Peculiar features of kink dynamics in inhomogeneous DNA

Yakushevich, L. V.; Krasnobaeva, L. A.

doi:10.1134/s0006350908010041

Cited by 11 publications

(3 citation statements)

References 13 publications

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“…Quasi-homogeneous approximation. In the quasi-homogeneous approximation, proposed in [Yakushevich, Krasnobaeva, 2008], the model Eqs. (4) take the form:…”

Section: B Gry Modelmentioning

confidence: 99%

On the computer experiments of Kasman

Grinevich¹,

Yakushevich²

2019

CRM

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Институт биофизики клетки Российской академии наук-обособленное подразделение Федерального государственного бюджетного учреждения науки «Федеральный исследовательский центр «Пущинский научный центр биологических исследований Российской академии наук», Россия, 142290, Московская обл., г. Пущино, ул. Институтская, д. 3 2 Федеральное государственное бюджетное учреждение науки «Институт теоретической и экспериментальной биофизики Российской академии наук», Россия, 142290, Московская обл., г. Пущино, ул. Институтская, д. 3

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“…Quasi-homogeneous approximation. In the quasi-homogeneous approximation, proposed in [Yakushevich, Krasnobaeva, 2008], the model Eqs. (4) take the form:…”

Section: B Gry Modelmentioning

confidence: 99%

On the computer experiments of Kasman

Grinevich¹,

Yakushevich²

2019

CRM

View full text Add to dashboard Cite

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“…To make it possible to apply the approach of McLaughlin and Scott for inhomogeneous sequences, the method of concentrations can be used [26,27]. According to the method, the coefficients of the initial model equations are averaged in the following way:…”

Section: Methods Of Concentrationsmentioning

confidence: 99%

Траектории Кинков ДНК В Последовательностях, Содержащих Кодирующие Области Генов

Якушевич¹,

Yakushevich²

2017

Math.Biol.Bioinf.

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Coding regions (CDS) being an integral part of any gene sequence, play an important role in the process of transcription. One of the tasks associated with the CDS regions, consists in the modeling of the passage of transcription bubbles named also open states or DNA kinks through the coding regions. In this paper, we present a simple and convenient approach to the modeling of the passage. It includes the calculation of the energy profile of the sequence and reducing the initial task to the modeling of the movement of a quasi particle in the field with this energy profile. To illustrate the method, we present the results of the calculations of the trajectories of the DNA kinks moving in the sequence of gene coding interferon alpha 17 (IFNA17) that consists of the three regions: the coding region and the two regions with unknown functional properties. To analyze the kink dynamics, we apply approximation where the DNA parameters are being averaged separately over each of the three regions. In the absences of dissipation, the total kink energy is constant. At the same time the kink velocity is constant only inside each of the regions. In the presence of dissipation, the total kink energy decreases. It is shown that the greater the total initial energy of the kink, the faster the energy decrease. It is suggested that the proposed approach could be useful in finding the ways to govern the movement of transcription bubbles at the first stage of the process of transcription.

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“…This approach was developed later in the works of Yomosa [14], Takeno and Homma [9], Zhang [23]. The theme was continued in the works of Salerno [13], Cuenda and Sanchez [4], Gaeta [2], Yakushevich [16,19,20,22], who improved the mechanical model by taking into account effects of asymmetry, helicity, dissipation and inhomogeneity of the molecule. These models were successfully applied to study the dynamics of open states in infinitely long double DNA chains.…”

Section: Introductionmentioning

confidence: 99%

Biomechanics of DNA: Rotational Oscillations of Bases

Yakushevich

2021

JNMP

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In the present paper we investigate the rotational oscillations of the nitrous bases that form a central base pair in a short DNA fragment consisting of three base pairs. For this purpose we use a simple mechanical model of the DNA fragment where the bases are imitated by pendulums, and the interactions between the bases are imitated by springs. It is suggested that the pendulums of the central pair oscillate, and the pendulums of neighboring pairs located at the edges of the fragment are immovable. The model takes into account the hydrogen bonds between the bases in pairs, the stacking interactions between neighboring base pairs and the helicity of the DNA structure. We derived the Lagrangian of the model system and the nonlinear equations of motions. Parameters of the equations were considered in details. We found solutions of the equations in the homogeneous case when the fragment contained only identical base pairs: Adenine-Thymine (AT) or Guanine-Cytosine (GC). The trajectories of the model system in the configuration space were also constructed in this approximation.

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Peculiar features of kink dynamics in inhomogeneous DNA

Cited by 11 publications

References 13 publications

On the computer experiments of Kasman

On the computer experiments of Kasman

Траектории Кинков ДНК В Последовательностях, Содержащих Кодирующие Области Генов

Biomechanics of DNA: Rotational Oscillations of Bases

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