Programmable low-cost DNA-based platform for viral RNA detection

Lifeng Zhou; Arun Richard Chandrasekaran; Jibin Abraham Punnoose; Gaston Bonenfant; Stephon Charles; Oksana Levchenko; Pheonah Badu; Cassandra Cavaliere; Cara T. Pager; Ken Halvorsen

The functionality of our DNA nanoswitches is largely enabled by DNA nanotechnology, which has become a well-established field that uses DNA as a functional material to fabricate nanostructures. 43, 44 Biosensing is a particularly promising application of DNA nanotechnology, 45 and reconfigurable DNA devices 46 have been demonstrated for the detection of DNA, 46 RNA, 47,48 proteins, 49 and pH. 50 However, most designs are complex and require laborious readout with advanced microscopy that reduces their practicality. A few approaches have overcome this practicality hurdle to provide widely useful solutions to problems in biological imaging (e.g. DNA-PAINT in super-resolution microscopy 51 and DNA scaffolds for NMR 52 and cryo-EM 53 ) and biosensing (e.g. detection of lysosomal disorders 54 and mapping cellular endocytic pathways 55 ). Our DNA nanoswitches take a reductionist approach, resulting in assays that are robust and sensitive, yet simple to adapt and don't require multiple steps or expensive equipment. With this work, we add viral detection to the existing suite of DNA nanoswitch assays that already includes protein 40 Our simple DNA nanoswitch-based assay for detection of viral RNA overcomes some limitations of currently available methods for clinical detection of RNA viruses in resource-limited areas. These challenges include 1) robust detection without enzymes or equipment, 2) maintaining low-cost and simplicity, and 3) providing specificity and versatility.