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DNA bendability--a novel feature in E. coli promoter recognition
O N Ozoline1, A A Deev, E N Trifonov
1Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region. ozoline@venus.iteb.serpukhov.su
Journal of Biomolecular Structure & Dynamics
|April 27, 1999
Summary
Bacterial promoter DNA exhibits a regular arrangement of flexible base-pair steps, suggesting a helical writhe that aids RNA polymerase binding. This unique DNA structure may be crucial for promoter recognition.
Area of Science:
- Structural biology
- Molecular genetics
- Biophysics
Background:
- Bacterial promoters are crucial DNA regions for gene transcription initiation.
- Understanding DNA structure and its role in protein binding is key to gene regulation.
Purpose of the Study:
- To analyze the distribution of deformable base-pair steps in bacterial promoters.
- To investigate the structural and functional implications of these DNA features for RNA polymerase recognition.
Main Methods:
- Analysis of DNA base-pair step deformability.
- Identification of periodic patterns in DNA sequences.
- Correlation analysis with known promoter elements (e.g., -35 hexamer).
Main Results:
- A regular positioning of TA and TG stacks with a period of 5.6 bp was detected.
- This periodicity suggests a sequence-dependent helical writhe (superhelix) in promoter DNA.
- Flexible base-pair steps correlate with rotational DNA setting on RNA polymerase, consistent with DNase I footprinting data.
- A negative correlation exists between deformable base-pair stacks and the -35 canonical hexamer.
Conclusions:
- Bacterial promoter DNA possesses a unique structural feature involving deformable base-pair steps and helical writhe.
- This structural characteristic likely facilitates RNA polymerase binding and promoter recognition.
- The findings suggest a novel element in promoter function beyond the canonical -35 hexamer.