Label-free multiplex detection of miRNA-assayed hydrogel barcode using a low-aspect-ratio micropore sensor

We report a rapid and label-free multiplex sensing of target miRNAs using hydrogel barcodes and a low-aspect-ratio micropore device. A 6-bit hydrogel barcode representing codes 0 and 1 was fabricated using flow lithography and functionalized with probe DNA. Subsequently, the probe DNA was assayed with the target miRNA at a specific concentration. The barcode particles in the solution were translocated through a low-aspect-ratio micropore, and the current signal between the cis and trans electrodes was measured. Therefore, the micropore sensor successfully detected the encoded data of the 6-bit hydrogel barcodes. We analyzed signals, such as overshoot, peak drop, and translocation time, to determine the appropriate parameter and subsequently the target miRNA concentration. We observed that the magnitude of the overshoot signal was significantly associated with the concentration of the target miRNA, matched with finite element method (FEM) analysis results. The micropore sensor individually detected the four types of miRNAs in conjunction with the encoded data and achieved a detection limit of 10 pM. In addition, this micropore sensor enabled multiplex sensing of four types of encoded barcodes assayed with different miRNAs in each sample at once.