Detection of Coronaviruses Using RNA Toehold Switch Sensors
Abstract
:1. Introduction
2. Results
2.1. RNA Toehold Switch Sensor Design and Screening
2.2. Sensitivity of Toehold Switch Sensors
2.3. Connecting RT-LAMP with RNA Toehold Reaction
2.4. Sensitivity of the Modified RT-LAMP-Coupled Toehold Reaction on Contrived Samples
2.5. Reduction of the Overall Turnaround Time
2.6. Specificity of the Modified RT-LAMP-Coupled Toehold Reaction
3. Discussion
4. Materials and Methods
4.1. Toehold Switch Design
4.2. Paper Preparation
4.3. Cell-Free Reaction
4.4. Synthetic Target RNA Synthesis and Toehold Switch Sensor Screening
4.5. Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP)
4.6. Saliva Inactivation with Heat and Stabilization Solution
4.7. Specificity Test
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
Abbreviations
RT-LAMP | Reverse transcription loop-mediated isothermal amplification |
rRT-PCR | Real-time reverse transcription polymerase chain reaction |
NASBA | Nucleic acid sequence-based amplification |
RBS | Ribosome binding site |
CPRG | Chlorophenol red-D-galactopyranoside |
CPR | Chlorophenol red |
URT | Upper respiratory tract sample |
LRT | Lower respiratory tract sample |
FIP | Forward inner primer |
BIP | Backward inner primer |
RPA | Recombinase polymerase amplification |
TX | in vitro transcription |
TL | in vitro translation |
References
- Corman, V.M.; Eckerle, I.; Bleicker, T.; Zaki, A.; Landt, O.; Eschbach-Bludau, M.; van Boheemen, S.; Gopal, R.; Ballhause, M.; Bestebroer, T.M.; et al. Detection of a novel human coronavirus by real-time reverse-transcription polymerase chain reaction. Eurosurveillance 2012, 17, 20285. [Google Scholar] [CrossRef] [Green Version]
- Heo, N.S.; Oh, S.Y.; Ryu, M.Y.; Baek, S.H.; Park, T.J.; Choi, C.; Huh, Y.S.; Park, J.P. Affinity Peptide-guided Plasmonic Biosensor for Detection of Noroviral Protein and Human Norovirus. Biotechnol. Bioprocess Eng. 2019, 24, 318–325. [Google Scholar] [CrossRef]
- Woo, C.H.; Jang, S.; Shin, G.; Jung, G.Y.; Lee, J.W. Sensitive fluorescence detection of SARS-CoV-2 RNA in clinical samples via one-pot isothermal ligation and transcription. Nat. Biomed. Eng. 2020, 4, 1168–1179. [Google Scholar] [CrossRef] [PubMed]
- Corman, V.M.; Landt, O.; Kaiser, M.; Molenkamp, R.; Meijer, A.; Chu, D.K.; Bleicker, T.; Brünink, S.; Schneider, J.; Schmidt, M.L.; et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Eurosurveillance 2020, 25, 2000045. [Google Scholar] [CrossRef] [Green Version]
- Guo, L.; Ren, L.; Yang, S.; Xiao, M.; Chang, D.; Yang, F.; Dela Cruz, C.S.; Wang, Y.; Wu, C.; Xiao, Y.; et al. Profiling Early Humoral Response to Diagnose Novel Coronavirus Disease (COVID-19). Clin. Infect. Dis. 2020, 71, 778–785. [Google Scholar] [CrossRef] [Green Version]
- Patrick, D.M.; Petric, M.; Skowronski, D.M.; Guasparini, R.; Booth, T.F.; Krajden, M.; McGeer, P.; Bastien, N.; Gustafson, L.; Dubord, J.; et al. An Outbreak of Human Coronavirus OC43 Infection and Serological Cross-reactivity with SARS Coronavirus. Can. J. Infect. Dis. Med. Microbiol. 2006, 17, 330–336. [Google Scholar] [CrossRef]
