ECHO-FISH for gene transcript detection in neuronal and other cells and subcellular compartments

Abstract

Fluorescence in situ hybridization (FISH) has been widely used in a variety of applications such as karyotyping, cytogenotyping, cancer diagnosis, species specification, and gene-expression analysis. With detection sensitivity and stringency, FISH provides detailed information on tissue-specific, cell-specific, and subcellular gene expression. Despite the versatile applications developed in both academia and clinical sectors, FISH remains a labor-intensive and time-consuming technique. Herein we describe a quick and simple FISH protocol (ECHO-FISH: e xciton- c ontrolled h ybridization-sensitive fluorescent o ligonucleotide- FISH ) using oligonucleotide probes that are doubly labeled with thiazole orange dyes. The fast hybridization kinetics and quick fluorescence activation of the new probes simplifies the conventional FISH protocols and reduces the amount of time to process the samples. Furthermore, hybridization-sensitive fluorescence emission of the probes allows monitoring dynamic behaviors of RNA in living cells.