Upconversion‐Linked Branched DNA Hybridization Assay for the Detection of Bacteriophage M13

Abstract The demand for highly sensitive methods of pathogen detection drives the development of new diagnostic assays. While nucleic acid amplification methods such as PCR are very sensitive and remain widely used, they may be limited in complex sample matrices due to the presence of polymerase inhibitors. On the other hand, the direct detection of nucleic acids by DNA hybridization assays is simple but typically less sensitive. This work combines a branched DNA (bDNA) hybridization assay with upconversion nanoparticle (UCNP) labels to enhance the sensitivity of DNA detection. The anti‐Stokes emission of UCNP labels enables measurements without optical background interference. The bDNA assay relies on a series of oligonucleotide probes creating a branched structure with several binding sites for biotinylated amplification probes and streptavidin‐conjugated UCNPs. Several configurations of the bDNA assay are investigated to achieve the highest signal amplification and the lowest background signal. The optimal configuration of bDNA assay yields a limit of detection (LOD) of 5.9 × 10⁴ cfu mL⁻¹ for the target DNA of the bacteriophage M13. The upconversion‐linked bDNA assay is easily adaptable to other target DNAs by adjusting the oligonucleotide probes.