RTL2DNA: An automatic flow of large-scale DNA-based logic circuit design

DNA computing is a new kind of computation for solving complex problems with significant parallelism. Research findings indicate that DNA-based logic systems can be useful in many biomedical applications such as early cancer detection. DNA logic systems have been applied successfully to detect the risky patterns of nucleotide-based cancer biomarkers (microRNAs). Detection of real diseases requires large-scale DNA-based logical systems. Therefore, the issue of large-scale DNA-based logic circuits is a crucial research topic. In this paper, an automatic design flow is proposed to facilitate the design, verification, and physical implementation of multi-stage and large-scale DNA logic circuits. Digital Microfluidic Biochips (DMFB) have been used recently as a promising platform for efficient implementation of DNA-based computing systems and circuits. We used this technology as the physical platform for implementation of DNA-based circuits. Our experiments and implementations show the feasibility, accuracy, efficiency, and simplicity of the proposed design flow. Final DNA reactions that are synthesized by the proposed design flow are verified and simulated using stochastic DNA-reaction simulators to prove the correctness of the proposed design flow. This design flow can open a new horizon for researchers and scientists to design, implement, and evaluate the DNA-based logic systems. (c) 2023 Sharif University of Technology. All rights reserved.