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Helical phasing between DNA bends and the determination of bend direction
1Yale University School of Medicine, Department of Molecular Biophysics and Biochemistry, New Haven, CT 06510.
Nucleic Acids Research
|December 10, 1987
Summary
Determining DNA bend direction is challenging. This study reveals how linking DNA bends reveals their relative orientation, aiding in understanding DNA structure and protein interactions.
Area of Science:
- Molecular Biology
- Biophysics
- Genetics
Background:
- DNA bending influences biological processes like replication and transcription.
- Electrophoresis is used to study DNA fragment mobility, but determining bend direction is difficult.
Purpose of the Study:
- To develop a method for determining the direction of DNA bends.
- To investigate the orientation of bends in kinetoplast DNA and at the gamma delta resolvase binding site.
Main Methods:
- Linking protein-induced and protein-independent DNA bends with variable-length DNA segments.
- Analyzing the electrophoretic mobility of these constructs using polyacrylamide gel electrophoresis.
- Correlating mobility minima with DNA helical turns to determine bend orientation.
Main Results:
- Electrophoretic mobility showed a sinusoidal variation with linker length.
- Mobility minima occurred predictably with each DNA helical turn added to the linker.
- The A5-6 tracts in kinetoplast DNA bend towards the minor groove.
- The gamma delta resolvase binding site I bends towards the major groove.
Conclusions:
- The method allows for the determination of relative DNA bend directions.
- The findings provide insights into the structural organization of kinetoplast DNA.
- The study elucidates the groove preference of DNA bending induced by the gamma delta resolvase.