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

Abstract

Viral detection is critical for controlling disease spread and progression. Recent emerging threats including the Zika and Ebola virus outbreaks highlight the cost and difficulty in responding rapidly. In low-resource areas, a key obstacle is quick and accurate detection of viruses near the point of care. To address these challenges, we develop a platform for low-cost and rapid detection of viral RNA with DNA nanoswitches designed to mechanically reconfigure in response to specific viruses. Using Zika virus as a model system, we show non-enzymatic detection of viral RNA to the attomole level, with selective and multiplexed detection between related viruses and viral strains. For clinical-level sensitivity in biological fluids, we paired the assay with a sample preparation step using either RNA extraction or isothermal preamplification. Our assay can be performed with minimal or no lab infrastructure, and is readily adaptable (with ~24-hour development time) to detect other viruses. Given this versatility, we expect that further development and field implementation will improve our ability to detect emergent viral threats and ultimately limit their impact.

Ribonuclease-Responsive DNA Nanoswitches

“…For use in a biological context, the biostability of DNA nanoswitches is an important factor. In previous work, we and others have demonstrated the detection of nucleic acid and protein biomarkers in 10%–20% serum, 9 , 11 as well as in human urine, 12 showing the inherent stability of DNA nanoswitches for use in real-life applications. Results in FBS and cell lysates demonstrated in this work further establish the potential of the DNA nanoswitch assay in in vitro applications.…”

“…Our DNA nanoswitch is a versatile biomolecular platform with broad applications. 10 , 12 – 14 , 17 The use of RNase provides an additional tool to manipulate DNA nanoswitches. Our DNA nanoswitch assay adds to the suite of available techniques for monitoring RNase activity.…”

Biosensors: frontiers in rapid detection of COVID-19

“…This assay requires only a sample preparation step using either RNA extraction or isothermal pre-amplification. Recently, similar authors also evaluated such automated DNA nano-switches to detect SARS-CoV-2 RNA in human saliva (Zhou et al 2020a ). A novel DNA hydrogel formation by isothermal amplification of complementary target (DhITACT-TR) system has been successfully used for detection of the MERS virus, which is highly sensitive and could be diagnosed by the naked eye, as well as fluorescent detection within a short time (Fig.…”

Application of DNA-Nanosensor for Environmental Monitoring: Recent Advances and Perspectives

“…Peptide nucleic acid and DNA/RNA-functionalized NPs have been used for detection of the SARS-CoV-2 (COVID 19) using plasmonic colorimetric, localized surface plasmon resonance, and plasmonic photothermal technique–based approach [ 134 ]. DNA nanoswitches have been designed to detect highly infectious pathogenic zika virus and SARS-CoV-2 viruses in saliva samples [ 135 ] (Fig. 9 ).…”

“…The asterisk denotes a band of contaminating cellular DNA following RNA isolation. Reproduced with permission from Zhou et al, American Association for the Advancement of Science [ 135 ] …”