DNA kinks behavior in the potential pit-trap

Larisa A. Krasnobaeva; Ludmila V. Yakushevich; Larisa A. Krasnobaeva; Ludmila V. Yakushevich

doi:10.3934/biophy.2022012

AIMS Biophysics

2022, Volume 9, Issue 2: 130-146. doi: 10.3934/biophy.2022012

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DNA kinks behavior in the potential pit-trap

Larisa A. Krasnobaeva ^1,2,
Ludmila V. Yakushevich ^{3
,
,}

1.
Siberian State Medical University, 634050 Tomsk, Moscow traсt 2, Russia
2.
Tomsk State University, 634050 Tomsk, Lenin Avenue 36, Russia
3.
Institute of Cell Biophysics, Russian Academy of Sciences, 142290 Pushchino. Institutskaya str. 3, Moscow region, Russia

Received: 10 May 2022 Revised: 31 May 2022 Accepted: 07 June 2022 Published: 10 June 2022

For better understanding the role of dynamic factors in the DNA functioning, it is important to study the internal mobility of DNA and, in particular, the movement of nonlinear conformational distortions -kinks along the DNA chains. In this work, we study the behavior of the kinks in the pPF1 plasmid containing two genes of fluorescent proteins (EGFP and mCherry). To simulate the movement, two coupled nonlinear sine-Gordon equations that describe the angular oscillations of nitrogenous bases in the main and complementary chains and take into account the effects of dissipation and the action of a constant torsion field. To solve the equations, approximate methods such as the quasi-homogeneous approximation, the mean field method, and the block method, were used. The obtained solutions indicate that two types of kinks moving along the double strand can be formed in any part of the plasmid. The profiles of the potential fields in which these kinks are moving are calculated. The results of the calculations show that the lowest energy required for the kink formation, corresponds to the region located between the genes of green and red proteins (EGFP and mCherry). It is shown that it is in this region a pit trap is located for both kinks. Trajectories of the kinks in the pit-trap and nearby are constructed. It is shown that there are threshold values of the torsion field, upon reaching which the kinks behavior changes dramatically: there is a transition from cyclic motion inside the pit-trap to translational motion and exit from the potential pit-trap.
- plasmid pPF1,
- EGFP and mCherry genes,
- potential energy profile,
- kink dynamics,
- 2D and 3D trajectories
Citation: Larisa A. Krasnobaeva, Ludmila V. Yakushevich. DNA kinks behavior in the potential pit-trap[J]. AIMS Biophysics, 2022, 9(2): 130-146. doi: 10.3934/biophy.2022012

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Abstract

For better understanding the role of dynamic factors in the DNA functioning, it is important to study the internal mobility of DNA and, in particular, the movement of nonlinear conformational distortions -kinks along the DNA chains. In this work, we study the behavior of the kinks in the pPF1 plasmid containing two genes of fluorescent proteins (EGFP and mCherry). To simulate the movement, two coupled nonlinear sine-Gordon equations that describe the angular oscillations of nitrogenous bases in the main and complementary chains and take into account the effects of dissipation and the action of a constant torsion field. To solve the equations, approximate methods such as the quasi-homogeneous approximation, the mean field method, and the block method, were used. The obtained solutions indicate that two types of kinks moving along the double strand can be formed in any part of the plasmid. The profiles of the potential fields in which these kinks are moving are calculated. The results of the calculations show that the lowest energy required for the kink formation, corresponds to the region located between the genes of green and red proteins (EGFP and mCherry). It is shown that it is in this region a pit trap is located for both kinks. Trajectories of the kinks in the pit-trap and nearby are constructed. It is shown that there are threshold values of the torsion field, upon reaching which the kinks behavior changes dramatically: there is a transition from cyclic motion inside the pit-trap to translational motion and exit from the potential pit-trap.

Conflict of interest

All authors declare no conflicts of interest in this paper.

References

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