Improving DNA capture on microarrays by integrated repeated denaturing

Sequence-specific sepsis-related DNA capture and fluorescent labeling in monoliths prepared by single-step photopolymerization in microfluidic devices

Fast determination of antibiotic resistance is crucial in selecting appropriate treatment for sepsis patients, but current methods based on culture are time consuming. We are developing a microfluidic platform with a monolithic column modified with oligonucleotides designed for sequence-specific capture of target DNA related to the Klebsiella pneumoniae carbapenemase (KPC) gene. We developed a novel single-step monolith fabrication method with an acrydite-modified capture oligonucleotide in the polymerization mixture, enabling fast monolith preparation in a microfluidic channel using UV photopolymerization. These prepared columns had a threefold higher capacity compared to monoliths prepared in a multistep process involving Schiff-base DNA attachment. Conditions for denaturing, capture and fluorescence labeling using hybridization probes were optimized with synthetic 90-mer oligonucleotides. These procedures were applied for extraction of a PCR amplicon from the KPC antibiotic resistance gene in bacterial lysate obtained from a blood sample spiked with E. coli. The results showed similar eluted peak areas for KPC amplicon extracted from either hybridization buffer or bacterial lysate. Selective extraction of the KPC DNA was verified by real time PCR on eluted fractions. These results show great promise for application in an integrated microfluidic diagnostic system that combines upstream blood sample preparation and downstream single-molecule counting detection.

Rapid, sensitive and real-time multiplexing platform for the analysis of protein and nucleic-acid biomarkers

We describe a multiplexing technology, named Evalution, based on novel digitally encoded microparticles in microfluidic channels. Quantitative multiplexing is becoming increasingly important for research and routine clinical diagnostics, but fast, easy-to-use, flexible and highly reproducible technologies are needed to leverage the advantages of multiplexing. The presented technology has been tailored to ensure (i) short assay times and high reproducibility thanks to reaction-limited binding regime, (ii) dynamic control of assay conditions and real-time binding monitoring allowing optimization of multiple parameters within a single assay run, (iii) compatibility with various immunoassay formats such as coflowing the samples and detection antibodies simultaneously and hence simplifying workflows, (iv) analyte quantification based on initial binding rates leading to increased system dynamic range and (v) high sensitivity via enhanced fluorescence collection. These key features are demonstrated with assays for proteins and nucleic acids showing the versatility of this technology.

Bacteria microarrays as sensitive tools for exploring pathogen surface epitopes and recognition by host receptors

We have developed a readily adaptable microarray technology for high-throughput screening of pathogen-binding biomolecules and inhibitors of pathogen–counter-receptor interactions, based on the generation of bacteria microarrays.