A PNA microarray platform for miRNA expression profiling using on-chip labeling technology

MicroRNAs (miRNAs) are short, non-coding RNAs that play a critical role in development, metabolism and other fundamental biological processes, and are also important in diseases such as cancer. To study miRNA expression levels in a systematic and parallel manner, we have developed a highly sensitive, specific and reproducible microarray for miRNA expression profiling using the Peptide Nucleic Acids (PNA) probes which have higher affinity and greater specificity for binding to RNA than do DNA probes. We developed a PNA microarray assay that optimizes PNA probe, hybridization conditions, and on-PNA chip labeling method. In this PANArray™ miRNA method, unlabeled RNA is hybridized to the PNA microarray and labeled by enzymatic ligation of pCp-Cy3 on the chip. This assay showed high reproducibility and low cross-hybridization for miRNAs belonging to the let-7 family and the miR-181 family, which differ by a single nucleotide. The PNA microarray (PANArray™ miRNA) is a rapid throughput technology for analyzing expression profiles with high fidelity, and could prove to be a powerful tool for cancer research, diagnosis and prognosic assessment.