The regulation of the mechanisms by which genomic information dictates cellular behavior is one of the most important and urgent research topics in the postgenomic era. Chemically modified nucleic acids would be key players in sensitive, quantitative, and real-time detection of specific transcripts. In this article, we review recent advances in nucleic acid detection using exciton-controlled hybridization-sensitive fluorescent oligonucleotide (ECHO) probe technologies. In ECHO probes, a hybridization-dependent fluorescent nucleotide regulated by the H-aggregation of thiazole orange dyes is incorporated into specific sequence contexts. ECHO probe serves as a fluorescent detection readout for target nucleic acids. In addition, auxiliary chemical functional modules such as pH sensitivity, photolabile ability, and enhanced hybridization property have been introduced into ECHO probes to accommodate a broad range of biological applications.
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