Ammonium ion at low concentration stabilizes the G-quadruplex formation by telomeric sequence

Area of Science:

• Biochemistry and Molecular Biology
• Structural DNA Research
• Chemical Biology

Background:

• Telomeric DNA sequences can form G-quadruplex structures, which are non-canonical DNA secondary structures.
• G-quadruplex stability is influenced by various counterions, with potassium (K+) and strontium (Sr2+) typically requiring higher concentrations for stabilization.
• Understanding the role of different ions in G-quadruplex formation is crucial for exploring their biological functions and therapeutic potential.

Purpose of the Study:

• To investigate the ability of ammonium ions (NH4+) to induce and stabilize G-quadruplex structures in a synthetic telomeric DNA analog.
• To compare the stabilizing effect of NH4+ with other known G-quadruplex stabilizing ions like K+ and Sr2+.
• To explore the conformational dynamics and stability of NH4+-bound G-quadruplexes under varying conditions.

Main Methods:

• Synthesis of a telomeric DNA analog, d(G4T2G4T2G4T2G4).
• Spectroscopic analysis, including circular dichroism (CD) spectroscopy, to study G-quadruplex formation and conformation.
• Thermal denaturation studies to assess the stability of the G-quadruplex structure in the presence of NH4+ and other ions.

Main Results:

• The synthetic telomeric DNA analog formed a G-quadruplex structure in the presence of NH4+ at concentrations as low as 1 mM.
• NH4+ demonstrated a stabilizing effect on the G-quadruplex, requiring lower concentrations compared to K+ or Sr2+.
• Circular dichroism studies indicated that NH4+ promotes intramolecular G-quadruplex formation over intermolecular associations, even at high temperatures (up to 100°C).

Conclusions:

• Ammonium ions are effective in stabilizing G-quadruplex structures at very low concentrations, suggesting a unique interaction mechanism possibly related to their ionic radius.
• The G-quadruplex formed in NH4+ environments exhibits distinct conformational properties and stability, being sensitive to intercalators like Actinomycin D and ions like Tb3+.
• The findings suggest potential future applications for NH4+-stabilized G-quadruplexes in areas requiring precise structural control at low ion concentrations.