Atomic force microscopy of DNA in aqueous solutions

Area of Science:

• Biophysics
• Materials Science
• Nanotechnology

Background:

• Atomic force microscopy (AFM) is a powerful tool for imaging biological molecules.
• Imaging DNA in aqueous solutions presents challenges due to substrate adhesion and tip-sample interactions.
• Previous methods required extensive sample preparation, limiting real-time observation.

Purpose of the Study:

• To develop and validate a method for imaging DNA on mica in aqueous solutions using AFM.
• To investigate the structural integrity and conformational changes of DNA under different imaging conditions.
• To explore potential applications of AFM for studying DNA-related processes in hydrated environments.

Main Methods:

• Thorough dehydration of DNA on mica using propanol or vacuum baking.
• Utilizing scanning electron microscope (SEM)-deposited tips for AFM imaging.
• Imaging DNA in both propanol and aqueous buffer solutions.
• Comparative analysis of DNA dimensions (height, width, length) under varying conditions.

Main Results:

• Successful imaging of DNA in aqueous solutions was achieved with proper dehydration and SEM tips.
• DNA dimensions (height, width) were larger in aqueous solutions compared to propanol.
• DNA length remained consistent with B-DNA in aqueous solutions but shortened to A-DNA upon re-imaging in propanol.
• Observed imaging of RNA polymerase bound to DNA and effective disaggregation of salt-DNA complexes.

Conclusions:

• AFM can effectively image DNA in aqueous solutions with appropriate sample preparation and tip modification.
• The method allows for the observation of DNA structural dynamics and interactions in hydrated states.
• This technique holds promise for studying DNA processes in real-time within aqueous environments.