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Related Experiment Video

Updated: May 15, 2026

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

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

Published on: May 12, 2023

Guanine base stacking in G-quadruplex nucleic acids.

Christopher Jacques Lech¹, Brahim Heddi, Anh Tuân Phan

¹Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.

Nucleic Acids Research

|December 27, 2012

Summary

This summary is machine-generated.

Guanine base stacking significantly impacts G-quadruplex stability and higher-order structures. Computational analysis reveals distinct energy landscapes for stacked G-tetrads, explaining structural preferences in parallel G-quadruplexes.

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Published on: September 19, 2017

Area of Science:

Structural biology
Biophysics
Computational chemistry

Background:

G-quadruplexes are nucleic acid structures formed by stacked guanine tetrads.
These structures can stack to form higher-order assemblies, notably in telomeric DNA and RNA.
Understanding guanine base stacking is crucial for G-quadruplex stability and function.

Purpose of the Study:

To investigate the influence of guanine base stacking on G-quadruplex stability.
To characterize stacking geometries in G-quadruplex cores and interfaces.
To computationally examine the energy landscapes of stacked G-tetrads.

Main Methods:

Structural survey of the Protein Data Bank for G-quadruplex stacking geometries.
Quantum mechanical computations to determine stacked G-tetrad energy landscapes.
Molecular dynamics simulations to explain observed structural preferences.

Main Results:

Experimentally observed G-tetrad stacking geometries at stacked G-quadruplex interfaces exhibit significant energy differences (up to 12 kcal/mol).
AMBER molecular mechanics calculations of stacking energy align well with quantum mechanical results.
Molecular dynamics simulations explain the preference for 5'-5' stacking in parallel G-quadruplexes due to accessible tetrad stacking modes.

Conclusions:

Guanine base stacking is a critical determinant of G-quadruplex stability and higher-order structure formation.
Computational methods accurately model the energy landscapes governing G-quadruplex stacking.
The study provides structural insights into the preferred stacking orientations of parallel G-quadruplexes.