Krasnobaeva

  3. Institute of Cell Biophysics, Russian Academy of Sciences, 142290, Pushchino, Moscow oblast, Russia

    L. V. Yakushevich

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  1. L. A. Krasnobaeva
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Correspondence to L. V. Yakushevich.

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The authors declare that they have no conflict of interest. This article does not contain any studies involving animals or human subjects performed by any of the authors.

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Translated by T. Tkacheva

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Krasnobaeva, L.A., Yakushevich, L.V. The Dynamic and Statistical Properties of DNA Kinks. BIOPHYSICS 65, 22–27 (2020). https://doi.org/10.1134/S0006350920010091

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