Investigation of the probability of occurrence of denaturation bubbles during 2H/1H exchange in a DNA molecule

Authors

  • Elkina A.A. Kuban State University, Krasnodar, Russian Federation
  • Malyshko V.V. Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, Rostov-on-Don, Russian Federation
  • Gerasimenko E.O. Кубанский государственный технологический университет, Краснодар, Russian Federation
  • Litvinov D.A. MBOU Lyceum No. 4 of the city of Krasnodar, Krasnodar, Russian Federation
  • Goldobin I.N. MBOU Lyceum No. 4 of the city of Krasnodar, Krasnodar, Russian Federation
  • Dzhimak S.S. Kuban State University, Krasnodar, Russian Federation

UDC

51-76; 53.01

DOI:

https://doi.org/10.31429/vestnik-18-3-46-55

Abstract

In this work, the role of single substitutions of protium for deuterium in the formation of bubbles was investigated using the methods of mathematical modeling. It is shown that the probability of the formation of bubbles of a certain length (from 8 to 27 nucleotides) depends on the localization of the deuterium atom in the DNA molecule and can differ significantly from the probability of the appearance of open states in general. It should be noted that, although in most cases the differences in the occurrence of open states in deuterium-free DNA in comparison with the same molecule, which includes a single 2H/1H substitution, is when exposed to Ecr (in the range from 270 to 290 10-25 Nm) a fairly low value: the maximum increase in the number of open states was about 4.1% (when replacing hydrogen isotopes in the 301st pair of nitrogenous bases), a decrease in the number of open states was observed by less than 2.7 % (when replacing hydrogen isotopes in 20th pair of nitrogenous bases); the change in the probability of occurrence of DNA bubbles of various lengths, in turn, was already a significantly more significant value: a decrease to 83% and an increase to 71% when replacing hydrogen isotopes in the 284th and 376th pairs of nitrogenous bases, respectively.

Keywords:

deuterium, mathematical modeling of open states of DNA, DNA, bubbles of denture, hydrogen bond

Acknowledgement

Исследование выполнено при финансовой поддержке РФФИ и администрации Краснодарского края в рамках научного проекта № 20-41-235002 и государственного задания ЮНЦ РАН (№ АААА-А19-119040390083-6).

Author Infos

Anna A. Elkina

младший научный сотрудник НИЧ Кубанского государственного университета, старший научный сотрудник лаборатории проблем распределения стабильных изотопов в живых системах Южного научного центра РАН

e-mail: 013194@mail.ru

Vadim V. Malyshko

канд. мед. наук, доцент кафедры общей хирургии Кубанского государственного медицинского университета, научный сотрудник лаборатории проблем распределения стабильных изотопов в живых системах Южного научного центра РАН

e-mail: intro-2@rambler.ru

Evgeniy O. Gerasimenko

профессор, д-р техн. наук, профессор кафедры технологии жиров, косметики, товароведения, процессов и аппаратов Кубанского государственного технологического университета

e-mail: rosmaplus@gmail.com

Danil A. Litvinov

учащийся МБОУ лицей № 4 города Краснодара

e-mail: litvi2003@gmail.com

Ivan N. Goldobin

учащийся МБОУ лицей № 4 города Краснодара

e-mail: wody04@mail.ru

Stepan S. Dzhimak

канд. биол. наук, ведущий научный сотрудник лаборатории проблем распределения стабильных изотопов в живых системах Южного научного центра РАН, доцент кафедры радиофизики и нанотехнологий Кубанского государственного университета

e-mail: jimack@mail.ru

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Issue

2021. Vol. 18. No. 3

Section

Physics

Pages

46-55

Submitted

2021-09-23

Published

2021-09-30

How to Cite

Elkina A.A., Malyshko V.V., Gerasimenko E.O., Litvinov D.A., Goldobin I.N., Dzhimak S.S. Investigation of the probability of occurrence of denaturation bubbles during 2H/1H exchange in a DNA molecule. Ecological Bulletin of Research Centers of the Black Sea Economic Cooperation, 2021, vol. 18, no. 3, pp. 46-55. DOI: https://doi.org/10.31429/vestnik-18-3-46-55 (In Russian)

Copyright (c) 2021 Elkina A.A., Malyshko V.V., Gerasimenko E.O., Litvinov D.A., Goldobin I.N., Dzhimak S.S.

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