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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Biotechnology

Background:

  • DNA aptamers form secondary structures for small-molecule ligand binding.
  • These structures are stable and useful for developing molecular tools in diagnostics and monitoring.
  • Adenosine triphosphate (ATP) aptamers are explored for their binding capabilities.

Purpose of the Study:

  • To investigate adenosine triphosphate (ATP)-binding aptamers for simultaneous detection of ATP and thioflavin T (ThT).
  • To explore the role of the G-quadruplex (G4) motif in modulating aptamer ligand binding properties.
  • To engineer aptamer variants with enhanced binding affinity and dual-ligand recognition.

Main Methods:

  • Utilized fluorescently labeled and label-free detection methods.
  • Constructed extended aptamer variants with increased G-quadruplex units (three or four G-quartets).
  • Performed equilibrium binding assays and electrospray ionization mass spectrometry (ESI-MS) analysis.

Main Results:

  • The native aptamer forms a G-quadruplex (G4) structure with two G-quartets, both involved in binding.
  • Extended G4 aptamer variants exhibited significantly stronger affinity for ATP (Kd range 0.040-0.042 μM) compared to the native aptamer (0.15 μM).
  • Label-free and ESI-MS analyses confirmed dual binding of both ThT and ATP to the engineered G4 constructs.

Conclusions:

  • The G-quadruplex (G4) motif is crucial for optimal ATP binding in these aptamers.
  • Modulating the G4 structure enhances ATP binding affinity and enables simultaneous binding of multiple ligands.
  • These findings facilitate the design of advanced molecular tools for biomarker monitoring and ligand binding studies.