Pyrene as a sensitive probe for DNA conformational changes due to protonation

Area of Science:

• Molecular Spectroscopy
• Biophysical Chemistry
• DNA Structure

Background:

• Planar molecules like pyrene can exhibit optical activity when interacting with chiral environments.
• The interaction between small molecules and DNA is crucial for understanding DNA structure and function.
• Circular Dichroism (CD) spectroscopy is a powerful tool for probing molecular interactions and conformational changes.

Purpose of the Study:

• To investigate the influence of pH on the binding of pyrene to duplex DNA.
• To characterize the conformational changes in DNA induced by protonation.
• To determine the sequence specificity of pyrene binding to DNA at different pH values.

Main Methods:

• Circular Dichroism (CD) spectroscopy was used to monitor the optical activity of pyrene upon binding to DNA.
• pH titrations were performed to study the cooperative nature of the observed spectral changes.
• Differential Scanning Calorimetry (DSC) or melting temperature analysis was employed to assess DNA stability.
• Studies with synthetic polynucleotides were conducted to evaluate sequence specificity.

Main Results:

• Pyrene binding to DNA induced positive Cotton effects in neutral/basic solutions, which reversed to negative CD bands in acidic solutions.
• The pH-induced CD sign reversal was a cooperative process, indicating a significant conformational change in the DNA duplex.
• Protonation of DNA led to a stable duplex state with a 40°C decrease in melting temperature compared to the neutral state.
• Pyrene exhibited distinct sequence preferences: binding to dA-dT sequences in neutral DNA and dG-dC sequences in protonated DNA.

Conclusions:

• The observed sign reversal of induced Cotton effects for pyrene is a direct consequence of DNA protonation and associated conformational alterations.
• DNA protonation induces a significant structural transition, favoring binding to guanine-rich sequences.
• These findings highlight the sensitivity of DNA structure to pH and its impact on small molecule interactions and sequence recognition.