Ultrasensitive Multiplexed MicroRNA Quantification on Encoded Gel Microparticles Using Rolling Circle Amplification

There is great demand for flexible biomolecule analysis platforms that can precisely quantify very low levels of multiple targets directly in complex biological samples. Herein we demonstrate multiplexed quantification of microRNAs (miRNAs) on encoded hydrogel microparticles with subfemtomolar sensitivity and single-molecule reporting resolution. Rolling circle amplification (RCA) of a universal adapter sequence that is ligated to all miRNA targets captured on gel-embedded probes provides the ability to label each target with multiple fluorescent reporters and eliminates the possibility of amplification bias. The high degree of sensitivity achieved by the RCA scheme and the resistance to fouling afforded by the use of gel particles are leveraged to directly detect miRNA in small quantities of unprocessed human serum samples without the need for RNA extraction or target-amplification steps. This versatility has powerful implications for the development of rapid, noninvasive diagnostic assays.