Our system’s strong points are that it gives outputs in order with time intervals. We can program order as we want.
Here we examine whether our system behaves properly in the simulation.
These results above show that the system seems to behave properly, but we need to check that the system changes order of outputs to actually say its behavior is proper. So third, we simulated how the system works when system accepts B-A input.
As we designed, the system gave B then A outputs in order. This prove our system can recognize input DNA and change its outputs as we coded.
Each concentration related to the system, so we checked the behavior of time intervals when the concentrations of each component are changed.
Following are the results of simulations when concentration of input, templates, gates were changed (Fig.4,5,6,7). Each result shows that time interval can be arranged by concentration of components.
・Our system gives outputs as coded in the input DNA in order.
・Our system gives outputs with time intervals and the interval can be arranged by changing concentrations of the components of the system.
Our system is described by differential equations obtained from chemical reaction formulas. We solved them by using numerical software (Scilab).
Condition of simulating is as follows.
Input DNA concentration: 10nM
Template1 concentration: 10nM
Template2 concentration: 10nM
Liposome1 concentration: 10nM
Liposome2 concentration: 10nM
Gate1 concentration: 10nM
Gate2 concentration: 10nM
Simulation time: 100[sec]
Values of chemical parameters are as follows.
Only Parameter of Reaction of gate and keyDNA is 1.0×10^6 because the toehold is short.