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Atomic Force Microscopy

Atomic Force Microscopy

Atomic force microscopy (AFM) is a type of scanning probe microscopy that can analyze topographic details of various specimens like ceramics, glass, polymers, and biological samples. AFM offers over 1000 times more resolution than the optical imaging system. Images generated from AFM are three-dimensional surface profiles, offering an advantage over the flat, two-dimensional images from other imaging techniques.
The AFM Probe
The probe is regarded as the heart of any AFM setup and comprises the...

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Updated: Jun 20, 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

Direct visualization of G-quadruplexes in DNA using atomic force microscopy.

Kelly J Neaves¹, Julian L Huppert, Robert M Henderson

¹Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK.

Nucleic Acids Research

|August 22, 2009

Summary

This summary is machine-generated.

G-rich DNA forms G-quadruplex structures during transcription, impacting DNA processes. Atomic force microscopy visualized these structures and their regulatory role in preventing further transcription.

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Area of Science:

Molecular Biology
Biophysics
Genetics

Background:

G-quadruplexes in G-rich DNA regions are implicated in transcription and replication.
The mechanism of G-quadruplex formation with a complementary strand is not well understood.

Purpose of the Study:

To investigate G-quadruplex formation in RNA/DNA hybrid structures during transcription.
To elucidate the structural consequences and regulatory role of G-quadruplexes in a specific DNA sequence.

Main Methods:

Atomic Force Microscopy (AFM) was used to image DNA structures.
In vitro transcription of a plasmid containing the murine immunoglobulin Sgamma3 switch region was performed.
RNase H treatment and varying cation concentrations (K+, Na+, Li+) were employed to analyze structural stability.

Main Results:

Stable RNA/DNA hybrid loops containing G-quadruplexes were visualized using AFM.
G-quadruplex formation in the non-RNA portion was consistent with computational predictions.
Hybrid formation and G-quadruplexes inhibited further transcription, suggesting a regulatory function.
The presence of loops, blobs, or spurs was cation-dependent, correlating with G-quadruplex stability.

Conclusions:

AFM directly observed structural changes associated with G-quadruplex formation in RNA/DNA hybrids.
G-quadruplex formation acts as a transcriptional roadblock, indicating a regulatory role in gene expression.
Cation choice significantly influences G-quadruplex stability and formation during transcription.