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Related Experiment Video

Updated: Jun 19, 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

Molecular models for intrastrand DNA G-quadruplexes.

Federico Fogolari¹, Haritha Haridas, Alessandra Corazza

¹Dipartimento di Scienze e Tecnologie Biomediche, Università di Udine, Piazzale Kolbe 4 - 33100 Udine, Italy. federico.fogolari@uniud.it

BMC Structural Biology

|October 9, 2009

Summary

Researchers modeled G-quadruplex DNA structures, which are important for gene regulation. These novel molecular models, based on existing structures, can aid in interpreting experimental data for G-quadruplex sequences.

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Single-molecule Manipulation of G-quadruplexes by Magnetic Tweezers

Single-molecule Manipulation of G-quadruplexes by Magnetic Tweezers

Published on: September 19, 2017

Area of Science:

Biochemistry
Structural Biology
Bioinformatics

Background:

G-quadruplex (G4) motifs, characterized by G(3)X(n1)G(3)X(n2)G(3)X(n3)G(3) sequences, are overrepresented in human gene promoter regions.
These G4 structures play a crucial role in gene regulation, yet few are structurally characterized in databases.
There is a growing interest in understanding these unusual DNA structures.

Purpose of the Study:

To generate feasible G-quadruplex structures using molecular modeling.
To provide reliable models for interpreting experimental data related to G-quadruplex DNA.

Main Methods:

Utilized existing G-quadruplex DNA structures from the Nucleic Acid Database.
Selected and clustered fragments with specific G-rich motifs (three adjacent Gs separated by loops).
Assembled G-quadruplex structures based on fragment superimposability and steric compatibility.

Main Results:

Generated molecular models for numerous G(3)X(n1)G(3)X(n2)G(3)X(n3)G(3) sequences.
Identified that not all topologies are achievable for every sequence due to steric hindrance and fragment superimposability.
Developed a method for constructing G-quadruplex models from experimentally observed fragments.

Conclusions:

The generated molecular models are reliable as they are derived from existing quadruplex structures.
These models can assist in the interpretation of experimental findings concerning G-quadruplex DNA.
The study provides a valuable resource for researchers investigating G-quadruplex structures and their functions.