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Maximum independent set problem is the core issue in NP-complete problems, many problems can be transformed into the maximum independent set problems to solve, so design a good algorithm for solving the problem is very necessary. Molecular beacon is a hairpin-shaped fluorescent probe, which can hybridize with target sequence that is complement to its loop sequence. The specificity of molecular beacon is as high as single base mismatch detection. In this paper, molecular beacon is as for probe, to separation and detection all of the independent sets, finally by observing the fluorescence to determine whether or not the solution is existence. At the same time, in the establishment of the initial data pool, only one type of DNA molecules was synthesized. In the calculation process, the model does not require the restriction enzyme digestion, gel electrophoresis etc.. These steps may avoid possible computational errors and data loss; at the same time, the algorithm also has easy code and reading solution.