Crowding and confinement act in concert to slow DNA diffusion within cell-sized droplets

Dynamics of biological macromolecules, such as DNA, in crowded and confined environments are critical to understanding cellular processes such as transcrip-tion, infection, and replication. However, the combined effects of cellular confine-ment and crowding on macromolecular dynamics remain poorly understood. Here, we use differential dynamic microscopy to investigate the diffusion of large DNA molecules confined in cell-sized droplets and crowded by dextran polymers. We show that confined and crowded DNA molecules exhibit universal anomalous subdiffusion with scaling that is insensitive to the degree of confinement and crowding. However, effective DNA diffusion coefficients D-eff decrease up to 2 or-ders of magnitude as droplet size decreases-an effect that is enhanced by increased crowding. We mathematically model the coupling of crowding and confinement by combining polymer scaling theories with confinement-induced depletion effects. The generality and tunability of our system and models render them applicable to elucidating wide-ranging crowded and confined systems.

Automated summary

This study uses differential dynamic microscopy to investigate the diffusion of large DNA molecules confined in cell-sized droplets and crowded by dextran polymers. The results show that confined and crowded DNA molecules exhibit universal anomalous subdiffusion, with the degree of confinement and crowding having minimal impact. However, as droplet size decreases, the effective DNA diffusion coefficients decrease significantly, and this effect is enhanced by increased crowding.