Diffusion of DNA in active and passive enzyme baths

Enzymes—catalyzing protein complexes—have been shown to exhibit enhanced diffusion in the presence of their substrate, potentially creating the makings of a molecular-scale active matter system. Directly quantifying the enhanced diffusion of an enzyme can be challenging due to the difficulty of reliably imaging/tracking its motion. Differential Dynamic Microscopy (DDM), which combines real-time video microscopy with Fourier analysis of light scattering has been shown to accurately quantify the diffusion of diffraction limited molecules, such as single-stranded DNA (ssDNA). We use ssDNA as a diffusion probe in enzymatic (urease) baths to characterize activity. We investigate if the presence of bulk enzymatic activity can affect the diffusion of passive molecules – in this case, ssDNA. We characterize our enzyme baths through UV-vis spectroscopy to determine the linear range and timescale of activity. These experiments on the activity of enzyme baths have the potential to unlock a large design space for molecular-scale active matter.