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Rapid Sequential In Situ Multiplexing With DNA-Exchange-Imaging
Johannes B Woehrstein,
Maier S. Avendaño,
Ron C.J. Schackmann,
Jason J. Zoeller,
Shan Shan H. Wang,
Paul W Tillberg,
Sylvain W Lapan,
Edward S Boyden,
Joan S Brugge,
Pascal S Kaeser,
George M Church,
Sarit S Agasti,
Posted 20 Mar 2017
bioRxiv DOI: 10.1101/112227 (published DOI: 10.1021/acs.nanolett.7b02716)
Posted 20 Mar 2017
To decipher the molecular mechanism of biological function, it is critical to map the molecular composition of individual cells in the context of their biological environment in situ. Immunofluorescence (IF) provides specific labeling for molecular profiling. However, conventional IF methods have finite multiplexing capabilities due to spectral overlap of the fluorophores. Various sequential imaging methods have been developed to circumvent this spectral limit, but are not widely adopted due to the common limitation of requiring multi-rounds of slow (hours to overnight in practice) immunostaining. To overcome this speed restriction and develop a practical platform for rapid in situ multiplexing, we describe here DNA-Exchange-Imaging, which allows single-step immunostaining with DNA-barcoded antibodies, followed by rapid (minutes) buffer exchange of fluorophore-bearing DNA imager strands. By eliminating the need for multiple rounds of immunostaining, DEI enables rapid spectrally unlimited sequential imaging. The programmability of DNA-Exchange-Imaging further allows us to adapt it to diverse microscopy platforms (with Exchange-Confocal, Exchange-SIM, Exchange-STED, and Exchange-PAINT demonstrated here), achieving highly multiplexed in situ protein visualization in diverse samples (including neuronal and tumor cells as well as fresh-frozen or paraffin-embedded tissue sections) and at multiple desired resolution scales (from ~300 nm down to sub-20-nm). Validation highlights include 8-target imaging using single-channel Exchange-Confocal in tens of micron thick retina tissue sections in 2-3 hours (as compared to days required in principle by previous methods using comparable equipment), and 8-target super-resolution imaging with ~20 nm resolution using Exchange-PAINT in primary neurons. These results collectively suggest DNA-Exchange as a versatile, practical platform for rapid, highly multiplexed in situ imaging, potentially enabling new applications ranging from basic science, to drug discovery, and to clinical pathology.
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