1.Dependence of the E. coli promoter strength and physical parameters upon the nucleotide sequence.
Andrey Y BEREZHNOY ; Yuriy G SHCKORBATOV
Journal of Zhejiang University. Science. B 2005;6(11):1063-1068
The energy of interaction between complementary nucleotides in promoter sequences of E. coli was calculated and visualized. The graphic method for presentation of energy properties of promoter sequences was elaborated on. Data obtained indicated that energy distribution through the length of promoter sequence results in picture with minima at -35, -8 and +7 regions corresponding to areas with elevated AT (adenine-thymine) content. The most important difference from the random sequences area is related to -8. Four promoter groups and their energy properties were revealed. The promoters with minimal and maximal energy of interaction between complementary nucleotides have low strengths, the strongest promoters correspond to promoter clusters characterized by intermediate energy values.
AT Rich Sequence
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genetics
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Base Sequence
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Chromosome Mapping
;
methods
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DNA, Bacterial
;
genetics
;
Escherichia coli
;
genetics
;
Molecular Sequence Data
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Promoter Regions, Genetic
;
genetics
;
Sequence Analysis, DNA
;
methods
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Transcription, Genetic
;
genetics
2.Regularities in the E. coli promoters composition in connection with the DNA strands interaction and promoter activity.
Andrey Yu BEREZHNOY ; Yuriy G SHCKORBATOV ; Kiryu HISANORI
Journal of Zhejiang University. Science. B 2006;7(12):969-973
The energy of interaction between DNA strands in promoters is of great functional importance. Visualization of the energy of DNA strands distribution in promoter sequences was achieved. The separation of promoters in groups by their energetic properties enables evaluation of the dependence of promoter strength on the energetic properties. The analysis of groups (clusters) of promoters distributed by the energy of DNA strands interaction in -55, -35, -10 and +6 sequences indicates their connection with the transcriptional activity.
DNA, Bacterial
;
genetics
;
Escherichia coli
;
genetics
;
Promoter Regions, Genetic
;
Sequence Analysis, DNA