MFN: Explainable DNA triple helixes Stabilized Design based on mCGR and flow network

DNA triple helix structure, as a highly specific gene targeting tool, enable gene regulation by precisely identifying and binding to target DNA sequences. However, the limits of design quality and efficiency affect their wide application in gene therapy. Therefore, in this paper, we propose an antiparallel DNA triple helixes design method-MFN based on matrix chaotic game representation (mCGR) and flow network. Leveraging the structural characteristics of DNA sequences, this method employs the mCGR algorithm to construct an initial matrix, generating a set of DNA sequences that conform to foundational constraints. Then, these sequences are mapped as stream network nodes to screen crosstalk structures by path search, and the whole process is observable and interpretable. Experimental results show that MFN significantly improves the design efficiency of triple helix structure and reduces crosstalk phenomenon. Wet experiments further verify the effectiveness of the method. In summary, MFN achieves an efficient and high-quality design of DNA triple helixes and provides a new idea for targeted gene therapy.