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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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Related Experiment Video

Updated: Sep 17, 2025

High-Speed Atomic Force Microscopy Imaging of DNA Three-Point-Star Motif Self Assembly Using Photothermal Off-Resonance Tapping

High-Speed Atomic Force Microscopy Imaging of DNA Three-Point-Star Motif Self Assembly Using Photothermal Off-Resonance Tapping

Published on: March 22, 2024

Quantifying complexity in DNA structures with high resolution Atomic Force Microscopy.

Elizabeth P Holmes¹, Max C Gamill¹, James I Provan^2,3

¹School of Chemical, Materials and Biological Engineering, University of Sheffield, Sheffield, UK.

Nature Communications

|July 2, 2025

Summary

This summary is machine-generated.

This study introduces a new automated pipeline combining Atomic Force Microscopy (AFM) and deep learning to analyze DNA topology. This method quantifies DNA length, conformation, and complex topological structures with high resolution.

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Last Updated: Sep 17, 2025

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Published on: March 22, 2024

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Atomic Force Microscopy Investigations of DNA Lesion Recognition in Nucleotide Excision Repair

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Area of Science:

Molecular Biology
Biophysics
Genomics

Background:

DNA topology is crucial for cellular functions and genome stability.
Quantifying DNA topology in complex molecules is technically challenging.
Existing methods lack the throughput and resolution for detailed analysis.

Purpose of the Study:

To develop a high-throughput, high-resolution method for quantifying DNA topology.
To analyze the structure and topology of complex DNA molecules, including replication intermediates and recombination products.
To investigate the impact of surface immobilization on DNA topology.

Main Methods:

High-resolution Atomic Force Microscopy (AFM) combined with a novel automated deep-learning pipeline.
Deep learning for DNA backbone tracing and identification of crossing points.
Coarse-grained simulations to model surface immobilization effects.

Main Results:

The pipeline accurately quantifies length, conformation, and topology of individual DNA molecules.
Analysis of stalled replication intermediates (theta structures, late products) and E. coli Xer recombination products (plasmids, knots, catenanes).
Quantification of surface immobilization effects on twist-writhe partitioning.

Conclusions:

The developed pipeline offers unprecedented resolution and throughput for DNA topology analysis.
This method enables detailed structural and topological studies of biologically relevant DNA molecules.
The findings provide insights into how DNA topology regulates fundamental biological processes.