Fabrication of a structure-specific RNA binder for array detection of label-free microRNA.

MicroRNAs (miRNAs) are a class of small non-coding RNAs (19 – 25 nucleotides) that regulate gene expression in viruses, plants, and animals. Over 700 miRNAs are already identified in humans with thousands more expected to be found. Accumulated studies have reported distinct miRNA expression patterns in various human diseases, showing great potential of miRNA profiling in clinical applications such as diagnosis and drug efficacy evaluation. Microarray-based detection offers an efficient method for profiling large numbers of miRNA expressions simultaneously. Currently, most miRNA labeling methods utilize direct or indirect enzymatic labeling reactions against target miRNAs prior to (or sometimes after) hybridization to chip surface probes. Here we fabricated a novel structure specific RNA binding protein, which stably binds to double-stranded RNAs with a 2-nt 3' overhang. Acting like an antibody, this RNA binder allowed us to universally detect hybridized miRNAs on array surfaces without the need of any enzymatic amplification or labeling reactions.