Probing DNA structure with optical super-resolution: from plasmids to bacterial chromosome

Bacterial DNA is about 1.6 mm long yet packed inside a micron size cell. Despite tight packing, the nucleoid manages to guide the major physiological processes in the cell such as gene expression, DNA replication and cell division. How the nucleoid is organized in a structure that is both dense and yet accessible to cell machinery is still unclear. A polymer physics theory suggests a possible solution: a fractal globule structure that keeps DNA unknotted and allows for an easy release of DNA loops.

We probe the E. Coli nucleoid structure using a scanning Fluorescence Correlation spectroscopy (sFCS) approach we developed earlier to study DNA in solutions. We have upgraded sFCS with optical super-resolution, tested the technique measuring the structure of relaxed and superhelical plasmids, and moved on then to measure the whole nucleoids gently released from bacteria.

Our preliminary data support the fractal globule organization of the bacterial nucleoid.