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Atomic Force Microscopy

Atomic Force Microscopy (AFM) is a class of Scanning Probe Force Microscopy (SPM). AFM probes force interactions between a probe (AFM tip) and the sample, and return topographic images that reflects the change of those interactions.

Pictured - SEM image of an AFM probe

Atomic Force Microscopy

AFM basics

Atomic Force Microscopy (AFM) probes force interactions between a probe (AFM tip) and the sample, includes but not limited to, Van der Waals interactions, electrostatic interactions, capillary forces, other types of long and short range adhesive and repulsive forces (it should be noted that these interactions are not mutually exclusive). It detects the change of interactions by monitoring the deflection of laser focused on the cantilever (part of AFM probe), which then are used to map the surface topography through its feedback system that maintains those interactions constant.

Mechanistic diagram of how AFM works

 

AFM images are intensity images. The Z values are intensity information such as height, amplitude, phase, etc. The following image is an example AFM height image that we obtained from experiments showing DNA-MutSβ interactions.

 

 

Due to the complexity of AFM techniques and sample constructs, AFM can be done with a substantial degree of flexibility and be used to probe different kinds of interactions. In addition to conventional AFM imaging on dried sample, our lab has also worked on imaging in fluid, electrostatic force microscopy (EFM) imaging, combined AFM-fluorescence imaging. Our lab and campus resources also enable us to pioneer cutting edge frontier of latest AFM researches such as fast imaging in biological native fluid environment.

 

DNA imaged in fluid using Cypher AFM. You can see distortions on part of the DNA during the video.

 

What can we learn from AFM?

  • Protein-DNA Interactions: 

    • Binding affinities
    • Binding specificities
    • Stoichiometry
    • Structural Features
      • Protein-induced DNA bending and looping

  • Protein-Protein Interactions:

    • Binding affinities
    • Stoichiometry
    • Structural features of complexes

  • DNA Conformations:

    • Bending
    • Supercoiling
    • Looping

  • Dual Resonance Frequency Enhanced Electrostatic Microscopy (DREEM):

    • Protein and DNA electrostatic properties
    • Visualize DNA path inside proteins

Our current and past studies using AFM can be found below, or navigated through the ‘Atomic Force Microscopy’ category on the left sidebar.

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