First published 2 September 2013
Predator prey molecular landscapes
Adrien Padirac, Alexandre Baccouche, Fujii Teruo, Andre Estevez-Torres, Yannick Rondelez
This paper describes the use of molecular programming techniques to build synthetic in vitro and spatially distributed reactions networks with tailored topologies. The basic workflow is to use synthetic DNA strands to encode the topologies of molecular interactions of the reaction network. The actual dynamic of the system is provided by enzymatic reactions controlled and templated by these DNA strands. Here we focus on the implementation of a molecular predator-prey ecosystem. We thus create two autocatalytic DNA amplifications reactions and connect them through predation—the second DNA-species consumes the first one to fuel its growth. We also ensure that these species have a limited lifetime in the test tube. We are therefore able to detect sustained oscillations of the two molecular species, as predicted and observed for real ecosystems. This is the first time that predator prey oscillations are observed in a chemical system. We further expand the analogy between chemical and animal networks by introducing additional interactions such as symbiosis, the mutually beneficial interaction between two species. Interestingly, competition also arises quite naturally from the physical substrate that is used in the modeling process and displays remarkable dynamic consequences such as synchronization or chaos. Finally we report the construction of spatially distributed chemical ecosystems, and the observation of their spatiotemporal behaviors, in particular traveling and spirals dual waves of molecular hunts.