In vitro evolution of molecular cooperation in CATCH, a cooperatively coupled amplification system

Background: One of the key issues in the investigation of evolution is how complex systems evolved from simple chemical replicators. Theoretical work proposed several models in which complex replicating systems are kineticall y stabilized. The development of powerful isothermal amplification techniqu e allows complex nucleic acid based evolving in vitro systems to be set up, which may then serve to verify experimentally current theories of evolutio n. Recently such a system based on the 3SR (self-sustained sequence replica tion) reaction has been established to investigate the evolution of coopera tion: the trans-cooperatively coupled CATCH (cooperative amplification by c ross hybridization). Results: Over four rounds of serial transfer, the cooperatively coupled two species CATCH system evolved into a more complex cooperative four species system, which then was overgrown by CATCH-derived RNA-Z-like hairpin specie s. In contrast to the classical RNA-Z species, these molecules have complem entary loop sequences and self-amplify using a dual mechanism that includes concentration-dependent phases of noncooperative and cooperative amplifica tion. Conclusions: The evolution of a cooperative system, under conditions that w ere alternately unfavorable and favorable for cooperative amplification, le d to a system showing facultative cooperation. This principle of facultativ e cooperation preserves the complexity of the system investigated and could have general implications for the evolution and stabilization of cooperati on under oscillating reaction conditions.