DNA-Sequence-Encoded Rolling Circle Amplicon for Single-Cell RNA Imaging

The expression and spatial profile of multiple RNA species at high precision in single cells is key information for understanding cellular behaviors and functions. Fluorescence microscopy is a powerful tool for imaging RNAs, but its multiplexing ability is limited by the number of spectrally distinct fluorophores. Here, we present a DNA-sequence-encoded fluorescence barcoding method, termed sequence-encoded amplicon (SeqEA), enabling highly multiplexed imaging of RNAs in single cells with single-molecule and single-nucleotide resolution. SeqEA exploits a thermodynamically tuning DNA hybridization approach for precisely encoding rolling circle amplicons with discrete fluorescence intensities as fluorescence barcodes, allowing for multiplexed tagging single-molecule RNAs. As a proof of principle, we have demonstrated its ability for simultaneously visualizing nine mRNA species and evaluated the coordination and spatial pattern of breast-cancer-associated oncogene expression. SeqEA provides a single-cell analysis platform for investigating the gene expression network and molecular mechanism of disease development.