Role of divalent cations on DNA polymorphism under low ionic strength conditions

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• The conformational flexibility of DNA is crucial for various biological processes.
• Poly(dG-m5dC) can adopt different helical structures, including left-handed and right-handed forms.
• Environmental factors, such as ion concentration, significantly influence DNA conformation.

Purpose of the Study:

• To investigate the conformational properties of poly(dG-m5dC) under varying low salt conditions.
• To determine the role of divalent cations, specifically magnesium (Mg+2), in stabilizing DNA conformations.
• To elucidate the transition mechanisms between left-handed and right-handed forms of poly(dG-m5dC).

Main Methods:

• Circular dichroism spectroscopy to determine polynucleotide conformation.
• Atomic absorption spectroscopy to quantify cation concentrations.
• Ion exchange chromatography and extensive dialysis for sample preparation and ion manipulation.

Main Results:

• Extensive dialysis against low salt buffers (Na-cacodylate, Tris-EGTA) induced a left-handed poly(dG-m5dC) conformation.
• Dilution or stringent purification led to a transition to the right-handed conformation.
• Left-handed forms correlated with high Mg+2 levels (≥190/1000 nucleotides), while right-handed forms had low Mg+2 levels (≤45/1000 nucleotides).
• Re-addition of MgCl2 restored the left-handed conformation.

Conclusions:

• The left-handed conformation of poly(dG-m5dC) under specific low salt conditions is primarily mediated by bound Mg+2 ions.
• Even chelating agents like EDTA may not fully remove tightly bound Mg+2, preserving the left-handed structure.
• Divalent cation concentration is a critical determinant of poly(dG-m5dC) helical structure.