A deep-red fluorogenic antimicrobial peptide for rapid wash-free staining and detection of bacteria

Fluorescent probes for rapid staining and detection of bacteria are needed for the diagnostics of bacterial infections as a measure for mitigating the dissemination of antibiotic resistance. Here we report the design, synthesis and characterization of bacteria-targeting fluorogenic peptides incorporating Alared, an environmentally sensitive fluorescent unnatural amino acid based on the Nile Red fluorophore. The new peptide-based probe named UNR-1 displayed deep-red emission (λmax = 665 nm) and enabled rapid add-and-read fluorescence staining of Gram-positive and Gram-negative bacteria under no-wash conditions, while also exhibiting selectivity over mammalian cells. The probe was compatible with fluorescence microscopy and flow cytometry and was used for the detection of E. coli in conditions mimicking bacteriuria.