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Related Experiment Video

Updated: May 29, 2026

In Vitro Chemical Mapping of G-Quadruplex DNA Structures by Bis-3-Chloropiperidines
05:32

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Published on: May 12, 2023

Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process.

Roman V Reshetnikov1, Jiri Sponer, Olga I Rassokhina

  • 1Department of Boiengineering and Bioinformatics, Lomonosov Moscow State University, GSP-1, Leninskie Gory, Moscow, 119991, Russian Federation.

Nucleic Acids Research
|September 7, 2011
PubMed
Summary
This summary is machine-generated.

This study reveals how ions bind to DNA quadruplexes. It shows ions are exchanged within the DNA structure, a process crucial for aptamer stability and function.

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Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis
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Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis
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Published on: January 7, 2017

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Computational Chemistry

Background:

  • Thrombin-binding aptamers (G-DNA) are crucial in diagnostics and therapeutics.
  • Understanding ion binding is key to aptamer stability and function.

Purpose of the Study:

  • To elucidate the atomistic mechanisms of ion binding to a 15-mer G-DNA aptamer.
  • To investigate the role of aptamer loops in ion binding dynamics.

Main Methods:

  • Explicit solvent molecular dynamics simulations (4 µs total).
  • Hybrid quantum mechanics/molecular mechanics (QM/MM) approach.
  • Isothermal titration calorimetry (ITC).

Main Results:

  • Ion binding to G-DNA is a complex, multi-pathway process influenced by cation type.
  • Aptamer loops modulate ion entry routes and stabilize the structure.
  • Observed the first atomistic-resolution, spontaneous exchange of internal cations within the G-DNA aptamer.

Conclusions:

  • Ion exchange is facilitated by the simultaneous binding of incoming and expulsion of internal ions.
  • This exchange mechanism minimizes structural destabilization of the aptamer.
  • Provides critical insights into aptamer-ion interactions for rational design.