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Open AccessCommunication

Hybridization Chain Reactions Targeting the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

1
Department Biomedical Engineering, National Taiwan University, Taipei 10617, Taiwan
2
Department of Medical Biotechnology and Laboratory Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
3
Graduate Institute of Bio-Electronics and Bio-Informatics, National Taiwan University, Taipei 10617, Taiwan
4
Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu 30011, Taiwan
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2020, 21(9), 3216; https://doi.org/10.3390/ijms21093216
Received: 19 April 2020 / Revised: 28 April 2020 / Accepted: 29 April 2020 / Published: 1 May 2020
(This article belongs to the Section Molecular Microbiology)
In this work, hybridization chain reactions (HCRs) toward Severe Acute Respiratory Syndrome Coronavirus 2 (SARS–CoV-2) nucleocapsid phosphoproteins gene loci and human RNase P are proposed to provide an isothermal amplification screening tool. The proposed chain reactions target the complementary DNA (cDNA) of SARS–CoV-2, with loci corresponding to gold-standard polymerase chain reaction (PCR) loci. Four hybridization chain reaction reactions are demonstrated herein, targeting N1/N2/N3 loci and human RNase P. The design of the hybridization chain reaction, herein, is assisted with an algorithm. The algorithm helps to search target sequences with low local secondary structure and high hybridization efficiency. The loop domain of the fuel hairpin molecule H1 and H2, which are the tunable segments in such reactions, are used as an optimization parameter to improve the hybridization efficiency of the chain reaction. The algorithm-derived HCR reactions were validated with gel electrophoresis. All proposed reactions exhibit a hybridization complex with a molecular mass >1.5k base pairs, which is clear evidence of chain reaction. The hybridization efficiency trend revealed by gel electrophoresis corresponds nicely to the simulated data from the algorithm. The HCR reactions and the corresponding algorithm serve as a basis to further SARS–CoV-2 sensing applications and facilitate better screening strategies for the prevention of on-going pandemics. View Full-Text
Keywords: SARS–CoV-2; hybridization chain reaction; algorithm SARS–CoV-2; hybridization chain reaction; algorithm
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Wu, T.-H.; Chang, C.-C.; Yang, C.-H.; Lin, W.-Y.; Ee, T.J.; Lin, C.-W. Hybridization Chain Reactions Targeting the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Int. J. Mol. Sci. 2020, 21, 3216.

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