Screening assays.

Real-time PCR assays containing 30 different color-coded molecular beacons were carried out, each assay initiated with 100,000 linearized target plasmids that contained a copy of the V3 region of the 16S ribosomal RNA gene from a different bacterial species. The unique duplex color combination that arose in each of the 15 screening assays unambiguously identified the species-specific target sequence that was initially present in each sample. A control assay containing a target plasmid from Streptococcus pyogenes, for which there were no molecular beacon probes, gave a very low background signal in all six colors, and remained low throughout the course of the assay.