Design of molecular systems for artificial pattern formation and gene regulation

Can we engineer matter that shapes itself ? To elucidate this question we have built molecular systems that mimic two essential features of life: pattern formation and gene regulation. We have designed an active reconstituted system composed of kinesin clusters and microtubules. Depending on their concentrations, we have rationally reported dynamic patterns such as local and global contractions, active flows and a new 3D regular pattern consisting of a corrugated active nematic sheet with tunable wavelength and dynamics. We have combined this active fluid with a programmable chemical reaction network composed of short DNA strands and enzymes. In particular we have observed the propagation of a DNA reaction-diffusion front in an active environment; they form then a complex system in which two patterning mechanisms - active matter and reaction-diffusion - are coupled to shape a material, which is reminiscent of morphogenetic processes happening during embryo development. Finally, we have used de novo engineered RNA translational regulators and have showed that a cell-free transcription-translation system composed of recombinant proteins can provide valuable information about the performances of in silico designed riboregulators. We hope that these approaches will help in the design of out-of-equilibrium materials with new properties.