Selective binding of tumor suppressor p53 protein to topologically constrained DNA: Modulation by intercalative drugs

Area of Science:

• Molecular Biology
• Biochemistry
• Genetics

Background:

• The tumor suppressor protein p53 plays a critical role in cellular responses to DNA damage.
• DNA supercoiling is a fundamental property influencing DNA structure and protein interactions.
• Understanding p53's DNA binding preferences is crucial for comprehending its function.

Purpose of the Study:

• To investigate the selective binding of wild-type p53 to negatively and positively supercoiled DNA.
• To explore how DNA topology modulation affects p53-DNA interactions.
• To analyze the impact of intercalating drugs on p53's binding affinity and specificity.

Main Methods:

• Utilized intercalating drugs (chloroquine, ethidium bromide, etc.) to modulate DNA supercoiling levels.
• Studied p53 binding to supercoiled and linear DNA using various concentrations of modulators.
• Analyzed DNA topoisomer distributions to assess binding selectivity based on superhelix density.

Main Results:

• p53 binding to negatively supercoiled DNA decreased as supercoiling was relaxed by intercalators.
• p53 preferentially bound to DNA that formed positive superhelices.
• p53 retained binding to specific sequences in topologically unconstrained linear DNA.
• p53 selectively binds DNA molecules with higher numbers of negative or positive superturns.

Conclusions:

• p53 exhibits selective binding to both negatively and positively supercoiled DNA.
• DNA topology significantly influences p53's binding preferences.
• These findings suggest potential biological roles for p53 in regulating DNA topology-dependent processes.