Multiplexed hydrogel microparticle suspension arrays for facile ribosomal RNA integrity assays

Reliable RNA integrity assay is important for a wide range of applications in genomics and diagnostics, yet the existing technologies have certain limitations such as large amount of sample required, high cost of equipment and/or long turnaround times. We report a simple assay method to analyze bacterial ribosomal RNA (rRNA) from complex total RNA samples utilizing shape-encoded and single-stranded DNA-conjugated hydrogel microparticle suspension arrays with no need for target amplification and under standard fluorescence imaging conditions. We show that our simple microparticle-based sensing scheme is reliable, sequence-specific and presents a responsive binding behavior to target RNA concentrations. Moreover, the relative stability of 16S and 23S rRNA can be assessed in a simple shape encoding-based multiplexed format. Combined, these findings represent a significant step toward cheap, fast, simple, and reliable assays for the analysis of rRNA and general RNA integrity.