# A microfluidic platform for extraction and analysis of bacterial genomic DNA

## TL;DR

A new microfluidic platform enables the extraction and analysis of bacterial genomic DNA without damaging it.

## Contribution

The platform allows for the first time sequential extraction and analysis of bacterial nucleoids without fragmentation.

## Key findings

- The microfluidic system successfully extracts and analyzes single chromosomes from B. subtilis cells.
- On-chip lysis allows genome expansion and removal of DNA-binding proteins.
- The platform enables controlled addition of exogeneous proteins to trapped DNA.

## Abstract

Bacterial cells organize their genomes into a compact hierarchical structure called the nucleoid. Studying the nucleoid in cells faces challenges because of the cellular complexity while in vitro assays have difficulty in handling the fragile megabase-scale DNA biopolymers that make up bacterial genomes. Here, we introduce a method that overcomes these limitations as we develop and use a microfluidic device for the sequential extraction, purification, and analysis of bacterial nucleoids in individual microchambers. Our approach avoids any transfer or pipetting of the fragile megabase-size genomes and thereby prevents their fragmentation. We show how the microfluidic system can be used to extract and analyze single chromosomes from B. subtilis cells. Upon on-chip lysis, the bacterial genome expands in size and DNA-binding proteins are flushed away. Subsequently, exogeneous proteins can be added to the trapped DNA via diffusion. We envision that integrated microfluidic platforms will become an essential tool for the bottom-up assembly of complex biomolecular systems such as artificial chromosomes.

We introduce a microfluidic platform for isolating and analyzing bacterial nucleoids, which allows for the sequential extraction, purification, and investigation of fragile bacterial chromosomes in a controlled environment.