DNA conformation determines the size of DNA-histone H1 nanoscale clusters

Biological liquid-liquid phase separation has attracted considerable attention because of its essential biological functions. Numerous studies have been conducted to elucidate the molecular properties of host and client biomolecules in liquid condensates. However, most of the previous investigations have focused on well-grown micrometer-scale condensates, and consequently, information on small clusters with sizes smaller than the optical diffraction limit is very limited due to the lack of appropriate spectroscopic techniques. In this study, we apply two-dimensional fluorescence lifetime correlation spectroscopy and fluorescence lifetime correlation spectroscopy to elucidate the conformational properties of DNA in nanoscale DNA-histone H1 clusters. The results reveal that DNA and histone H1 form two distinct types of nanoscale clusters with different hydrodynamic radii, in which DNA adopts markedly different conformations. These findings suggest that DNA conformation plays a key role in determining the size of nanoscale clusters. Our results, therefore, provide important insights into the relationship between the growth of liquid condensates and the conformational states of host biomolecules.