Molecular program based on switching toehold exchange reaction for cell type identification

Accurate identification of cell lines is crucial during the development of cell-based medical products. Recent work has shown that DNA-based molecular computing is powerful for simultaneously sensing and analyzing complex molecular information. Here, we designed a molecular program based on a switching toehold exchange reaction that can integrate the sensing of multiple mRNAs and simultaneously perform logical analysis of the detected mRNA information to directly report the cell type identification results. As a demonstration, we successfully achieved the converting of molecular program as fluorescent probes for in situ detection of mRNA in living cells, and further scaled up the molecular program for identification of cellular differentiation of direct reprogramming of human fibroblasts to hepatocytes. Owing to its sequence design flexibility and scalability, this molecular program will have broad applications in bioscience, biomedical engineering and personalized medicine.