Detection of the cellular and tissue distributions of RNA species is critical in our understanding of the regulatory mechanisms underlying cellular and tissue differentiation. Here, we show that an atomic force microscope tip modified with 27-acid dendron, a cone shaped molecule with 27 monomeric units forming its base, can be successfully used to map the spatial distribution of mouse Pax6 mRNA on sectioned tissues of the mouse embryonic neocortex. Scanning of the sectioned tissue with a 30-mer DNA probe attached to the apex of the dendron resulted in detection of the target mRNA on the tissue section, permitting mapping of the mRNA distribution at nanometer resolution. The unprecedented sensitivity and resolution of this process should be applicable to identification of molecular level distribution of various RNAs in a cell.
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