High-quality mapping of DNA-protein complexes by dynamic scanning force microscopy

Area of Science:

• Biophysics
• Materials Science
• Nanotechnology

Background:

• Studying the structure of biomolecular complexes like DNA and streptavidin (STV) is crucial for understanding biological processes.
• Previous studies using scanning force microscopy (SFM) have limitations in resolving fine structural details, especially for soft samples.
• Existing models often attribute enlarged lateral sizes to tip geometry, which may not fully account for tip-sample interactions with soft matter.

Purpose of the Study:

• To investigate the structural characteristics of DNA and streptavidin (STV) biomolecular complexes, nanocircles, and aggregates.
• To enhance the resolution and detail obtained from dynamic scanning force microscopy (SFM) for soft biological samples.
• To assess the validity of current SFM models concerning tip-sample interactions for soft materials.

Main Methods:

• Utilized dynamic scanning force microscopy (SFM) to image biomolecular complexes.
• Employed an improved dynamic mode incorporating a specialized feedback circuit, termed Q-control.
• Compared imaging results under identical conditions with and without the Q-control enhancement.

Main Results:

• The Q-control enhanced dynamic SFM mode significantly improved the observation of structural details in DNA and STV complexes.
• Finer structural features were discernible compared to standard SFM techniques under similar conditions.
• The improved imaging suggests that the influence of tip geometry on lateral size measurements needs re-evaluation for soft samples.

Conclusions:

• The Q-control technique offers superior resolution for imaging soft biomolecular assemblies.
• Established models correlating enlarged lateral size with SFM tip geometry require modification when applied to soft, deformable samples.
• This study highlights the importance of advanced AFM modes for accurate characterization of soft matter at the nanoscale.