Towards Optical Super-Resolution Measurement of the Structure of Dense DNA Solutions

Chromatin organization has long been hypothesized to adopt a fractal globule structure, yet comprehensive experimental validation remains elusive. I will present the steps we have done towards measuring chromatin's structure factor through a combination of scanning fluorescence correlation spectroscopy (sFCS) with advanced super-resolution optics. Initially focusing on dense, non-concatenated ring polymer melts as a simplified test model, the project encountered significant technical hurdles, notably extreme photon count rates and detector afterpulsing artifacts. These challenges were successfully addressed by implementing fluorescence-lifetime correlation spectroscopy (FLCS), optimizing labeling strategies, refining buffer conditions, and developing improved sample preparation protocols. Additionally, novel calibration standards were created to precisely characterize the optical system. The resulting sFCS-gSTED setup achieved sub-diffraction resolution, clearly distinguishing structural differences between dilute and semi-dilute DNA solutions. Although definitive evidence for fractal globule organization is still pending, this work lays a robust technical foundation, opening exciting avenues for future structural investigations of bacterial nucleoids, eukaryotic chromosomes, and other densely packed DNA systems.