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Biological Chemistry

Chemical reaction lights the way for tracking microRNA in living organisms

Imaging probes provide first-ever technique for visualizing small RNA sequences that control gene expression in vivo

by Alla Katsnelson, special to C&EN
June 13, 2016 | APPEARED IN VOLUME 94, ISSUE 24

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Credit: ACS Cent. Sci.
Nucleic acid-based probes illuminate expression of target microRNA sequences in neural cells (top) and cells involved in tail and fin development (bottom) in live zebrafish embryos.
Credit: ACS Cent. Sci.
Nucleic acid-based probes illuminate expression of target microRNA sequences in neural cells (top) and cells involved in tail and fin development (bottom) in live zebrafish embryos.

Researchers have developed a light-induced chemical reaction that visualizes RNA in live zebrafish embryos without interfering with cell processes. In previous work, the team applied the method to cells in culture. But now the researchers have developed the method as the first technique for detecting specific strings of nucleic acids in live vertebrates that doesn’t require genetically modifying the organisms. What’s more, the method is sensitive enough to visualize the expression of microRNAs, which are small noncoding RNAs that act as puppet masters of gene expression (ACS Cent. Sci. 2016, DOI: 10.1021/acscentsci.6b00054). Nicolas Winssinger, Marcos Gonzalez-Gaitan, and colleagues at the University of Geneva designed two nucleic acid probes that each complement and bind to adjacent halves of a target microRNA sequence. The researchers conjugated one probe to a ruthenium complex that absorbs visible light and the other to a rhodamine dye that lights up when its azide bonds are cleaved. When the probes attach to the target sequence, the two reagents come close enough to react. Shining a light on the sample activates the ruthenium, which reduces the azide in the rhodamine conjugate and thereby allows it to fluoresce. The researchers designed probes against three different microRNAs: one expressed in neural cells, another in muscle cells, and a third in cells involved in forming the pectoral tail and fins. After the embryos were exposed to light for 30 minutes, confocal imaging revealed that each probe set illuminated the expected type of tissue and the probes tracked microRNA expression over time during embryo development.

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