Exponential Fluorescent Amplification of Individual Nucleic Acids Using Clampfish Probes

Non-enzymatic, high-gain signal amplification methods with single-cell, single-molecule resolution are in great need. We present click-amplifying FISH (clampFISH) for the fluorescent detection of nucleic acids that combines the specificity of oligonucleotides with bioorthogonal click chemistry in order to achieve high specificity and extremely high-gain (>400x) signal amplification in single cells. We show that clampFISH signal enables detection of RNA species with low magnification microscopy and separation of cells by RNA levels via flow cytometry. Additionally, we show that the modular design of clampFISH probes enables multiplexing of RNA and DNA, that the locking mechanism prevents probe detachment in expansion microscopy, and that clampFISH can be applied to tissue samples.