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Atomic Force Microscopy

Atomic Force Microscopy

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Updated: Jul 18, 2026

Force Spectroscopy of Single Protein Molecules Using an Atomic Force Microscope

Force Spectroscopy of Single Protein Molecules Using an Atomic Force Microscope

Published on: February 28, 2019

Probing Interactions within the synaptic DNA-SfiI complex by AFM force spectroscopy.

Alexey V Krasnoslobodtsev¹, Luda S Shlyakhtenko, Yuri L Lyubchenko

¹Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA.

Journal of Molecular Biology

|November 28, 2006

Summary

Single-molecule force spectroscopy reveals the stability of the SfiI-DNA complex before cleavage. Dynamic force spectroscopy elucidated the role of the DNA spacer region in SfiI-DNA complex stability and dissociation kinetics.

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Area of Science:

Biochemistry
Molecular Biology
Biophysics

Background:

SfiI restriction enzyme functions as a tetramer, binding two DNA recognition sites.
The SfiI-DNA complex is a model for studying protein-DNA interactions.
Properties of the SfiI-DNA complex before DNA cleavage remain unclear.

Purpose of the Study:

To analyze the strength and stability of the SfiI-DNA complex using single-molecule force spectroscopy.
To investigate the dissociation mechanism and energy landscape of the SfiI-DNA complex.
To determine the role of the DNA spacer region in complex stability.

Main Methods:

Single-molecule force spectroscopy (SMFS) was employed to probe SfiI-DNA interactions.
Approach-retraction cycles were used to measure rupture forces of the synaptic complex.
Dynamic force spectroscopy (DFS) analyzed the force loading rate dependence of dissociation.

Main Results:

The SfiI-DNA complex exhibits similar rupture forces in different experimental setups.
Dissociation of the SfiI-DNA complex is characterized by a single energy barrier.
The 5 bp spacer region in the DNA recognition site influences SfiI-DNA complex stability and off-rates.

Conclusions:

SMFS provides insights into the pre-cleavage stability of the SfiI-DNA complex.
DFS reveals a single energy barrier for SfiI-DNA complex dissociation.
The DNA spacer sequence significantly impacts SfiI-DNA complex stability and dissociation kinetics.