Edorium Journal of

Bioinformatics

 
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Original Article
 
Differences in the energy of DNA strands interaction in the near start-codon sequences of three bacterial genomes
Papirny Maxim A.1, Pasiuga Vladimir N.2, Shckorbatov Yuriy G.3
1Post-graduate student, National Scientific Centre "ISSAR" NAAS, Kharkiv, Ukraine.
2Researcher, Research Institute of Biology, V. N. Karazin Kharkiv National University, Kharkiv, Ukraine.
3Head of Department of Genetics, Research Institute of Biology, V. N. Karazin Kharkiv National University, Kharkiv, Ukraine.

Article ID: 100001B02PA2015
doi:10.5348/B02-2015-1-OA-1

Address correspondence to:
Yuriy G. Shckorbatov
Office - V. N Karazin Kharkiv National University
Institute of Biology, pl. Svobody 4
Kharkiv 61022
Ukraine
Phone: +380(57)7075262

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How to cite this article
Papirny MA, Pasiuga VN, Shckorbatov YG. Differences in the energy of DNA strands interaction in the near start-codon sequences of three bacterial genomes. Edorium J Bioinforma 2015;1:1–8.


Abstract
Aims: The energy of DNA strands interaction (DSI) can regulate binding of enzymes and regulatory proteins to DNA in gene promoter and upstream region. The purpose of this work was to investigate the mean value of the energy DSI in the near promoter zone (± 200 nucleotides) of three bacterial genomes.
Methods: We used the computer analysis for assessment of the energy of DSI in 90 in direct orientation and 90 genes in reverse orientation for every genome in proximity of start codon for E. coli, B. subtilis, and S. typhimurium genomes.
Results: The DSI energy in genes of three tested bacterial species decreases in the prepromoter zone and comes to the elevated level in the coding zone of gene. The assessed mean energy of DSI differs in all tested species. It is higher (in absolute value) in genes of E. coli and S. typhimurium than in genes of B. subtilis in the prepromoter and promoter zone (area from -200 to -1). The DSI energy in the promoter and prepromoter zones (from -150 to -1 nucleotides) and in coding zone (from + 51 to + 150 nucleotides) is lower in genes of S. typhimurium and B. subtilis with reverse orientation than in directly oriented genes. In genes of E. coli such regularity was not observed.
Conclusion: The proposed approach- the assessment of the DSI energy in the genomes is a perspective tool for determination differences in genotype between the organisms of different systematic position. For instance, the observed similarity in DSI in the near promoter zone between E. coli and S. typhimurium and difference in DSI to B. subtilis may be connected with the relative systematic proximity between E. coli and S. typhimurium and relative systematic distance of B. subtilis from these species.

Keywords: Bacillus subtilis, DNA strands interaction energy, Escherichia coli, Gene activity regulation, Gene orientation, Salmonella typhimurium

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Author Contributions:
Papirny Maxim A. – Substantial contributions to conception and design, Acquisition of data, Analysis and interpretation of data, Drafting the article, Critical revision of the article, Final approval of the version to be published
Pasiuga Vladimir N. – Substantial contributions to conception and design, Acquisition of data, Analysis and interpretation of data, Drafting the article, Critical revision of the article, Final approval of the version to be published
Shckorbatov Yuriy G. – Substantial contributions to conception and design, Acquisition of data, Analysis and interpretation of data, Drafting the article, Critical revision of the article, Final approval of the version to be published
Guarantor of submission
The corresponding author is the guarantor of submission.
Source of support
None
Conflict of interest
Authors declare no conflict of interest.
Copyright
© 2015 Papirny Maxim A. et al. This article is distributed under the terms of Creative Commons Attribution License which permits unrestricted use, distribution and reproduction in any medium provided the original author(s) and original publisher are properly credited. Please see the copyright policy on the journal website for more information.



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