Conformational lability of poly(dG-m5dC):poly(dG-m5dC)

Area of Science:

• Molecular Biology
• Biophysics
• Structural Biology

Background:

• Poly(dG-m5dC):poly(dG-m5dC) is known for its conformational flexibility.
• DNA can adopt different conformations, such as the B and Z forms, depending on environmental conditions.
• Understanding these conformational changes is crucial for comprehending DNA function and regulation.

Purpose of the Study:

• To investigate the acid-mediated conformational hysteresis of poly(dG-m5dC):poly(dG-m5dC).
• To characterize the properties of the acid-induced Z conformation.
• To explore the reversibility and factors influencing DNA conformational transitions.

Main Methods:

• Acid-base titration of poly(dG-m5dC):poly(dG-m5dC) solutions.
• Thermal melting studies (UV spectrophotometry) to assess DNA stability.
• Ethidium bromide binding assays to compare B and Z forms.
• EDTA treatment to investigate the role of metal ions.

Main Results:

• An acid-mediated Z conformation was observed in low sodium concentrations, a condition typically favoring the B form.
• The acid-mediated Z conformation is thermally stable, melting directly into single strands around 100°C.
• The B form DNA exhibited biphasic melting with conversion to the Z form before denaturation.
• Ethidium binding was weaker in the acid-mediated Z form compared to the B form.
• Both acid-mediated and thermally induced Z conformations were reversed by EDTA, suggesting involvement of metal ions.

Conclusions:

• Poly(dG-m5dC):poly(dG-m5dC) displays significant conformational lability, including acid-mediated Z-form induction and hysteresis.
• The Z conformation induced by acid is highly stable and exhibits distinct binding properties.
• DNA conformational transitions are reversible and sensitive to ionic strength, pH, and trace metal ions.