DNA nanotechnology for nucleic acid analysis: Detection of RNA and dsDNA amplicon using multifunctional DNAzyme nanomachine (DNM)

Abstract

DNA has long been recognized as a promising material for biotechnological applications. Here, we demonstrate how DNA nanotechnology can enhance the sensing of practically important forms of nucleic acid analytes, including folded singlestranded RNA (ssRNA) and double-stranded DNA (dsDNA) amplicons. We designed and optimized a multifunctional DNAbased sensor incorporating the catalytic DNAzyme 10-23, named here DNAzyme-based molecular machine (DNM), and compared its performance with that of the classical binary 10-23 DNAzyme (BiDz) probe in detecting ssDNA, ssRNA, and dsDNA targets. The newly developed sensor exhibited up to 100 and 20-fold lower limits of detection (LOD) for ssDNA and ssRNA, respectively. Unlike traditional BiDz, DNM was capable of detecting as little as 1 µL of dsDNA amplicon (2 nM) within a 30 min assay, achieving excellent target specificity. We suggested an explanation of the nucleic acid complexes' behaviour with the respect to Gibbs energy.2