Deciphering the molecular mechanism of DNA-protein interactive co-condensates

Double-stranded DNA (dsDNA)-protein co-condensates (DPCs) play a crucial role in various fundamental cellular processes. Despite their significance, the molecular mechanisms governing DPCs remain elusive. To address this gap, we employed dsDNA and the transcription factor (TF) p53 as a model system to investigate a special case— dsDNA-protein interactive co-condensates (DPICs), where neither dsDNA nor the protein demonstrates phase-separation capacity. Through a combination of diverse experimental assays and theoretical methodologies, our investigation reveals that p53 acts as a bridge between different DNA duplexes, facilitating the DPIC formation. Using atomic force microscopy-based force spectroscopy (AFM-FS), we measured the viscoelastic properties of these DPICs. Additionally, we analyzed the phase diagram of DPICs, uncovering two distinctive transition behaviors: a phase transition between viscoelastic fluid and viscoelastic solid, and a morphology transition between DPICs with droplet-like morphology and “pearl chain”-like structure. Finally, we established the relationship between DNA-protein interaction strength, relaxation time, and condensate morphology.