Abstract: The present invention relates to methods of isolating cells, generating cell lines, and detecting RNAs in cells using signaling probes that produce a signal upon hybridization to a target sequence. Other methods that utilize the signaling probe include methods of detecting or quantifying the effect of an agent on RNAs in a cell, methods of quantifying the level of RNA expression, methods for identifying genetic recombinational events in living cells and methods of generating a transgenic animal using the isolated cells. The invention also provides protease probes. Signaling probes and protease probes that form stem-loop structures, three-arm junction structures, and dumbbell structures are provided.

Abstract: The present invention relates to methods of isolating cells, generating cell lines, and detecting RNAs in cells using signaling probes that produce a signal upon hybridization to a target sequence. Other methods that utilize the signaling probe include methods of detecting or quantifying the effect of an agent on RNAs in a cell, methods of quantifying the level of RNA expression, methods for identifying genetic recombinational events in living cells and methods of generating a transgenic animal using the isolated cells. The invention also provides protease probes. Signaling probes and protease probes that form stem-loop structures, three-arm junction structures, and dumbbell structures are provided.