A Mathematical Model for Basepair Opening in a DNA Double Helix

Drobotenko, M. I.; Джимак, С. С.; Svidlov, Alexander; Басов, А. А.; Lyasota, O. M.; Барышев, М. Г.

doi:10.1134/s0006350918020069

Cited by 11 publications

(7 citation statements)

References 15 publications

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“…Existing mathematical models of DNA are discussed in a number of reviews [ 27 , 28 , 29 ]. However, to describe the effects caused by the introduction of deuterium atoms to hydrogen bonding between base pairs, the upgraded Yakushevich model was chosen [ 30 , 31 , 32 , 33 ], which allows to take into consideration the energy of the hydrogen bonds between pairs of nitrogenous bases. Due to the introduction of an additional term, this model allows to consider the effects of dissipation caused by the viscosity of the medium surrounding the DNA molecule.…”

Section: Introductionmentioning

confidence: 99%

Inequality in the Frequency of the Open States Occurrence Depends on Single 2H/1H Replacement in DNA

et al. 2020

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In the present study, the effect of 2H/1H isotopic exchange in hydrogen bonds between nitrogenous base pairs on occurrence and open states zones dynamics is investigated. These processes are studied using mathematical modeling, taking into account the number of open states between base pairs. The calculations of the probability of occurrence of open states in different parts of the gene were done depending on the localization of the deuterium atom. The mathematical modeling study demonstrated significant inequality (dependent on single 2H/1H replacement in DNA) among three parts of the gene similar in length of the frequency of occurrence of the open states. In this paper, the new convenient approach of the analysis of the abnormal frequency of open states in different parts of the gene encoding interferon alpha 17 was presented, which took into account both rising and decreasing of them that allowed to make a prediction of the functional instability of the specific DNA regions. One advantage of the new algorithm is diminishing the number of both false positive and false negative results in data filtered by this approach compared to the pure fractile methods, such as deciles or quartiles.

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Section: Introductionmentioning

confidence: 99%

Inequality in the Frequency of the Open States Occurrence Depends on Single 2H/1H Replacement in DNA

et al. 2020

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“…At first, the bond breaking corresponds to angular deviations of 180 • from the equilibrium position, so it is not clear how the "closing" of breaks can be described using "kinks". Secondly, the sine-Gordon equation models a simplified coupling in base pairs of pendulums, which leads to a significant change in the nature of the solution with a decrease in the amplitude of angular vibrations of nucleobases by about 100 times [53]. In third place, there is another drawback to this model [12], which is that fluctuations of bases in extreme pairs are not taken into account.…”

Section: Discussionmentioning

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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“…lums: nitrogenous bases correspond to the rotating pendulums, sugar-phosphate chains of the DNA molecule correspond to the elastic thread to which the pendulums are attached, and the elastic coupling of the pendulums is equivalent to the hydrogen bonding of complementary nitrogenous bases. The behavior of the mechanical system consisting of n pairs of pendulums is described by the Cauchy problem for a system of 2n ordinary differential equations [15,16].…”

Section: Aqueous Solutions In Biological Systemsmentioning

confidence: 99%

Influence of the 2H/1H Isotope Composition of the Water Environment on the Probability of Denaturation Bubble Formation in a DNA Molecule

et al. 2021

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A Mathematical Model for Basepair Opening in a DNA Double Helix

Cited by 11 publications

References 15 publications

Inequality in the Frequency of the Open States Occurrence Depends on Single 2H/1H Replacement in DNA

Inequality in the Frequency of the Open States Occurrence Depends on Single 2H/1H Replacement in DNA

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

Influence of the 2H/1H Isotope Composition of the Water Environment on the Probability of Denaturation Bubble Formation in a DNA Molecule

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