Dissipative Gated and Cascaded DNA Networks

Nucleic acid based, out-of-equilibrium, dissipative networks driven by nucleic acid fuels coupled to the nicking enzyme, Nt.BbvCI, are presented. One set of experiments includes a functional module consisting of a duplex and two fluorophore-labeled strands. The fuel-triggered activation of the functional module leads to a supramolecular intermediate composed of a template bound to the two fluorophore-labeled strands. Nicking of the fuel strand by Nt.BbvCI yields "waste"products, resulting in the regeneration of original system. The transient dissipative behavior of the systems is probed by following the FRET signal generated by the fluorophore labels associated with the intermediate supramolecular complex. The second set of experiments introduces two functional modules activated in parallel by the fuel strand. Using two inhibitors, I1 or I2, the selective gated dissipative operation of the networks is demonstrated. Finally, experiments presenting the intercommunication and cascading of two dissipative networks are introduced. Subjecting the networks to the fuel strands leads to intercommunication between the networks by strand-transfer and strand-feedback processes, allowing the cascaded dissipative operation of the assembly. The experimental results of the different dissipative systems are accompanied by kinetic models and computational simulations. The computational simulations provide useful means to predict the dissipative transient patterns of the systems at different auxiliary conditions.