Rapidemic, a versatile and label-free DNAzyme-based platform for visual nucleic acid detection

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

Abstract In the last three decades, there have been recurring outbreaks of infectious diseases, brought to light with the recent outbreak of coronavirus disease 2019 (COVID-19). Attempts to effectively contain the spread of infectious diseases have been hampered by the lack of rapidly adaptable, accurate, and accessible point-of-care diagnostic testing. In this study, we present a novel design of a label-free DNAzyme-based detection method called Rapidemic. This assay combines recombinase polymerase amplification (RPA) with linear strand-displacement amplification (LSDA) and guanine-quadruplex (GQ) DNAzyme-catalysed colour-changing reaction. The colorimetry basis of the signal readout omits the need for extensive instrumentation. Moreover, the primer-based sequence detection of RPA gives Rapidemic a potential to be rapidly adapted to target a new sequence. As a proof of concept, we developed the assay to detect isolated genomic DNA of Saccharomyces cerevisiae . The use of low-pH buffers and the optimization of the dilution rates from each preceding reaction to the next showed to be successful strategies to enable visible detection with this method. These findings demonstrate for the first time that a label-free DNAzyme-based detection method can be coupled to RPA and LSDA for nucleic acid detection.

Authors 16

1. Marijn van den Brink Aachen

   Leiden University

   Affiliation as printed

   Leiden University

2. Sebastian Tommi Tandar Aachen

   Leiden University

   Affiliation as printed

   Leiden University

3. Tim A. P. van den Akker Aachen

   Leiden University

   Affiliation as printed

   Leiden University

4. Sinisha Jovikj Aachen

   Leiden University

   Affiliation as printed

   Leiden University

5. Violette Defourt Aachen

   Leiden University

   Affiliation as printed

   Leiden University

6. Tom G. B. Langelaar Aachen

   Leiden University

   Affiliation as printed

   Leiden University

7. Tijn O. Delzenne Aachen

   Leiden University

   Affiliation as printed

   Leiden University

8. Kelly van Strien Aachen

   Leiden University

   Affiliation as printed

   Leiden University

9. Amber W. Schonk Aachen

   Leiden University

   Affiliation as printed

   Leiden University

10. Aukje J. A. M. Beers Aachen

    Leiden University

    Affiliation as printed

    Leiden University

11. Eugene Golov Aachen

    Leiden University

    Affiliation as printed

    Leiden University

12. Güniz Özer Bergman Aachen

    Leiden University

    Affiliation as printed

    Leiden University

13. Joey J. W. D. Meijdam Aachen

    Leiden University

    Affiliation as printed

    Leiden University

14. Marjolein E. Crooijmans Aachen

    Leiden University

    Affiliation as printed

    Leiden University

15. Dennis Claessen corresponding Aachen

    Leiden University

    Affiliation as printed

    Leiden University

16. Johannes H. DE WINDE corresponding Aachen

    Leiden University

    Affiliation as printed

    Leiden University