Adaptive DNA computing algorithm by using PCR and restriction enzyme

In this paper, we introduce a new adaptive DNA computing algorithm by using Polymerase Chain Reaction (PCR). The adaptive algorithm is designed based on Adleman-Lipton (1995) paradigm of DNA computing. However, unlike the Adleman-Lipton architecture, a cutting operation has been introduced to the algorithm and the mechanism in which the molecules used by computation were feedback to the next cycle was devised. Moreover, amplification by PCR is performed in the molecule used by feedback and a concentration difference arises in the base sequence can be used again. By doing this, the molecules which serve as a solution candidate can be narrowed down and the optimal solution can be detected easily. From the application point of view, a simulation has been carried out on the shortest path problem and the validity of the proposed adaptive algorithm is stated from the results of the simulation. Finally, we go on to propose applying adaptive algorithm to the chemistry experiment which used the actual DNA molecules for solving a universal problem.