Energetics of pPF1 plasmid kinks

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

doi:10.3934/bioeng.2025018

AIMS Bioengineering

2025, Volume 12, Issue 3: 383-396. doi: 10.3934/bioeng.2025018

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Research article

Energetics of pPF1 plasmid kinks

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

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

Received: 22 May 2025 Revised: 05 August 2025 Accepted: 11 August 2025 Published: 15 August 2025

Kinks are known in mathematics as special solutions of nonlinear partial differential equations (NLPDEs) and in biology as models of open states of DNA formed during replication, transcription, and denaturation. The characteristics of the formation and movement of kinks in various DNAs are currently being actively studied. However, the dynamic behavior of kinks formed and propagated in the recently synthesized plasmid pPF1 remains poorly understood, and the issue of kink energetics has not yet been considered. This paper considers the energetics of kinks moving in the potential field of the plasmid pPF1, the sequence of which consists of 5557 base pairs and includes the genes of fluorescent proteins Egfp and mCherry, separated by a small intermediate region, as well as the gene of resistance to kanamycin (Kan). The paper presents the calculations of the energy profiles of the plasmid potential field, as well as the time dependence of the energy, size, and propagation velocity of kinks along these strands. Considerable attention is paid to the study of the influence of DNA torque on the energy of kinks. It is shown that the form of the curves of dependence on time is completely determined by the magnitude of the torque. Thus, at torque values below threshold values, the energy curves have the form of damped oscillations; at torque values above the threshold values, the energy curves change smoothly. Estimates of these threshold values are provided.
- pPF1 plasmid,
- DNA open states,
- kink energy,
- kink size,
- kink velocity
Citation: Ludmila V. Yakushevich, Larisa A. Krasnobaeva. Energetics of pPF1 plasmid kinks[J]. AIMS Bioengineering, 2025, 12(3): 383-396. doi: 10.3934/bioeng.2025018

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Abstract

Kinks are known in mathematics as special solutions of nonlinear partial differential equations (NLPDEs) and in biology as models of open states of DNA formed during replication, transcription, and denaturation. The characteristics of the formation and movement of kinks in various DNAs are currently being actively studied. However, the dynamic behavior of kinks formed and propagated in the recently synthesized plasmid pPF1 remains poorly understood, and the issue of kink energetics has not yet been considered. This paper considers the energetics of kinks moving in the potential field of the plasmid pPF1, the sequence of which consists of 5557 base pairs and includes the genes of fluorescent proteins Egfp and mCherry, separated by a small intermediate region, as well as the gene of resistance to kanamycin (Kan). The paper presents the calculations of the energy profiles of the plasmid potential field, as well as the time dependence of the energy, size, and propagation velocity of kinks along these strands. Considerable attention is paid to the study of the influence of DNA torque on the energy of kinks. It is shown that the form of the curves of dependence on time is completely determined by the magnitude of the torque. Thus, at torque values below threshold values, the energy curves have the form of damped oscillations; at torque values above the threshold values, the energy curves change smoothly. Estimates of these threshold values are provided.

Conflict of interest

All authors declare no conflicts of interest in this paper.

References

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