Visualization of DNA and protein-DNA complexes with atomic force microscopy

Area of Science:

• Biophysics
• Materials Science
• Biochemistry

Background:

• Atomic Force Microscopy (AFM) is a powerful tool for visualizing biological molecules at the nanoscale.
• Traditional AFM sample preparation for DNA and protein-DNA complexes can be limited by ionic strength, pH, and the need for divalent cations.
• Developing robust and versatile surface chemistries is crucial for advancing high-resolution molecular imaging.

Purpose of the Study:

• To describe a novel sample preparation technique for AFM imaging of DNA and protein-DNA complexes.
• To introduce the aminopropyl silatrane (APS)-mica surface as a versatile substrate for biomolecular imaging.
• To provide detailed protocols for surface functionalization and sample preparation.

Main Methods:

• Chemical functionalization of mica surfaces with aminopropyl silatrane (APS) to create an APS-mica surface.
• Characterization of the APS-mica surface's binding properties for nucleic acids and nucleoprotein complexes.
• Detailed description of sample preparation methodologies for AFM imaging.
• Inclusion of protocols for APS synthesis and purification.

Main Results:

• The APS-mica surface effectively binds DNA and protein-DNA complexes.
• Stable imaging is achieved over a wide range of ionic strengths and pH values.
• The method functions effectively in the absence of divalent cations.
• Demonstration of AFM imaging capabilities with representative images of DNA and protein-DNA complexes.

Conclusions:

• The APS-mica surface offers a robust and adaptable platform for AFM imaging of DNA and protein-DNA complexes.
• This preparation technique overcomes limitations of previous methods, enabling imaging under diverse experimental conditions.
• The provided protocols facilitate the application of this advanced AFM sample preparation method in various research settings.