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The biological Deoxyribonucleic acid (DNA) strand is found to be a promising computing unit. DNA computing is attracted as one method which gives us suitable answers for optimization problems. Proportional Integral Derivative (PID) control schemes have been widely used in industrial fields. Since the PID parameters have a great influence on the stability and performance of the control system, many approaches have been proposed to determine them. In this article, we propose double helix structured DNA algorithms to design the type of PID controller and optimize the PID parameters. The structure of DNA computing is provided. It is applied into the optimal design of PID controller system. A computer simulation shows that we can get satisfactory results with the proposed method.