Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Video

Updated: Jun 19, 2026

Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis
08:09

Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis

Published on: January 7, 2017

Cation localization and movement within DNA thrombin binding aptamer in solution.

Marko Trajkovski1, Primoz Sket, Janez Plavec

  • 1Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia.

Organic & Biomolecular Chemistry
|October 30, 2009
PubMed
Summary

The thrombin binding aptamer forms a G-quadruplex structure with ammonium ions, revealing specific ion binding sites and structural details. This G-quadruplex folding is influenced by ion concentration and base pair interactions.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Characterization of the Interaction of Known G-quadruplex Ligands With a Minimal i-Motif Structure.

Chemistry (Weinheim an der Bergstrasse, Germany)·2026
Same author

Epirus-yellow (EY): A dual naked-eye colorimetric and NIR fluorimetric chemosensor for the rapid, sensitive, and selective detection of Sn<sup>2</sup>.

Food chemistry·2026
Same author

Unraveling the NMR structures of G-quadruplex-forming aptamers acting as inhibitors of High Mobility Group Box 1 (HMGB1) pathological activity.

International journal of biological macromolecules·2026
Same author

Stromatolites from Lake Ashenge, Ethiopia: Controls on Biosignature Preservation in Extreme Alkaline Environments.

Astrobiology·2026
Same author

Selective Delivery of Anticancer Natural G-Quadruplex Ligands by the AT11 Aptamer for Gastric Cancer Treatment.

Journal of medicinal chemistry·2025
Same author

Glyoxal as Single Crosslinker for Mechanically Blown, Condensed and Hydrolyzable Tannin Foams.

Polymers·2025

Area of Science:

  • Biochemistry
  • Structural Biology
  • Nucleic Acid Chemistry

Background:

  • The thrombin binding aptamer (TBA) is a 15-mer oligonucleotide known to form a stable G-quadruplex structure.
  • Cation binding is crucial for the stability and function of G-quadruplex structures.
  • Understanding ion-G-quadruplex interactions is key to aptamer-based drug design and diagnostics.

Purpose of the Study:

  • To investigate the folding topology and cation binding properties of the thrombin binding aptamer in the presence of ammonium ions.
  • To elucidate the specific binding site and affinity of ammonium ions within the G-quadruplex core.
  • To characterize the dynamics of ion exchange and the influence of structural features on ion accessibility.

Main Methods:

  • Solution-state Nuclear Magnetic Resonance (NMR) spectroscopy was employed to study the G-quadruplex structure.

More Related Videos

DNAzyme 10-23 - Based Nanomachines for Nucleic Acid Recognition
07:16

DNAzyme 10-23 - Based Nanomachines for Nucleic Acid Recognition

Published on: February 9, 2024

Aptamer-Based Target Detection Facilitated by a 3-Stage G-Quadruplex Isothermal Exponential Amplification Reaction
03:38

Aptamer-Based Target Detection Facilitated by a 3-Stage G-Quadruplex Isothermal Exponential Amplification Reaction

Published on: October 6, 2022

Related Experiment Videos

Last Updated: Jun 19, 2026

Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis
08:09

Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis

Published on: January 7, 2017

DNAzyme 10-23 - Based Nanomachines for Nucleic Acid Recognition
07:16

DNAzyme 10-23 - Based Nanomachines for Nucleic Acid Recognition

Published on: February 9, 2024

Aptamer-Based Target Detection Facilitated by a 3-Stage G-Quadruplex Isothermal Exponential Amplification Reaction
03:38

Aptamer-Based Target Detection Facilitated by a 3-Stage G-Quadruplex Isothermal Exponential Amplification Reaction

Published on: October 6, 2022

  • Isotopic labeling with (15)NH(4)(+) was used for ion localization and binding studies.
  • Titration experiments were performed to assess the effect of sodium ion concentration.

    • Main Results:

    • The thrombin binding aptamer folds into an antiparallel unimolecular G-quadruplex in the presence of (15)NH(4)(+) ions.
    • Ammonium ions bind specifically between the G-quartets with an equilibrium binding constant of 190 M(-1).
    • Structural analysis revealed a noncanonical T4-T13 base pair and out-of-plane bending of G2 and G11, influencing ion access and exchange.

    Conclusions:

    • Ammonium ions stabilize the G-quadruplex structure, although less so than potassium ions.
    • The identified binding site and structural features provide insights into the cation selectivity and dynamics of G-quadruplexes.
    • This study enhances the understanding of aptamer-cation interactions, relevant for therapeutic applications.