Development of a rapid bead-based microfluidic platform for DNA hybridization using single- and multi-mode interactions for probe immobilization

Abstract The demand for portable, rapid, sensitive and low-cost DNA detection systems that could be used for rapid diagnostic of disease and infection has greatly motivated the development of new DNA detection platforms in recent years. However, these platforms are often highly complex, requiring an excessively long time of analysis and/or suffer from inadequate sensitivity. Here we report a rapid and simple bead-based microfluidic platform to detect a specific 22-mer DNA sequence via hybridization, serving as a model of a miRNA biomarker for tumor and cardiovascular diseases. Commercial nanoporous chromatography beads were used as solid support for probe DNA immobilization, using either a single-mode electrostatic interaction or multi-mode interactions (electrostatic and hydrophobic). Using a mass balance approach, a probe density of 2.4 × 10 13 ± 18 % ( ± RSD%) molecules/cm 2 was quantified in optimized conditions, which was found to provide hybridization efficiencies above 95 % and a hybridization dissociation constant below 1 nM. Comparing targets with different optical labels, namely Atto 430LS, quantum dots and horseradish peroxidase, the lowest limit of detection of 9.5 ± 1.1 pM was achieved with an assay time of 10 min using a quantum dot label coupled with a multi-mode immobilization. These results highlight the potential of the system to be applied as a simple and highly sensitive DNA hybridization platform, achieving low pM sensitivities without the need of a DNA amplification procedure.