A system for fabricating nucleic acid polyominoe and a method thereof are disclosed, according to some embodiments of a present invention. The system includes an input module for receiving inputs for nucleic acid sequences and type of configurations. A processing module generates an optimized set of nucleic acid sequences and shapes based on the inputs; and an output module outputs the fittest and optimized polyominoe structure. The polyominoe includes an elementary block including at least two ssDNA sequences. A number of the blocks assemble together into different heterogeneous shapes. The shapes further merge into the target larger structure- polyominoe due to the self-organizing property of the DNA sequences and many sequences to many shapes configuration.