Self-assembly algorithm is a new computing model based on molecular which is regarded as data storage and operator. In order to improve the specificity and detection sensitivity of self-assembly algorithm, for the first time, both the PNA molecules and gold nanoparticles are introduced into the model for computing, and also a simple 0–1 programming problem is taken for example to interpret this model. Analysis shows the introduction of the two is feasible in the biological operation, and both the accuracy and dependability of the computation model are improved. At the same time, the detection method becomes more flexible to be introduced into other self-assembly algorithm models.