Hybridization-initiated exonuclease resistance strategy for simultaneous detection of multiple microRNAs

Abstract

Multiple miRNA detection is often limited by sample, time-consuming, and complicated procedures. To address such challenges, we present a relatively simple and amplification-free fluorescent strategy based on hybridization-initiated exonuclease resistance for simultaneous detection of multiple miRNAs in a single tube. Single-stranded linear DNA probes were designed with dual roles of capture and reporter DNA, i.e. each DNA probe was labeled with biotin at the 3′-end for signal readout and amino at the 5′-end for probe immobilization. After target miRNAs specifically hybridized with the corresponding probes, the formation of double-stranded probe-target duplex protected the biotin on the probe from Exonuclease I digestion, thus resulting in high fluorescent intensities through the reaction between biotin and streptavidin-phycoerythrin. Coupling with the 3-plex fluorescent microsphere-based assay system, herein we successfully demonstrated the simultaneous and quantitative measurement of three sequence-specific miRNAs at concentration range of 2.5 pM to 1.25 nM and detection limits of 2 pM. To meet high throughput and rapid turnaround time requirements, we have also exemplified that, even shortening the total reaction time within 1 h, wider linear response range and lower detection limit were guaranteed. We further applied this assay to detect endogenous target miRNA levels from five kinds of cancer cell line and one normal cell line HEK 293T. This simple and rapid strategy will hold great potential for monitoring of multiple miRNAs biomarkers in biomedical research and early clinical diagnosis.