Abstract: Oligonucleotide probes, kits, and methods useful for detecting more than one target nucleic acid at a time are provided. The invention provides oligonucleotides that interact with target nucleic acids to form first stage cleavage structures that are cleaved by a structure-specific nuclease. In an embodiment, the cleavage products of the first stage cleavage reactions interact with secondary cleavage oligonucleotides that are specific for each target nucleic acid and that are coupled to a solid support. The cleavage of the specific secondary cleavage oligonucleotides leads to detectible changes in fluorescence and is used to detect multiple target nucleic acids in one assay. In one embodiment, the solid support is a coded bead.