The DNA chains interaction energy in E. coli promoters in connection with their functional activity
Keywords:
promoters, promoter strength, nucleotide sequence, energy of interaction of DNA chains, physic properties of promoter
Abstract
The calculations of interaction energy of complementary nucleotides in promoter were performed. The methods of graphic representation of energetic promoter properties were elaborated. The data obtained indicate that the energy distribution through the promoter length has 3 minimums centered at the positions -35, -8 and +7 nucleotide number from the starting site of transcription. The most important sequence (Pribnow box) differs from the rest of promoter in its low energy of interaction between DNA chains. We defined 4 clusters in Pribnow box and in -35 sequences. The negative correlation between the mean DNA chains interaction energy in the clusters in Pribnow box and promoter strength was determined. Quite on the contrary in -35 box the mean DNA chains interaction energy directly correlate with promoter strength.
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References
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Spassky A, Kirkegaard K, Buc H. Changes in the DNA structure of the lac UVS promoter during formation open complex with Escherichia coli RNA polymerase. Biochemistry. 1985;24(11):2723-31.
Gralla JD. Activation and repression of E. coli promoters. Curr Opin Genet. 1996;6(5):526-30.
Roberts CW, Roberts JW. Base-specific recognition of the nontemplate strand of promoter DNA by E. coli RNA polymerase. Cell. 1996;3:495-501.
Guo Y, Gralla JD. Promoter opening via a DNA fork junctiou binding activity. Proc. Nat. Acad. Sci. 1998;95(20):1655-60.
Burr T, Mitchell J, Minchin S, Busby S. DNA sequence elements located immediately upstream of the -10 hexamer in Escherichia coli promoters: A systmeatic study. Nucleic Acids Res. 2000;28:1864-70.
Murakami KS, Masuda S, Campbell EA, Muzzin O, Darst SA. Structural basis of transcription initiation: An RNA polymerase holoenzyme-DNA complex. Science. 2002;296:1285-90.
Campbell EA, Muzzin O, Chlenov M, Sun JL, Olson CA, Weinman O, et al. Structure of the bacterial RNA polymerase promoter specificity o subunit. Mol. Cell. 2002;9:527-39.
Gourse RL, Ross W, Gaal T. UPs and downs in bacterial transcription initiation: Role of the a subunit of RNA polymerase in promoter recognition. Mol. Microbiol. 2000;37:687-95.
Guo Y, Gralla JD. Promoter opening via a DNA fork junction binding activity. Proc. Natl. Acad. Sci. 1998;95(20):11655-60.
Roberts CW, Roberts JW. Base-specific recognition of the nontemplate strand of promoter DNA by E. coli RNA polymerase. Cell. 1996;86(3):495-501.
Kajitani M, Ishihama A. Determination of the promoter strength in the mixed transcription system. II. Promoters of ribosomal RNA, ribosomal protein SI and recA protein operous from Escherichia coli. Nuclei Acids Research. 1983;11(12):3873-88.
Vogel SK, Schulz A, Rippe K. Binding affinity of Escherichia coli RNA polymerase holoenzyme for the glnAp2, nifH and nifL promoters. Nucleic Acids Research. 2002;30(18):4094-101.
Kanehisa M, Goto S, Kawashima S, Kuno Y, Hattori M. The KEGG resources for deciphering the genomel. Nucleic Acids Res. 2004;32:D277-80.
Mori H, Isono K, Horiuchi T, Miki T. Functional genomics of Escherich ia coli in Japan. Res Microbio. 2000;151:121-8.
Hisanori Kiryu, Taku Oshima, Kiyoshi Asai. Extracting relations between promoter sequences and their strengths from microarray data. Bioinformatics. 2005;21(7):1062-8.
Kudritskaya ZG, Danilov VI. Quantum mechanical study dipole approximation. J. Theor. Biol. 1976;59:301-18.
Spassky A, Kirkegaard K, Buc H. Changes in the DNA structure of the lac UVS promoter during formation open complex with Escherichia coli RNA polymerase. Biochemistry. 1985;24(11):2723-31.
Gralla JD. Activation and repression of E. coli promoters. Curr Opin Genet. 1996;6(5):526-30.
Roberts CW, Roberts JW. Base-specific recognition of the nontemplate strand of promoter DNA by E. coli RNA polymerase. Cell. 1996;3:495-501.
Guo Y, Gralla JD. Promoter opening via a DNA fork junctiou binding activity. Proc. Nat. Acad. Sci. 1998;95(20):1655-60.
Published
2006-06-06
Cited
How to Cite
Shckorbatov, Y. G., & Berezhnoy, A. Y. (2006). The DNA chains interaction energy in E. coli promoters in connection with their functional activity. Biophysical Bulletin, 1(17), 42-47. Retrieved from https://periodicals.karazin.ua/biophysvisnyk/article/view/12848
Section
Molecular biophysics
Copyright (c) 2006 Biophysical visnik
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