Pattern Recognition of microRNA Expression in Body Fluids Using Nanopore Decoding at Subfemtomolar Concentrations

[Image: see text] This paper describes a method for detecting microRNA (miRNA) expression patterns using the nanopore-based DNA computing technology. miRNAs have shown promise as markers for cancer diagnosis due to their cancer type specificity, and therefore simple strategies for miRNA pattern recognition are required. We propose a system for pattern recognition of five types of miRNAs overexpressed in bile duct cancer (BDC). The information of miRNAs from BDC is encoded in diagnostic DNAs (dgDNAs) and decoded electrically by nanopore analysis. With this system, we succeeded in the label-free detection of miRNA expression patterns from the plasma of BDC patients. Moreover, our dgDNA–miRNA complexes can be detected at subfemtomolar concentrations, which is a significant improvement compared to previously reported limits of detection (∼10(–12) M) for similar analytical platforms. Nanopore decoding of dgDNA-encoded information represents a promising tool for simple and early cancer diagnosis.