Issue August 2002

category image Volume 20
No. 1 (p 1-140)
August 2002
ISSN 0739-1102

Sequence-Dependent Flexibility in Promoter Sequences (p. 127-134)

The non-neighbor interactions between base-pairs were taken into account to calculate the angular parameters (Ω, ρ and τ) describing the orientation of successive base-pair planes and the translation parameters (Dy) along the long axis of base-pair steps for 36 independent tetramers. A statistical mechanical model was proposed to predict the DNA flexibility that is mainly related to the thermal fluctuations at individual base-pair steps. The DNA flexibility can be described by the root-mean-square deviation of the end-to-end distance of DNA helical structure. The present model was then used to investigate the extreme flexible pattern in prokaryotic and eukaryotic promoter sequences. The results demonstrated several extreme flexible regions related to functionally important elements exist both in prokaryotic promoters and in eukaryotic promoters, DNA flexibility and AT content are highly correlated. The probabilities finding flexibility pattern in promoter sequences were also estimated statistically. The biological implications were discussed briefly.

Lu Tsai1,2
Liaofu Luo3
Zhirong Sun1*

1Department of Biological Science and Biotechnology
Tsinghua University
Beijing, 100084, P. R. China.
2Department of Biological and Chemical Engineering
Baotou University of Iron and Steel Technology
Baotou, 014010, P. R. China
3Department of Physics
Inner Mongolia University
Hohhot, 010021, P. R. China
*sunzhr@mail.tsinghua.edu.cn

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