Programmable Dynamic Control of DNA Condensates

The formation of liquid condensates has been recently implicated as a mechanism of control in biological systems. While non-specific interactions between subunits are considered to be major drivers in the formation of natural condensates, molecules with programmable specific interactions are of particular interest to engineers and materials scientists. The toolkit of DNA nanotechnology has recently provided a framework to design and build subunits for liquid-liquid phase separation (LLPS) using DNA as a programmable biological polymer. Using DNA nanotechnology we are exploring the mechanisms and design rules by which condensates can be controlled through chemical reactions.<br/>Here, we demonstrate, by theory and experiment, how modification of the structure of DNA nanostar subunits affects their macroscopic condensation kinetics. By changing the various domains of the DNA monomer we achieve a predictable growth profile of the condensates. We conceive tunable and reversible dynamic control of condensate formation and dissolution by utilizing DNA strand displacement reactions that deactivate or reactivate the DNA monomer interaction domains. By changing DNA monomer design and sequence makeup, we explore the tunability of these reactions under different conditions. We quantify the temporal evolution of different designs of DNA condensates via fluorescence microscopy and report population-level kinetics of phase separation and condensate growth. We also develop a mean field theory of condensates under the impact of chemicals which disrupt their ability to phase separate, and show how the impact of said chemicals leads to phase diagrams for the system which have similar features to the standard temperature control. We show how this control is dependent on various factors under our direction, such as the concentrations of the chemicals involved, the valency of the nanostars and the size of the nanostars. Our results provide a versatile DNA-based toolkit for designing and controlling macroscopic condensates through sequence design methods. This toolset may be useful to build synthetic membraneless organelles whose formation can be temporally controlled via chemical reactions.