- Meyer, B.; Drosten, C.; Müller, M.A. Serological assays for emerging coronaviruses: Challenges and pitfalls. Virus Res. 2014, 194, 175–183. [Google Scholar] [CrossRef]
- Lobato, I.M.; O’Sullivan, C.K. Recombinase polymerase amplification: Basics, applications and recent advances. Trends Analyt. Chem. 2018, 98, 19–35. [Google Scholar] [CrossRef] [PubMed]
- Gootenberg, J.S.; Abudayyeh, O.O.; Lee, J.W.; Essletzbichler, P.; Dy, A.J.; Joung, J.; Verdine, V.; Donghia, N.; Daringer, N.M.; Freije, C.A.; et al. Nucleic acid detection with CRISPR-Cas13a/C2c2. Science 2017, 356, 438–442. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Broughton, J.P.; Deng, X.; Yu, G.; Fasching, C.L.; Servellita, V.; Singh, J.; Miao, X.; Streithorst, J.A.; Granados, A.; Sotomayor-Gonzalez, A.; et al. CRISPR-Cas12-based detection of SARS-CoV-2. Nat. Biotechnol. 2020, 38, 870–874. [Google Scholar] [CrossRef] [Green Version]
- Pardee, K.; Green, A.A.; Ferrante, T.; Cameron, D.E.; DaleyKeyser, A.; Yin, P.; Collins, J.J. Paper-based synthetic gene networks. Cell 2014, 159, 940–954. [Google Scholar] [CrossRef] [Green Version]
- Pardee, K.; Green, A.A.; Takahashi, M.K.; Braff, D.; Lambert, G.; Lee, J.W.; Ferrante, T.; Ma, D.; Donghia, N.; Fan, M.; et al. Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components. Cell 2016, 165, 1255–1266. [Google Scholar] [CrossRef] [Green Version]
- Takahashi, M.K.; Tan, X.; Dy, A.J.; Braff, D.; Akana, R.T.; Furuta, Y.; Donghia, N.; Ananthakrishnan, A.; Collins, J.J. A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers. Nat. Commun. 2018, 9, 3347. [Google Scholar] [CrossRef]
- Hong, F.; Ma, D.; Wu, K.; Mina, L.A.; Luiten, R.C.; Liu, Y.; Yan, H.; Green, A.A. Precise and programmable detection of mutations using ultraspecific riboregulators. Cell 2020, 180, 1018–1032.e16. [Google Scholar] [CrossRef]
- Green, A.A.; Silver, P.A.; Collins, J.J.; Yin, P. Toehold switches: De-novo-designed regulators of gene expression. Cell 2014, 159, 925–939. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Kudla, G.; Murray, A.W.; Tollervey, D.; Plotkin, J.B. Coding-sequence determinants of gene expression in Escherichia coli. Science 2009, 324, 255–258. [Google Scholar] [CrossRef] [Green Version]
- Cianfrocco, M.A.; Lahiri, I.; DiMaio, F.; Leschziner, A.E. Cryoem-cloud-tools: A software platform to deploy and manage cryo-EM jobs in the cloud. J. Struct. Biol. 2018, 203, 230–235. [Google Scholar] [CrossRef]
- Zadeh, J.N.; Wolfe, B.R.; Pierce, N.A. Nucleic acid sequence design via efficient ensemble defect optimization. J. Comput. Chem. 2011, 32, 439–452. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Corman, V.M.; Albarrak, A.M.; Omrani, A.S.; Albarrak, M.M.; Farah, M.E.; Almasri, M.; Muth, D.; Sieberg, A.; Meyer, B.; Assiri, A.M.; et al. Viral shedding and antibody response in 37 patients with middle east respiratory syndrome coronavirus infection. Clin. Infect. Dis. 2016, 62, 477–483. [Google Scholar] [CrossRef] [Green Version]
- Pan, Y.; Zhang, D.; Yang, P.; Poon, L.L.M.; Wang, Q. Viral load of SARS-CoV-2 in clinical samples. Lancet Infect. Dis. 2020, 20, 411–412. [Google Scholar] [CrossRef]
