A colorful bunch: A series of fluorescent probes designed on the basis of fluorescence quenching caused by an excitonic interaction contain different dye moieties and fluoresce in various colors upon hybridization with their target nucleic acid. The picture shows simultaneous fluorescence in three colors in the nucleus of a cell containing an excess of three different microRNA strands. Left: differential interference contrast image.
Nuclease-resistant hybridization probes for long-term intracellular RNA imaging were synthesized. Newly designed probes with a 2'-O-MeRNA structure showed high resistance against nucleases, which is in contrast to the low resistance of DNA probes. These modified probes retained the function on the on-off switching of fluorescence emission in sensitive response to RNA recognition, based on the mechanism of interdye excitonic interaction, and functioned effectively for the long-term monitoring of RNA-stained living cells.
A series of near-infrared fluorescent probes were designed based on the concept of emission control caused by interdye excitonic interaction. The fluorescent probes showed very weak emission in the unhybridized state, whereas they emitted near-infrared fluorescence after hybridization with the complementary nucleic acid. The hybridization-dependent switching of fluorescence emission made it possible to monitor mRNA in human cells in the range of near-infrared wavelengths.
BackgroundImaging the behavior of RNA in a living cell is a powerful means for understanding RNA functions and acquiring spatiotemporal information in a single cell. For more distinct RNA imaging in a living cell, a more effective chemical method to fluorescently label RNA is now required. In addition, development of the technology labeling with different colors for different RNA would make it easier to analyze plural RNA strands expressing in a cell.Methodology/Principal FindingsTag technology for RNA imaging in a living cell has been developed based on the unique chemical functions of exciton-controlled hybridization-sensitive oligonucleotide (ECHO) probes. Repetitions of selected 18-nucleotide RNA tags were incorporated into the mRNA 3′-UTR. Pairs with complementary ECHO probes exhibited hybridization-sensitive fluorescence emission for the mRNA expressed in a living cell. The mRNA in a nucleus was detected clearly as fluorescent puncta, and the images of the expression of two mRNAs were obtained independently and simultaneously with two orthogonal tag–probe pairs.Conclusions/SignificanceA compact and repeated label has been developed for RNA imaging in a living cell, based on the photochemistry of ECHO probes. The pairs of an 18-nt RNA tag and the complementary ECHO probes are highly thermostable, sequence-specifically emissive, and orthogonal to each other. The nucleotide length necessary for one tag sequence is much shorter compared with conventional tag technologies, resulting in easy preparation of the tag sequences with a larger number of repeats for more distinct RNA imaging.
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