In our project, we proposed a system that releases molecules following the
information written on DNA. The features of this system are programmability and
scalability. To achieve our goals, we created two types of system, Enzyme system and
Enzyme-free system. In both of these systems, programmability and scalability are
confirmed through simulations. Results of the simulation are shown below.
Both Enzyme and Enzyme-free systems have a common limitation, which is that the same output cannot be released again. In concrete terms, input coded A-B-A is not accepted while input coded A-B-C is accepted.
The reaction rate constant is planned to be optimized by feed-backing the result of chemical reaction.
(1) Enzyme system
First we verified the programmability of Enzyme system. When information of input was a-b, output A-B was released in order. The same thing applies to input coded b- a. We can conclude that Enzyme system has programmability. By adjusting initial concentration, the time interval of the output was changed.
However, we found it difficult to adjust the time interval of the output arbitrarily. We
are searching for solution for this problem.
The simulation in which information of input was a-b-c to show the scalability is now proceeding by extending ordinary differential equations.
(2) Enzyme-free system
In the same manner as Enzyme system, we carried out the simulation of Enzyme-
free system. When information of input was a-b, output A-B was released in order.
The same result of the simulation was obtained when information of input was b-a as
well. Subsequently, we simulated the scalability. When information of the input was a-
b-c, output A-B-C was released. We can conclude that Enzyme-free system has both
programmability and scalability.
We found that a slight difference in the concentrations of components has a great effect on the intervals of output releasing, which makes it difficult to tune the whole reactions in detail.
We have to make experiments to confirm that the two systems have programmability, and Enzyme-free system has scalability. We have already finished designing the sequence of DNA. We have prepared all the materials and are about to go on experiments to prove these features.