Fluorogenic Monomethine Cyanine Dyes for Nucleolar RNA Imaging in Living Cells

In contrast to well -established DNA -selective dyes for live cell imaging, RNA -selective dyes have been less developed due to the challenge of making small molecule selectively target RNA over DNA. Two kinds of dyes (SYTO RNA select and Nucleolus Bright) are now commercially available for nucleolar RNA imaging in cells, but these two dyes are not applicable to living cells. Here we report on unsymmetrical monomethine cyanine dyes for imaging of nucleolar RNA in living cells, including green -emissive thiazole orange (TO: lambda,(em) = 532 nm) and its regioisomer (2TO: lambda,(em) = 532 nm), yellow -emissive benzo[c,d]indole-oxazolo[5,4-c]pyridine (BIOP: lambda,(em) = 570 nm), and deep -red emissive benzo[c,d]indole-quinoline (BIQ: lambda,(em) = 657 nm) and its derivative having an amino group -terminated side chain (BIQ-NH2: lambda,(em) = 665 nm). These cyanine-based probes were essentially non -fluorescent in the free state (phi(free): TO, 0.00042; 2TO, 0.00009; BIOP, 0.00038; BIQ, < 0.0001; BIQ-NH2, 0.00062), and the value of fluorescence quantum yield significantly increased in the bound state (phi(bound): TO, 0.16; 2TO, 0.11; BIOP, 0.52; BIQ, 0.0085; BIQ-NH2, 0.020). Among these probes, TO, 2TO and BIOP were even applicable to wash -free imaging of living cells due to their high brightness and/or remarkable light -up property. Considering their good photostability, low cytotoxicity and easy preparation as well, we expect that a series of these cyanine dyes would be a candidate for practical use toward spatiotemporal analysis of nucleolar RNA in living cells.