Computational encoding DNA sequence design is one of the most important steps in molecular computation. A lot of research work has been done to design reliable sequence library. A revised method based on the support system developed by Tanaka et al.is proposed here with different criteria to construct fitness function. Then we adapt particle swarm optimization (PSO) algorithm to our encoding problem. By using the new algorithm, a set of sequences with good quality is generated. The result also shows that our PSO- based approach could rapidly converge at the minimum level for an output of the simulation model. The celerity of the algorithm fits our requirements.