Construction of SHERLOCK-based sgRNA for SARS-CoV-2 Diagnostics from Indonesia

Handling a pandemic requires high sensitivity, high specificity, simple, fast, and flexible tests. How- ever, conventional test methods (RT-PCR and Rapid Antigen) have weaknesses in test efficiency. Specific High sensitivity Enzymatic Reporter un-LOCKing (SHERLOCK), is a new technology that can dete...

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Bibliographic Details
Published in:The New microbiologica 2022-07, Vol.45 (3), p.173-180
Main Authors: Narulita, Erlia, Widianto, Agung Haris, Wathon, Syubbanul
Format: Article
Language:English
Subjects:
Antigens
COVID-19 - diagnosis
COVID-19 Testing
Genomics
Humans
Indonesia - epidemiology
Locking
Melting point
Melting points
Molecular docking
Molecular Docking Simulation
Mutation
New technology
Nucleic acids
Optimization
Proteins
Proteomics
Sample preparation
SARS-CoV-2 - genetics
Sensitivity
Sensitivity analysis
Sensitivity and Specificity
Severe acute respiratory syndrome
Severe acute respiratory syndrome coronavirus 2
Spike Glycoprotein, Coronavirus
Spike protein
Viral diseases
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Summary:Handling a pandemic requires high sensitivity, high specificity, simple, fast, and flexible tests. How- ever, conventional test methods (RT-PCR and Rapid Antigen) have weaknesses in test efficiency. Specific High sensitivity Enzymatic Reporter un-LOCKing (SHERLOCK), is a new technology that can detect nucleic acids even with limited sample preparation, but with high sensitivity, high spec- ificity, rapidly, and flexibly. The key to the specificity of the SHERLOCK diagnostic method is the single guide RNA (sgRNA). The purpose of this study was to analyze the design of the SHERLOCK sgRNA, which has optimum potential to be used as a Cas13a marker to recognize the spike protein gene of the Receptor Binding Domain of the SARS-CoV-2 strain from Indonesia. The method used was an in-silico approach using genomic and proteomic data and molecular docking. This study used a sample of 37 genomic data representing 86 types of SARS-CoV-2 spike protein mutations in Indonesia. Based on the docking candidate results, sgRNA8 has the lowest energy to bind to the viral protospacer target SARS-CoV-2 and a high melting point value at 70.3°C, indicating that the sgRNA8 chain is the optimal candidate for sgRNA.
ISSN:1121-7138