Inequality in the Frequency of the Open States Occurrence Depends on Single <sup>2</sup>H/<sup>1</sup>H Replacement in DNA
In the present study, the effect of <sup>2</sup>H/<sup>1</sup>H 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 nu...
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| Format: | Article |
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MDPI AG
2020-08-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/25/16/3753 |
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| author | Alexander Basov Mikhail Drobotenko Alexandr Svidlov Eugeny Gerasimenko Vadim Malyshko Anna Elkina Mikhail Baryshev Stepan Dzhimak |
| author_facet | Alexander Basov Mikhail Drobotenko Alexandr Svidlov Eugeny Gerasimenko Vadim Malyshko Anna Elkina Mikhail Baryshev Stepan Dzhimak |
| author_sort | Alexander Basov |
| collection | DOAJ |
| description | In the present study, the effect of <sup>2</sup>H/<sup>1</sup>H 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 <sup>2</sup>H/<sup>1</sup>H 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. |
| first_indexed | 2024-03-10T17:16:36Z |
| format | Article |
| id | doaj.art-c58fd7ab49d34296a5db58b01eea9e21 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-10T17:16:36Z |
| publishDate | 2020-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-c58fd7ab49d34296a5db58b01eea9e212023-11-20T10:28:50ZengMDPI AGMolecules1420-30492020-08-012516375310.3390/molecules25163753Inequality in the Frequency of the Open States Occurrence Depends on Single <sup>2</sup>H/<sup>1</sup>H Replacement in DNAAlexander Basov0Mikhail Drobotenko1Alexandr Svidlov2Eugeny Gerasimenko3Vadim Malyshko4Anna Elkina5Mikhail Baryshev6Stepan Dzhimak7Kuban State Medical University, 350063 Krasnodar, RussiaKuban State University, 350040 Krasnodar, RussiaKuban State University, 350040 Krasnodar, RussiaKuban State Technological University, 350042 Krasnodar, RussiaKuban State Medical University, 350063 Krasnodar, RussiaKuban State University, 350040 Krasnodar, RussiaKuban State University, 350040 Krasnodar, RussiaKuban State University, 350040 Krasnodar, RussiaIn the present study, the effect of <sup>2</sup>H/<sup>1</sup>H 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 <sup>2</sup>H/<sup>1</sup>H 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.https://www.mdpi.com/1420-3049/25/16/3753deuteriumDNAmathematical modelopen statesrotational movements of nitrogenous basesdynamics of a double-stranded DNA molecule |
| spellingShingle | Alexander Basov Mikhail Drobotenko Alexandr Svidlov Eugeny Gerasimenko Vadim Malyshko Anna Elkina Mikhail Baryshev Stepan Dzhimak Inequality in the Frequency of the Open States Occurrence Depends on Single <sup>2</sup>H/<sup>1</sup>H Replacement in DNA Molecules deuterium DNA mathematical model open states rotational movements of nitrogenous bases dynamics of a double-stranded DNA molecule |
| title | Inequality in the Frequency of the Open States Occurrence Depends on Single <sup>2</sup>H/<sup>1</sup>H Replacement in DNA |
| title_full | Inequality in the Frequency of the Open States Occurrence Depends on Single <sup>2</sup>H/<sup>1</sup>H Replacement in DNA |
| title_fullStr | Inequality in the Frequency of the Open States Occurrence Depends on Single <sup>2</sup>H/<sup>1</sup>H Replacement in DNA |
| title_full_unstemmed | Inequality in the Frequency of the Open States Occurrence Depends on Single <sup>2</sup>H/<sup>1</sup>H Replacement in DNA |
| title_short | Inequality in the Frequency of the Open States Occurrence Depends on Single <sup>2</sup>H/<sup>1</sup>H Replacement in DNA |
| title_sort | inequality in the frequency of the open states occurrence depends on single sup 2 sup h sup 1 sup h replacement in dna |
| topic | deuterium DNA mathematical model open states rotational movements of nitrogenous bases dynamics of a double-stranded DNA molecule |
| url | https://www.mdpi.com/1420-3049/25/16/3753 |
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