Improved Templated Fluorogenic Probes Enhance the Analysis of Closely Related Pathogenic Bacteria by Microscopy and Flow Cytometry

2011-09-21T00:00:00Z (GMT) by Raphael M. Franzini Eric T. Kool
Templated fluorescence activation has recently emerged as a promising molecular approach to detect and differentiate nucleic acid sequences <i>in vitro</i> and in cells. Here, we describe the application of a reductive quencher release strategy to the taxonomic analysis of Gram-negative bacteria by targeting a single nucleotide difference in their 16S rRNA in a two-color assay. For this purpose, it was necessary to develop a release linker containing a quencher suitable for red and near-infrared fluorophores, and to improve methods for the delivery of probes into cells. A cyanine-dye labeled oligonucleotide probe containing the new quencher-release linker showed unprecedentedly low background signal and high fluorescence turn-on ratios. The combination of a fluorescein-containing and a near-IR emitting probe discriminated <i>E. coli</i> from <i>S. enterica</i> despite nearly identical ribosomal target sequences. Two-color analysis by microscopy and the first successful discrimination of bacteria by two-color flow cytometry with templated reactive probes are described.