In order to show the potential of photonic techniques for realizing nanoscale computing, we examined the operation of DNA reactions by optical manipulation of microdroplets that contain DNA. The processing procedures are reconfigurable owing to flexibility in manipulating the microdroplets. The method is effective in, for example, implementing DNA computations in limited-volumes at multiple positions in parallel, enhancing an operation rate, and decreasing sample consumption, and it can be a promising technique applicable to photonic DNA computing. A reaction scheme using a pair of hairpin DNA and linear DNA was examined to confirm the method. The reaction scheme provides exchange of the sequence of a sticky-end of a DNA conformation, and it is usable for DNA computation. Microdroplets that contain DNA components were contacted to each other to start the reaction. By observing fluorescence intensity, we confirmed the reaction of sequence-change in the optically manipulated microdroplet. The experimental result also showed that different reactions are implemented at separate positions simultaneously.