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Related Experiment Video

Updated: Feb 7, 2026

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

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Published on: January 7, 2017

Charge-dipole interactions in G-quadruplex thrombin-binding aptamer.

Hyun Woo Kim¹, Young Min Rhee, Seung Koo Shin

¹Center for Molecular Modeling and Simulation, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea.

Physical Chemistry Chemical Physics : PCCP

|August 4, 2018

Summary

Metal ions compete with DNA

Area of Science:

Biochemistry
Molecular Biology
Computational Chemistry

Background:

DNA forms complex structures via noncovalent interactions like hydrogen-bonding and base-stacking.
These interactions are crucial for stabilizing DNA structures such as G-quadruplexes (G4).

Purpose of the Study:

To investigate the role of electrostatic charge-dipole interactions in DNA G-quadruplex stability.
To examine how intercalating metal ions with varying charges and radii affect G4 structure and noncovalent interactions.

Main Methods:

All-atom molecular dynamics simulations were employed.
The thrombin-binding aptamer (TBA) G4 structure was studied with different metal ions (K+, Sr2+, Mn+).

Main Results:

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Electrostatic charge-dipole interactions were found to be competitive, not cooperative, with hydrogen-bonding and base-stacking.

Increasing metal ion charge enhanced charge-dipole interactions but weakened hydrogen-bonding and base-stacking.

Metal ion charge and ionic radius significantly influence G4 geometry and stability.

Conclusions:

The stability of the antiparallel G4 structure of TBA is sensitive to the balance of competing noncovalent interactions.
Electrostatic charge-dipole interactions play a critical, competitive role alongside hydrogen-bonding and base-stacking.
Metal ion properties, specifically charge and radius, are key determinants for G4 formation and stability.