Influence of Environmental Parameters on the Stability of the DNA Molecule

Svidlov, Alexander; Drobotenko, M. I.; Басов, А. А.; Gerasimenko, E. O.; Елкина, А. А.; Барышев, М. Г.; Nechipurenko, Yu. D.; Джимак, С. С.

doi:10.3390/e23111446

Cited by 9 publications

(3 citation statements)

References 47 publications

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“…The mathematical model of the angular movements of nitrogenous bases is based on the analogy between a DNA molecule and a mechanical system consisting of two chains of interconnected pendulums. At the same time, nitrogenous bases correspond to the rotating pendulums, and the sugar-phosphate chains of the DNA molecule correspond to the elastic thread to which these pendulums are attached; the hydrogen bond of a pair of complementary nitrogenous bases corresponds to the elastic bond of the corresponding pair of pendulums [25][26][27].…”

Section: Mathematical Modelmentioning

confidence: 99%

Genesis of Open States Zones in a DNA Molecule Depends on the Localization and Value of the Torque

Джимак

Svidlov

Елкина

et al. 2022

IJMS

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The formation and dynamics of the open states in a double-stranded DNA molecule are largely determined by its mechanical parameters. The main one is the torque. However, the experimental study of DNA dynamics and the occurrence of open states is limited by the spatial resolution of available biophysical instruments. Therefore, in this work, on the basis of a mechanical mathematical model of DNA, calculations of the torque effect on the process of occurrence and dynamics of open states were carried out for the interferon alpha 17 gene. It was shown that torsion action leads to the occurrence of rotational movements of nitrogenous bases. This influence is nonlinear, and an increase in the amplitude of the torsion action does not lead to an automatic increase in the amplitude of rotational movements and an increase in the zones’ open states. Calculations with a constant torsion moment demonstrate that open states zones are more often formed at the boundaries of the gen and in regions with a predominance of A–T pairs. It is shown, that for the occurrence of open states in the part of the gene that contains a small number of A–T pairs, a large amount of torque is required. When the torque is applied to a certain region of the gene, the probability of the formation of the open state depends on the content of A–T pairs in this region, the size of this region, and on the exposure time. For this mathematical model, open states zones can be closed when the torsion action stops. The simulation results showed that the values of the torsion moment required for the appearance of open states zones, in some cases, are close to experimentally measured (13–15 pN·nm).

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Section: Mathematical Modelmentioning

confidence: 99%

Genesis of Open States Zones in a DNA Molecule Depends on the Localization and Value of the Torque

Джимак

Svidlov

Елкина

et al. 2022

IJMS

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“…Moreover, the isotopic composition of the media, causing primarily a single 2 H/ 1 H replacement, affects the size of denaturation bubbles and the probability of their formation [24]. The angular model of DNA [25,26] makes it possible to take into consideration a quite wide range of external influences, such as the viscosity of the medium, the isotopic composition, and external forces [27][28][29][30]. In addition, stacking is also contemplated in the coefficient responsible for the elastic properties of the thread in this model.…”

Section: Introductionmentioning

confidence: 99%

Influence of a Single Deuterium Substitution for Protium on the Frequency Generation of Different-Size Bubbles in IFNA17

Basov,

Dorohova,

Malyshko

et al. 2023

IJMS

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The influence of a single 2H/1H replacement on the frequency generation of different-size bubbles in the human interferon alpha-17 gene (IFNA17) under various energies was studied by a developed algorithm and mathematical modeling without simplifications or averaging. This new approach showed the efficacy of researching DNA bubbles and open states both when all hydrogen bonds in nitrogenous base pairs are protium and after an 2H-substitution. After a single deuterium substitution under specific energies, it was demonstrated that the non-coding region of IFNA17 had a more significant regulatory role in bubble generation in the whole gene than the promoter had. It was revealed that a single deuterium substitution for protium has an influence on the frequency generation of DNA bubbles, which also depends on their size and is always higher for the smaller bubbles under the largest number of the studied energies. Wherein, compared to the natural condition under the same critical value of energy, the bigger raises of the bubble frequency occurrence (maximums) were found for 11–30 base pair (bp) bubbles (higher by 319%), 2–4 bp bubbles (higher by 300%), and 31 bp and over ones (higher by 220%); whereas the most significant reductions of the indicators (minimums) were observed for 11–30 bp bubbles (lower by 43%) and bubbles size over 30 bp (lower by 82%). In this study, we also analyzed the impact of several circumstances on the AT/GC ratio in the formation of DNA bubbles, both under natural conditions and after a single hydrogen isotope exchange. Moreover, based on the obtained data, substantial positive and inverse correlations were revealed between the AT/GC ratio and some factors (energy values, size of DNA bubbles). So, this modeling and variant of the modified algorithm, adapted for researching DNA bubbles, can be useful to study the regulation of replication and transcription in the genes under different isotopic substitutions in the nucleobases.

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“…The aim of this work is to study the effect of a single deuterium substitution at the frequency of hydrogen bond dissociation in IFNA17 in the range of the highest critical energies, based on the mechanical model of DNA [ 26 ], without simplifications and averaging [ 27 , 28 ].…”

Section: Introductionmentioning

confidence: 99%

Influence of Single Deuterium Replacement on Frequency of Hydrogen Bond Dissociation in IFNA17 under the Highest Critical Energy Range

Басов

Drobotenko

Svidlov

et al. 2022

IJMS

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The effect of single substitutions of protium for deuterium in hydrogen bonds between pairs of nitrogenous bases on the open states occurrence probability at high critical breaking energies of these bonds has been studied. The study was carried out using numerical methods based on the angular mathematical model of DNA. The IFNA17 gene was divided into three approximately equal parts. A comparison of the open states occurrence probability in these parts of the gene was done. To improve the accuracy of the results, a special data processing algorithm was developed. The developed methods have shown their suitability for taking into account the occurrence of open states in the entire range of high critical energies. It has been established that single 2H/1H substitutions in certain nitrogenous bases can be a mechanism for maintaining the vital activity of IFNA17 under critical conditions. In general, the developed method of the mathematical modeling provide unprecedented insight into the DNA behavior under the highest critical energy range, which greatly expands scientific understanding of nucleobases interaction.

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Influence of Environmental Parameters on the Stability of the DNA Molecule

Cited by 9 publications

References 47 publications

Genesis of Open States Zones in a DNA Molecule Depends on the Localization and Value of the Torque

Genesis of Open States Zones in a DNA Molecule Depends on the Localization and Value of the Torque

Influence of a Single Deuterium Substitution for Protium on the Frequency Generation of Different-Size Bubbles in IFNA17

Influence of Single Deuterium Replacement on Frequency of Hydrogen Bond Dissociation in IFNA17 under the Highest Critical Energy Range

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