Oscillator for self-assembled DNA nanomachines

Self-assembled DNA nanomachines have been energetically developed recently. We have invented an RNA-oscillator constructed with an autonomous biomolecular computing system in order to operate periodically DNA nanomachines driven by DNA/RNA hybridization. The biomolecular computing system, which we have developed, can convert RNA sequences from input strand to output strand by nucleic-acids hybridizations and enzymatic reactions at a constant temperature. A feedback network of the autonomous biomolecular computing system can oscillate. In this study, we simulated behaviors of the oscillator before in vitro experiments by describing each reaction step using simultaneous nonlinear differential equations. As the result of numerical simulation, we found that there were some conditions on which RNA concentrations could oscillate and the conditions depended on the balance between RNA production and degradation rates.