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Interaction effects of DNA, RNA-polymerase, and cellular fluid on the local dynamic behaviors of DNA

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Abstract

In view of the complex structure and environment, the dynamic analysis on deoxyribonucleic acid (DNA) is a challenge in the biophysics field. Considering the local interaction with ribonucleic acid (RNA)-polymerase as well as the dissipative effect of cellular fluid, a coupling sine-Gordon-type dynamic model is used to describe the rotational motions of the bases in DNA. First, the approximate symmetric form is constructed. Then, the wave form and the wave velocity of the kink solution to the proposed dynamic model are investigated by a Runge-Kutta structure-preserving scheme based on the generalized multi-symplectic idea. The numerical results indicate that, the strengthening of the local interaction between DNA and RNA-polymerase described by the coupling potential makes the form of the kink solution steep, while the appearance of the friction between DNA and cellular fluid makes the form of the kink solution flat. In addition, the appearance of the friction decreases the velocities of both the symplectic configuration and the anti-symplectic configuration with different degrees. The above findings are beneficial to comprehend the DNA transcription mechanism.

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Achknowlegements

The authors wish to thank Professor J. J. FENG of University of British Columbia and Professor G. DERKS of Surrey University for giving us several good suggestions. The authors also wish to thank the Fund of the Youth Innovation Team of Shaanxi Universities and the Seed Foundation of Qian Xuesen Laboratory of Space Technology for financial support.

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Authors and Affiliations

  1. School of Civil Engineering and Architecture, Xi’an University of Technology, Xi’an, 710048, China

    Weipeng Hu

  2. State Key Laboratory of Eco-Hydraulics in Northwest Arid Region of China, Xi’an University of Technology, Xi’an, 710048, China

    Weipeng Hu

  3. School of Mechanics, Civil Engineering and Architecture, Northwestern Polytechnical University, Xi’an, 710072, China

    Zichen Deng

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  1. Weipeng Hu
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  2. Zichen Deng
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Correspondence to Weipeng Hu.

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Project supported by the National Natural Science Foundation of China (Nos. 11972284 and 11672241), the Fund for Distinguished Young Scholars of Shaanxi Province of China (No. 2019JC-29), and the Open Foundation of State Key Laboratory of Structural Analysis of Industrial Equipment of China (No.GZ19103)

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Hu, W., Deng, Z. Interaction effects of DNA, RNA-polymerase, and cellular fluid on the local dynamic behaviors of DNA. Appl. Math. Mech.-Engl. Ed. 41, 623–636 (2020). https://doi.org/10.1007/s10483-020-2595-6

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  • DOI: https://doi.org/10.1007/s10483-020-2595-6

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