A new magnetic cell fishing approach based on hybridization chain reaction: HCR-MISH

This paper aims at presenting a new magnetic labelling approach based on in-situ hybridization for the specific capture of bacterial cells. This approach is inspired by HCR-FISH, which was recently proposed as a new sensitive method for the detection of environmental microorganisms using a combination of FISH (Fluorescent In Situ Hybridization) and HCR (Hybridization Chain Reaction). Here we propose to adapt the technique to allow grafting of superparamagnetic nanoparticles onto target bacteria and therefore to exploit magnetism instead of fluorescence for their subsequent isolation using a micro-magnet array. The feasibility of the approach was first assessed by isolating E. coli cells using a universal bacterial probe, Eub338. Then, specific targeting of Escherichia coli DH5a, Pseudomonas putida, and Acinetobacter sp. ADP1 were demonstrated using heterologous probes. For the purpose of comparison, both HCR-FISH and HCR-MISH experimental results are presented.