Search of the minimums of energy of interaction between complementary chains of DNA in promoter and coding parts of genes of E. coli

  • Y. G. Shckorbatov Kharkiv National University, Institute of Biology
  • M. A. Papirny Kharkiv National University, Department of Molecular Biology and Biotechnology
  • M. V. Kulik Kharkiv National University, Department of Molecular Biology and Biotechnology
Keywords: energy of interaction of DNA chains, composition of DNA, promoter, orientation of genes

Abstract

By means of computer analysis of nucleotide composition and the energy of interaction between DNA chains in promoter and coding regions of genes of E. coli was studied. It showed an increase in the content of adenine and thymine in the promoter region. There were no significant differences between the genes in the direct and reverse orientation. It was found the minimums in the energy a of the interaction of complementary DNA strands in genes of direct and reverse orientations of the promoter and coding regions are near the positions: -100, -70, - 40, +5, +20, +30. Sites -40, +5 are close to the known consensus sequences of nucleotides in the promoter affecting the activity of the gene. Sites -100, -70, +20, +30, according to our data, also have the energy decrease of the interaction of complementary strands of DNA, suggesting that they have regulatory significance. The interaction energy of the complementary strands of DNA is reduced not only in the promoter but also at the beginning of the coding gene. Growth in the energy of interaction of DNA in the coding region of a gene occurs after the 100th position. The interaction energy of DNA chain interaction is lower in genes of reverse orientation. Differences between direct and reverse sequences are statistically significant in the region from -150 to - 101 and from 1 to 51. Genes in the reverse orientation have the additional energy minims in positions: -140,-120, -25, and +40. In addition, genes with a reverse orientation have a minimum of the energy of interaction between DNA strands in the cite -85, while in the genes with a direct orientation the minimum of energy is in position about -80.

Downloads

Download data is not yet available.

Author Biographies

Y. G. Shckorbatov, Kharkiv National University, Institute of Biology

Kharkov, pl. Svobody 4, 61077, Ukraine
yury.g.shckorbatov@univer.kharkov.ua

M. A. Papirny, Kharkiv National University, Department of Molecular Biology and Biotechnology

Kharkov, pl. Svobody 4, 61077, Ukraine
max_papirny@mail.ru

M. V. Kulik, Kharkiv National University, Department of Molecular Biology and Biotechnology

Kharkov, pl. Svobody 4, 61077, Ukraine
max_papirny@mail.ru

References

1. Lewin B. Genes YIII. Upper Saddle River, New Jersey, Pearson Education Inc., 2004. 1002 p.

2. Morton R.A., Morton B.R. Separating the effects of mutation and selection in producing DNA skew in bacterial chromosomes. BMC Genomics 2007; 8: 369.

3. Lobry J.R., Sueoka N. Asymmetric directional mutation pressures in bacteria. Genome Biol. 2002; 3(10): research0058.1–research0058.14.

4. Mrazek J., Karlin S. Strand compositional asymmetry in bacterial and large viral genomes. Proc. Natl. Acad. Sci. USA. 1998; 178: 3720-3725.

5. Rocha C. The replication-related organization of bacterial genomes. Microbiology 150 2004; 220: 1609-1627.

6. Tillier E.R., Collins R.A. Replication orientation affects the rate and direction of bacterial gene evolution. J Mol. Evol. 2000; 51(5): 459-63.

7. Burland V., Plunkett G., Daniels D.L., Blattner F.R. DNA sequence and analysis of 136 kb of the Escherichia coli genome: organizational symmetry around the origin of replication // Genomics. 1993. V. 16: 551–561.

8. Ogasawara N., Yoshikawa H. Genes and their organization in the replication origin region of the bacterial chromosome // Mol. Microbiol. 1992. V. 6. P. 629–634.

9. Kunst, F., Ogasawara, N., Moszer, I. & 148 other authors. The complete genome sequence of the Gram-positive bacterium Bacillus subtilis // Nature 1997. V. 390. P.249–256.

10. Blattner F.R., Plunkett G., Bloch C.A. & 14 other authors. The complete genome sequence of Escherichia coli K-12 // Science. 1997. V. 240. P. 1453-1461.

11. Dervyn E., Ehrlich S.D. Two essential DNA polymerases at the bacterial replication fork. Science. 2001. V. 294. P. 1716-1719.

12. Yuzhakov, A., Turner, J. & O'Donnell, M. Replisome assembly reveals the basis for asymmetric function in leading and lagging strand replication // Cell. 1996. V. 86. P. 877–886.

13. Sponer J., Jurecka P., Hobza P. Accurate interaction energies of hydrogen-bonded nucleic acid Base Pairs // J. AM. CHEM. SOC. 2004. V. 126. P. 10142-10151.

14. Rocha E.P., Danchin A., Viari A. Universal replication biases in bacteria // Mol. Microbiol. 1999. V.32. P. 11–16/
Cited
How to Cite
Shckorbatov, Y. G., Papirny, M. A., & Kulik, M. V. (1). Search of the minimums of energy of interaction between complementary chains of DNA in promoter and coding parts of genes of E. coli. Biophysical Bulletin, 1(24). Retrieved from https://periodicals.karazin.ua/biophysvisnyk/article/view/3866
Issue
Vol. 1 No. 24 (2010): Біофізичний вісник
Section
Molecular biophysics

Authors who publish with this journal agree to the following terms:

  1. Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
  2. Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
  3. Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).