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The effects of DNA supercoiling on G-quadruplex formation
Doreen A T Sekibo1, Keith R Fox1
1Biological Sciences, Life Sciences Building 85, University of Southampton, Southampton SO17 1BJ, UK.
Nucleic Acids Research
|October 17, 2017
Summary
Negative supercoiling does not induce G-quadruplex formation in DNA plasmids. Studies show that supercoiling alone is insufficient to drive the formation of these four-stranded DNA structures.
Area of Science:
- Molecular Biology
- Genomics
- Biochemistry
Background:
- Guanine-rich DNA sequences can form four-stranded G-quadruplex structures.
- These G-rich sequences are prevalent in gene promoter regions.
- G-quadruplex formation competes with Watson-Crick duplex formation and requires strand dissociation.
Purpose of the Study:
- To investigate the role of negative supercoiling in promoting G-quadruplex formation in DNA plasmids.
- To determine if supercoiling can overcome the competition with duplex formation.
Main Methods:
- Using plasmids with multiple (G3T)n and (G3T4)n repeats.
- Employing dimethylsulphate (DMS), potassium permanganate, and S1 nuclease for probing DNA structure.
- Utilizing 2D gel electrophoresis of DNA topoisomers.
Main Results:
- Dimethylsulphate footprinting showed limited evidence of G-quadruplex formation in (G3T)n sequences, unaffected by supercoiling.
- Potassium permanganate did not detect exposed thymines in loop regions for either sequence type.
- (G3T4)n sequences were not protected from DMS and did not react with permanganate; no supercoil-dependent transitions were detected by S1 nuclease or 2D gel electrophoresis.
Conclusions:
- Negative supercoiling alone is insufficient to drive G-quadruplex formation in these DNA constructs.
- The presence of G-rich repeats in plasmids does not automatically lead to supercoil-induced G-quadruplex formation.