- Tomita, N.; Mori, Y.; Kanda, H.; Notomi, T. Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection of products. Nat. Protoc. 2008, 3, 877–882. [Google Scholar] [CrossRef] [PubMed]
- Notomi, T.; Okayama, H.; Masubuchi, H.; Yonekawa, T.; Watanabe, K.; Amino, N.; Hase, T. Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. 2000, 28, E63. [Google Scholar] [CrossRef] [Green Version]
- Nagamine, K.; Hase, T.; Notomi, T. Accelerated reaction by loop-mediated isothermal amplification using loop primers. Mol. Cell. Probes 2002, 16, 223–229. [Google Scholar] [CrossRef]
- Pasomsub, E.; Watcharananan, S.P.; Boonyawat, K.; Janchompoo, P.; Wongtabtim, G.; Suksuwan, W.; Sungkanuparph, S.; Phuphuakrat, A. Saliva sample as a non-invasive specimen for the diagnosis of coronavirus disease 2019: A cross-sectional study. Clin. Microbiol. Infect. 2020, in press. [Google Scholar] [CrossRef] [PubMed]
- Wyllie, A.L.; Fournier, J.; Casanovas-Massana, A.; Campbell, M.; Tokuyama, M.; Vijayakumar, P.; Warren, J.L.; Geng, B.; Muenker, M.C.; Moore, A.J.; et al. Saliva or Nasopharyngeal Swab Specimens for Detection of SARS-CoV-2. N. Engl. J. Med. 2020, 383, 1283–1286. [Google Scholar] [CrossRef]
- Myhrvold, C.; Freije, C.A.; Gootenberg, J.S.; Abudayyeh, O.O.; Metsky, H.C.; Durbin, A.F.; Kellner, M.J.; Tan, A.L.; Paul, L.M.; Parham, L.A.; et al. Field-deployable viral diagnostics using CRISPR-Cas13. Science 2018, 360, 444–448. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Meyerson, N.R.; Yang, Q.; Clark, S.K.; Paige, C.L.; Fattor, W.T.; Gilchrist, A.R.; Barbachano-Guerrero, A.; Sawyer, S.L. A community-deployable SARS-CoV-2 screening test using raw saliva with 45 minutes sample-to-results turnaround. MedRxiv 2020. [Google Scholar] [CrossRef]
- Pham, H.L.; Wong, A.; Chua, N.; Teo, W.S.; Yew, W.S.; Chang, M.W. Engineering a riboswitch-based genetic platform for the self-directed evolution of acid-tolerant phenotypes. Nat. Commun. 2017, 8, 411. [Google Scholar] [CrossRef] [PubMed]
- Jaroenram, W.; Kiatpathomchai, W.; Flegel, T.W. Rapid and sensitive detection of white spot syndrome virus by loop-mediated isothermal amplification combined with a lateral flow dipstick. Mol. Cell. Probes 2009, 23, 65–70. [Google Scholar] [CrossRef]
- Pardee, K.; Slomovic, S.; Nguyen, P.Q.; Lee, J.W.; Donghia, N.; Burrill, D.; Ferrante, T.; McSorley, F.R.; Furuta, Y.; Vernet, A.; et al. Portable, On-Demand Biomolecular Manufacturing. Cell 2016, 167, 248–259. [Google Scholar] [CrossRef] [PubMed] [Green Version]
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Park, S.; Lee, J.W. Detection of Coronaviruses Using RNA Toehold Switch Sensors. Int. J. Mol. Sci. 2021, 22, 1772. https://doi.org/10.3390/ijms22041772
Park S, Lee JW. Detection of Coronaviruses Using RNA Toehold Switch Sensors. International Journal of Molecular Sciences. 2021; 22(4):1772. https://doi.org/10.3390/ijms22041772
Chicago/Turabian StylePark, Soan, and Jeong Wook Lee. 2021. "Detection of Coronaviruses Using RNA Toehold Switch Sensors" International Journal of Molecular Sciences 22, no. 4: 1772. https://doi.org/10.3390/ijms22041772