Detecting miRNAs Using DNA Nanoswitches

M13mp18 nanoscaffold-based strip sensor for detecting influenza A virus (H1N1)

We report the development of an amplification-free nucleic acid assay using lateral flow test strips. M13mp18 nanoscaffold signal amplification permitted the visual detection of H1N1 RNA in 20 min. M13mp18 nanoscaffold supported a set of backbone, variable, detection, and modified oligonucleotides. A bridging-type FAM probe/H1N1 RNA/M13mp18 was used in the lateral flow test strip format. The bridging-type complexes were captured on the test zone. The lower limit of detection of specific H1N1 RNA was 1 pM. The method directly detected H1N1 RNA without amplification, eliminating the risk of amplicon contamination and lessening the chance of false positives. This biosensor has potential value for field testing in resource-limited settings and monitoring viral loads in recovering patients. The amplification-free lateral flow detection of RNA provides an alternative between amplification-based RNA assays and protein antigen assays for facilitating the rapid identification of H1N1 virus during point-of-care testing.

How to Perform miRacles: A Step-by-Step microRNA Detection Protocol Using DNA Nanoswitches

MicroRNAs are short non-coding RNAs involved in post-transcriptional gene regulation, and are increasingly considered to be biomarkers for numerous biological processes and human diseases. Current techniques used for microRNA detection can be expensive and labor-intensive, and typically require amplification, labeling, or radioactive probes. In this protocol, we describe a DNA nanoswitch-based microRNA detection assay termed  "miRacles": microRNA-activated conditional looping of engineered switches. This method uses conformationally responsive DNA nanoswitches that detect the presence of specific microRNAs with a simple and unambiguous gel-shift assay that can be performed on the benchtop. The assay is low cost, minimalistic, and capable of direct detection of specific microRNAs in unprocessed total RNA samples, with no enzymatic amplification, labeling, or special equipment. The protocol for detection of microRNAs in total RNA can be completed in as little as a few hours, making this assay a compelling alternative to qPCR and Northern blotting. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Preparation of DNA nanoswitches Basic Protocol 2: Detection of microRNAs from total RNA samples Support Protocol 1: Optional nanoswitch purification by PEG precipitation Support Protocol 2: Optional nanoswitch purification by liquid chromatography.