DNA length tunes the fluidity of DNA-based condensates

Fernando Muzzopappa (1) , Maud Hertzog (1) , Fabian Erdel (1)

1 MCD - Unité de biologie Moléculaire, Cellulaire et du Développement

Living organisms typically store their genomic DNA in a condensed form. Mechanistically, DNA condensation can be driven by macromolecular crowding, multivalent cations, or positively charged proteins. At low DNA concentration, condensation triggers the conformational change of individual DNA molecules into a compacted state, with distinct morphologies. Above a critical DNA concentration, condensation goes along with phase separation into a DNA-dilute and a DNA-dense phase. The latter DNA-dense phase can have different material properties and has been reported to be rather liquid-like or solid-like depending on the characteristics of the DNA and the solvent composition. Here, we systematically assess the influence of DNA length on the properties of the resulting condensates. We show that short DNA molecules with sizes below 1 kb can form dynamic liquid-like assemblies when condensation is triggered by polyethylene glycol and magnesium ions, binding of linker histone H1, or nucleosome reconstitution in combination with linker histone H1. With increasing DNA length, molecules preferentially condense into less dynamic more solid-like assemblies, with phage l-DNA with 48.5 kb forming mostly solid-like assemblies under the conditions assessed here. The transition from liquid-like to solid-like condensates appears to be gradual, with DNA molecules of roughly 1-10 kb forming condensates with intermediate properties. Titration experiments with linker histone H1 suggest that the fluidity of condensates depends on the net number of attractive interactions established by each DNA molecule. We conclude that DNA molecules that are much shorter than a typical human gene are able to undergo liquid-liquid phase separation, whereas longer DNA molecules phase separate by default into rather solid-like condensates. We speculate that the local distribution of condensing factors can modulate the effective length of chromosomal domains in the cell. We anticipate that the link between DNA length and fluidity established here will improve our understanding of biomolecular condensates involving DNA. The first three terms correspond to the ''external'' free energy of mixing, reflecting the arrangement of solvent and ''whole'' DNA molecules.

Domaines: Sciences du Vivant [q-bio]

Fernando Muzzopappa, Maud Hertzog, Fabian Erdel. DNA length tunes the fluidity of DNA-based condensates. Biophysical Journal, 2021, 120, pp.1288 - 1300. ⟨10.1016/j.bpj.2021.02.027⟩. ⟨hal-03411634⟩