HIV-integrase aptamer folds into a parallel quadruplex: a thermodynamic study

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• Guanine-rich sequences form G-quadruplex structures crucial for telomeres and gene regulation.
• Quadruplex oligonucleotides hold therapeutic and biotechnological potential.
• The HIV-integrase aptamer d(GGGT)(4) exhibits favorable thermodynamics, with prior NMR suggesting an antiparallel fold.

Purpose of the Study:

• To investigate the structural discrepancy between NMR and CD data for the d(GGGT)(4) aptamer.
• To determine the correct quadruplex topology of the d(GGGT)(4) aptamer using thermodynamic and optical methods.

Main Methods:

• Systematic thermodynamic analyses of d(GGGT)(4) and its sequence variants.
• Circular dichroism (CD) spectroscopy across a range of strand concentrations.
• Comparison of experimental data with proposed quadruplex folding models.

Main Results:

• Thermodynamic analyses consistently supported a parallel quadruplex fold for d(GGGT)(4) and its variants.
• CD studies did not indicate a structural transition with increasing strand concentration.
• The combined data strongly favor a parallel fold over an antiparallel one.

Conclusions:

• The d(GGGT)(4) aptamer adopts a parallel quadruplex structure.
• This finding reconciles conflicting structural data from NMR and CD.
• The study clarifies the structure of a therapeutically relevant G-quadruplex aptamer.