Studying Nucleoid-Associated Protein-DNA Interactions Using Polymer Microgels as Synthetic Mimics

Area of Science:

• Biochemistry
• Molecular Biology
• Biophysics

Background:

• Bacterial cell division is regulated by protein-DNA interactions.
• The nucleoid-associated protein SlmA negatively regulates division ring stability in Escherichia coli.
• Mimicking the dense DNA environment of the bacterial nucleoid is crucial for studying these interactions.

Purpose of the Study:

• To utilize microfluidically fabricated polymer microgels as a platform for analyzing protein-DNA interactions.
• To investigate the influence of charge and permeability on protein binding and diffusion within a simulated bacterial nucleoid.
• To explore the role of SlmA in bacterial cell division regulation using engineered microgels.

Main Methods:

• Fabrication of polymer microgels using microfluidics with polyethylene glycol and hyaluronic acid.
• Functionalization of microgels with short DNA binding sequences (SBS) for SlmA interaction.
• Analysis of SlmA protein binding specificity and accumulation on microgels under varying buffer conditions.
• Assessment of microgel permeability and its effect on protein diffusion.

Main Results:

• SlmA specifically bound to SBS-functionalized microgels, preferentially accumulating at the surface.
• Microgel charge did not significantly impact SlmA binding.
• Hyaluronic acid microgels demonstrated higher permeability, facilitating enhanced SlmA diffusion.
• Buffer composition allowed control over SlmA binding specificity.

Conclusions:

• Microfluidic microgels serve as effective platforms for reconstituting bacterial nucleoid environments.
• Hyaluronic acid-based microgels are suitable for mimicking bacterial nucleoids due to their permeability.
• This approach facilitates the bottom-up study of essential cellular processes in controlled environments.