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Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...

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Elongated thrombin binding aptamer: a G-quadruplex cation-sensitive conformational switch.

Aurore De Rache1, Iva Kejnovská, Michaela Vorlíčková

  • 1Université Libre de Bruxelles, Faculté des Sciences, Service de Chimie Analytique et Chimie des Interfaces, CP 255, Boulevard du Triomphe 2, 1050 Bruxelles, Belgium.

Chemistry (Weinheim an Der Bergstrasse, Germany)
|February 25, 2012
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Summary
This summary is machine-generated.

Elongating thrombin binding aptamers (TBA) changes their structure and stability. This ion-sensitive switch behavior, influenced by cations and redox markers, offers new possibilities for biosensor development.

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Area of Science:

  • Biotechnology
  • Molecular Biology
  • Biosensor Technology

Background:

  • Aptamer-based biosensors are crucial for high-performance protein detection.
  • Thrombin binding aptamer (TBA) is a G-quadruplex DNA sequence often modified for enhanced analytical performance.
  • Investigating structural modifications of TBA is key to optimizing biosensor applications.

Purpose of the Study:

  • To investigate the impact of 5'-end elongation on the structure and stability of thrombin binding aptamers (TBA).
  • To explore the potential of cation-induced structural changes in TBA for ion-sensitive biosensing applications.
  • To demonstrate the cation-dependent conformational switching behavior of elongated TBA sequences.

Main Methods:

  • Circular dichroism (CD) spectroscopy to analyze DNA folding and conformation.
  • UV spectroscopy melting curves to evaluate the stability of different aptamer structures.
  • Thermal difference spectra to confirm the G-quadruplex character of folded aptamers.

Main Results:

  • TBA consistently forms an antiparallel G-quadruplex with various cations.
  • Elongated aptamers exhibit cation-dependent structural polymorphism, adopting parallel or antiparallel conformations.
  • A specific redox marker, [Ru(NH(3))(6)](3+), induces a parallel conformation at low concentrations, reversible by K+ ions.

Conclusions:

  • 5'-end elongation of TBA introduces cation-dependent structural plasticity.
  • This ion-sensitive switch behavior in elongated TBAs is demonstrated and has potential for electrochemical biosensing.
  • The findings open new avenues for developing responsive devices and advanced biosensor platforms.