https://scholars.lib.ntu.edu.tw/handle/123456789/580738
Title: | Hybridization chain reactions targeting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) | Authors: | Wu T.-H Chang C.-C Yang C.-H Lin W.-Y Ee T.J CHII-WANN LIN |
Keywords: | apoptin; nucleocapsid phosphoprotein; ribonuclease P; unclassified drug; complementary DNA; algorithm; Article; computer model; controlled study; gel electrophoresis; gene amplification; gene locus; gene sequence; human; hybridization chain reaction; molecular weight; nonhuman; Severe acute respiratory syndrome coronavirus 2; simulation; Betacoronavirus; computer simulation; Coronavirus infection; genetics; isolation and purification; mass screening; nucleic acid amplification; pandemic; polymerase chain reaction; procedures; virology; virus pneumonia; Betacoronavirus; Computer Simulation; Coronavirus Infections; DNA, Complementary; Humans; Mass Screening; Nucleic Acid Amplification Techniques; Pandemics; Pneumonia, Viral; Polymerase Chain Reaction; Ribonuclease P | Issue Date: | 2020 | Journal Volume: | 21 | Journal Issue: | 9 | Source: | International Journal of Molecular Sciences | Abstract: | 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. ? 2020 by the authors. Licensee MDPI, Basel, Switzerland. |
URI: | https://www.scopus.com/inward/record.uri?eid=2-s2.0-85084220661&doi=10.3390%2fijms21093216&partnerID=40&md5=d68f46046bc32aad12997581d3b1878a https://scholars.lib.ntu.edu.tw/handle/123456789/580738 |
ISSN: | 16616596 | DOI: | 10.3390/ijms21093216 |
Appears in Collections: | 電機工程學系 |
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