Modeling B–A Transformations of the DNA Double Helix

Волков, С. Н.

doi:10.1007/s10867-005-1284-3

Cited by 7 publications

(10 citation statements)

References 19 publications

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“…Геликоидальный, согласно Толковому словарю, это как раз винтовой, спиральный [7]. Есть и название в английской литературе, где слово helix (геликоидальный) явно обозначено как Double Helix DNA Model [12]. В диссертации был замечен единичный случай употребления такого термина.…”

Section: Hysteresis Cycle -петля гистерезисаunclassified

Complex Cases of Translation of the English Terms in the Sphere of Mathematical Modeling of a Dna Molecule

Kovylyaeva¹

2018

Philology. Theory & Practice

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The article considers the complex cases of terms translation in the sphere of mathematical modeling of a DNA molecule. The main problem is the lack of specialized dictionaries on this topic. In the work, the author has found the Russian equivalents for 12 word combinations, which caused difficulties for the translator. The translation was carried out with the help of the Russian-English and explanatory dictionaries, as well as articles with similar topics. It should be mentioned that the translation used a visualization technique that helps to understand the meaning of the term. The list of translated words is useful to specialists in the sphere of theoretical physics, biophysics, and it needs to be expanded.

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Section: Hysteresis Cycle -петля гистерезисаunclassified

Complex Cases of Translation of the English Terms in the Sphere of Mathematical Modeling of a Dna Molecule

Kovylyaeva¹

2018

Philology. Theory & Practice

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“…In expression (1) Ṙ, ṙ are derivatives on time; k R and k r are the elastic constants, which describe the interactions along macromolecular chain for external and internal components; M means monomer mass, m is reduced mass of monomer link according to the pathway of conformational transformation. It is significant to note, that for DNA conformational pathways with joint motions of nucleic bases, the masses M and m have the same value for A•T and G•C pairs [44][45][46]. Potential function Φ(r) describes the change of monomer energy on the pathway of conformational transformation from the usual compact to the stretched helix form.…”

Section: Dna Macromolecule Under the Action Of External Forcementioning

confidence: 99%

“…But in the present study the simplest model with two dominated components is considered to understand the basic mechanism of threshold deformation in the double helix. Such twocomponent approach has been successfully used for the modeling of B-A transition in dsDNA [44][45][46], and under studies of the effects of DNA localized bending and unzipping [47][48][49]. The action of external force on DNA macromolecule in last papers is considered indirectly, as the change in external component stiffness.…”

Section: Dna Macromolecule Under the Action Of External Forcementioning

confidence: 99%

“…As known [4][5][6][7][8][9] for critical regime, when f cr =65 pN, the deformation of dsDNA with average nucleotide content comprises 0.7 of its length. Considering, that the stretch modulus of such dsDNA has average value (S=1100 pN), from expression (46) it can be calculated ae cr ≈1. This estimation is important for the evaluation of coupling parameter χ.…”

Section: Properties Of Overstretching Transition: Quantitative Estima...mentioning

confidence: 99%

“…So, accordingly to the estimations made (Tabl. 1), and expression (46), the overstretching deformation of heteronomous DNA should be larger for macromolecule fragments with smaller stiffness, that is, for A•T-rich fragments. Note, this conclusion is in accordance with results of [21], where the larger amplitudes of overstretching deformation are observed for A•T-rich DNA.…”

Section: Dependence On Nucleicleotide Content B-s and Fim Overstretch...mentioning

confidence: 99%

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Mechanism of Threshold Elongation of DNA Macromolecule

Волков¹

2016

Preprint

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The mechanism of threshold elongation (overstretching) of DNA macromolecules under the action of external force is studied within the framework of phenomenological approach. When considering the task it is taken into account that double-stranded DNA is a polymorphic macromolecule with a set of metastable states. Accordingly to proposed mechanism, DNA threshold elongation can take place as a cooperative structural transition of macromolecule to metastable form, which is stabilized by the external force. For the description of DNA overstretching, the model included external (stretching) and internal (conformation) displacement components is constructed. As assumed, both components are coupled on the pathway of double helix transformations. It is shown, that under force action DNA deformation proceeds in two stages. First one is the restructuring of the double helix, which leads to formation of conformational bistability in DNA macromolecule. On the second stage, the conformational transition and the deformation induced by it consistently cover the macromolecule as a threshold process. The propagation of overstretched deformation in bistable macromolecule occurs as the motion of transition boundaries (domain walls), which are topologically stable structural excitations. Using the proposed approach, the contributions to DNA overstretching process are determined. This is elastic stretching of the double helix, deformation induced by conformational changes in macromolecule before overstretching transition, and threshold elongation as such. The greatest contribution to overstretching process in DNA (more then 80%) is introduced by threshold elongation. As shown, the effect of threshold deformation in DNA double helix takes place due to the critical correspondence of acting force with elastic properties of macromolecule, and achieves by restructuring of the double helix. The comparison of calculated characteristics of overstretching process for heteronomous DNA with experimental data shows good agreement. Analysis of the results obtained, together with the available literature data allow to conclude, that overstretching transition in the double helix is dynamical process and can spread in DNA chain. In the same time, in DNA with A•T-rich content due to large dissipation the overstretching process leads to force induced melting transition, and should have nearly static character.

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Conformation impact in the deformation of DNA TATA-box

Kanevska

Волков

2022

Low Temperature Physics

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The ability to undergo specific deformation in response to conformational changes of some sites of the macromolecule is the key element of DNA genetic activity regulation in biological cells. The deformation of the definite sequences in DNA chain provides an accurate reading of genetic information and the process of protein synthesis passing. The model based on the analysis of conformational changes of the TATA nucleotide sequence in DNA double helix is developed. In addition to elastic components (bending, twisting), the presented model includes the conformational rearrangements of the TATA-box. Obtained form, value, and energy of DNA cite deformation allow to offer the probable mechanism of recognition of key DNA sequences and makes it possible to explain the high accuracy of the processes of reproducing of genetic information in biological cells. The formulated physical mechanism of DNA deformation can be one of the main principles of genetic information realization.

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Modeling B–A Transformations of the DNA Double Helix

Cited by 7 publications

References 19 publications

Complex Cases of Translation of the English Terms in the Sphere of Mathematical Modeling of a Dna Molecule

Complex Cases of Translation of the English Terms in the Sphere of Mathematical Modeling of a Dna Molecule

Mechanism of Threshold Elongation of DNA Macromolecule

Conformation impact in the deformation of DNA TATA-box

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