CAP binding to B and Z forms of DNA

Area of Science:

• Molecular Biology
• Biophysics
• Genetics

Background:

• The cyclic AMP receptor protein (CAP) is a crucial transcription factor in bacteria.
• Understanding CAP-DNA interactions is vital for deciphering gene regulation mechanisms.

Purpose of the Study:

• To investigate the conformational changes in DNA upon binding by CAP.
• To determine the binding stoichiometry and affinity of CAP for specific and non-specific DNA sequences.
• To compare CAP's binding preference for different DNA forms (B-DNA vs. Z-DNA).

Main Methods:

• Circular dichroism (CD) spectroscopy was employed to study CAP-DNA interactions.
• Spectroscopic titration was used to determine binding stoichiometry and affinity.
• Synthetic DNA copolymers were used to compare binding to B and Z DNA forms.

Main Results:

• CAP binding to its specific DNA sequence induced a B-DNA to "C-like" conformational change, distinct from non-specific binding.
• A 1:1 binding stoichiometry (CAP dimer to DNA) and a non-specific binding site size of 17 bp/dimer were determined.
• CAP exhibited a slight preference for binding the B-form over the Z-form of DNA.

Conclusions:

• CAP binding induces an optically detectable conformational change in DNA.
• The findings do not support CAP binding to a left-handed DNA form.
• CAP demonstrates a preference for the canonical B-DNA conformation over Z-DNA.