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DNA Topoisomerases

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Related Experiment Video

Updated: May 10, 2026

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

Published on: April 4, 2025

DNA quadruplex folding formalism--a tutorial on quadruplex topologies.

Andreas Ioannis Karsisiotis¹, Christopher O'Kane, Mateus Webba da Silva

¹School of Pharmacy & Pharmaceutical Sciences, Biomedical Sciences Research Institute, University of Ulster, Cromore Road, BT52 1SA, Coleraine, UK.

Methods (San Diego, Calif.)

|June 25, 2013

Summary

This study introduces a new formalism for understanding DNA quadruplex folding based on glycosidic bond angles. This method simplifies complex structures, aiding in the prediction of various quadruplex topologies.

Keywords:

Formalism Glycosidic bond angle NMR structure Quadruplex Quadruplex structure Tetrad

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Area of Science:

Structural biology
Biochemistry
Bioinformatics

Background:

DNA quadruplexes exhibit diverse topologies influenced by their surrounding environment.
Understanding these structures is crucial for various biological processes and therapeutic applications.

Purpose of the Study:

To develop a novel formalism for describing DNA quadruplex folding.
To establish a method for predicting quadruplex topologies based on structural features.
To provide a tutorial for applying this formalism to both unimolecular and multimolecular quadruplexes.

Main Methods:

Developing a formalism based on the glycosidic bond angle, relating base to sugar.
Reducing quadruplex stem description to two finite states of glycosidic bond angle ranges.
Analyzing the interdependency of loop types and groove widths within quadruplex stems.

Main Results:

The formalism allows for the description of relationships between loop types and groove widths.
Successfully predicted certain unimolecular quadruplex topologies.
Demonstrated general utility for understanding multimolecular folds and quadruplexes with more than three loops.

Conclusions:

The developed formalism provides a simplified yet comprehensive approach to understanding DNA quadruplex structures.
This method enhances the ability to predict and analyze complex quadruplex folding patterns.
The formalism is applicable to a wide range of quadruplex architectures, facilitating further research.