scholarly journals A Review on the Development of Gold and Silver Nanoparticles-Based Biosensor as a Detection Strategy of Emerging and Pathogenic RNA Virus

Sensors ◽  
2021 ◽  
Vol 21 (15) ◽  
pp. 5114
Author(s):  
Nadiah Ibrahim ◽  
Nur Diyana Jamaluddin ◽  
Ling Ling Tan ◽  
Nurul Yuziana Mohd Mohd Yusof
Keyword(s):  
Nucleic Acid ◽  
Biological Activities ◽  
Electrochemical Techniques ◽  
Immunological Methods ◽  
Viral Diseases ◽  
Clinical Samples ◽  
Test Accuracy ◽  
Risk Of Death ◽  
Detection Strategy ◽  
Signal Amplifier

The emergence of highly pathogenic and deadly human coronaviruses, namely SARS-CoV and MERS-CoV within the past two decades and currently SARS-CoV-2, have resulted in millions of human death across the world. In addition, other human viral diseases, such as mosquito borne-viral diseases and blood-borne viruses, also contribute to a higher risk of death in severe cases. To date, there is no specific drug or medicine available to cure these human viral diseases. Therefore, the early and rapid detection without compromising the test accuracy is required in order to provide a suitable treatment for the containment of the diseases. Recently, nanomaterials-based biosensors have attracted enormous interest due to their biological activities and unique sensing properties, which enable the detection of analytes such as nucleic acid (DNA or RNA), aptamers, and proteins in clinical samples. In addition, the advances of nanotechnologies also enable the development of miniaturized detection systems for point-of-care (POC) biosensors, which could be a new strategy for detecting human viral diseases. The detection of virus-specific genes by using single-stranded DNA (ssDNA) probes has become a particular interest due to their higher sensitivity and specificity compared to immunological methods based on antibody or antigen for early diagnosis of viral infection. Hence, this review has been developed to provide an overview of the current development of nanoparticles-based biosensors that target pathogenic RNA viruses, toward a robust and effective detection strategy of the existing or newly emerging human viral diseases such as SARS-CoV-2. This review emphasizes the nanoparticles-based biosensors developed using noble metals such as gold (Au) and silver (Ag) by virtue of their powerful characteristics as a signal amplifier or enhancer in the detection of nucleic acid. In addition, this review provides a broad knowledge with respect to several analytical methods involved in the development of nanoparticles-based biosensors for the detection of viral nucleic acid using both optical and electrochemical techniques.

Advances in Molecular Technologies and Platforms for the Diagnosis of Infectious Diseases

2013 ◽  
Vol 810 ◽  
pp. 77-125
Author(s):  
M. Rubayet Hasan
Keyword(s):  
Nucleic Acid ◽  
Infectious Diseases ◽  
Potential Method ◽  
Diagnostic Methods ◽  
Control Measures ◽  
Nucleic Acid Amplification ◽  
Microbial Pathogens ◽  
Immunological Methods ◽  
Clinical Samples ◽  
Single Test

nfectious microbial pathogens constitute the largest cause of morbidity and mortality worldwide. Early diagnosis and rapid infection control measures can lead to improved outcomes, earlier discharges and reduced nosocomial infections. Conventional diagnostic methods for infectious diseases such as microscopy, culture, and immunological methods, in most cases, are not universally applicable, less sensitive and could take from days to months to complete depending on the pathogen. Molecular assays based on nucleic acids such as polymerase chain reaction (PCR) have improved the sensitivity, specificity and turn-around time in diagnostic microbiology laboratories. These tests are particularly important to detect very low levels of pathogens in clinical samples, and for organisms that have long half-lives or are non-culturable. However, individual molecular tests are available for only a limited number of the more common infectious agents. Moreover, infectious disease events arising from novel pathogens or genetic variants have significantly increased, recently, for which, routine diagnostic methods are not yet available. Therefore, molecular methods and technologies capable of detecting multiple pathogens in a single test have become available over the last few years. Although, these methods are based on the conventional nucleic acid amplification and hybridization chemistry, enhanced multiplexing capability has been achieved through innovations in nucleic acid labeling techniques, and post-amplification analytic methods and instrumentation. The availability of these test kits brought a new level of convenience to the physicians ordering practices, and to the laboratory personnel, as they require very little hands on time. However, these tests are yet unaffordable to many laboratories, and in many cases, the sensitivity is poor compared to that of single-target, real-time PCR assays. Looking into the future, the revolutionary, next generation sequencing (NGS) technology is now being considered as a potential method for rapid identification of hundreds of pathogens, in an unbiased manner, with a single test that could significantly benefit patients who are critically ill with undiagnosed disease.

scholarly journals A CRISPR-Cas autocatalysis-driven feedback amplification network for supersensitive DNA diagnostics

2021 ◽  
Vol 7 (5) ◽  
pp. eabc7802
Author(s):  
Kai Shi ◽  
Shiyi Xie ◽  
Renyun Tian ◽  
Shuo Wang ◽  
Qin Lu ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Genomic Dna ◽  
Reaction Network ◽  
Clinical Samples ◽  
Great Promise ◽  
Base Specificity ◽  
Nucleotide Mutation ◽  
Positive Feedback Circuit ◽  
Stringent Target ◽  
And Function

Artificial nucleic acid circuits with precisely controllable dynamic and function have shown great promise in biosensing, but their utility in molecular diagnostics is still restrained by the inability to process genomic DNA directly and moderate sensitivity. To address this limitation, we present a CRISPR-Cas–powered catalytic nucleic acid circuit, namely, CRISPR-Cas–only amplification network (CONAN), for isothermally amplified detection of genomic DNA. By integrating the stringent target recognition, helicase activity, and trans-cleavage activity of Cas12a, a Cas12a autocatalysis-driven artificial reaction network is programmed to construct a positive feedback circuit with exponential dynamic in CONAN. Consequently, CONAN achieves one-enzyme, one-step, real-time detection of genomic DNA with attomolar sensitivity. Moreover, CONAN increases the intrinsic single-base specificity of Cas12a, and enables the effective detection of hepatitis B virus infection and human bladder cancer–associated single-nucleotide mutation in clinical samples, highlighting its potential as a powerful tool for disease diagnostics.

scholarly journals GraphBind: protein structural context embedded rules learned by hierarchical graph neural networks for recognizing nucleic-acid-binding residues

2021 ◽  
Author(s):  
Ying Xia ◽  
Chun-Qiu Xia ◽  
Xiaoyong Pan ◽  
Hong-Bin Shen
Keyword(s):  
Neural Networks ◽  
Nucleic Acid ◽  
Biological Activities ◽  
New Drugs ◽  
Superior Performance ◽  
Nucleic Acid Binding ◽  
Hierarchical Graph ◽  
Binding Residue ◽  
Binding Residues ◽  
Graph Neural Networks

Abstract Knowledge of the interactions between proteins and nucleic acids is the basis of understanding various biological activities and designing new drugs. How to accurately identify the nucleic-acid-binding residues remains a challenging task. In this paper, we propose an accurate predictor, GraphBind, for identifying nucleic-acid-binding residues on proteins based on an end-to-end graph neural network. Considering that binding sites often behave in highly conservative patterns on local tertiary structures, we first construct graphs based on the structural contexts of target residues and their spatial neighborhood. Then, hierarchical graph neural networks (HGNNs) are used to embed the latent local patterns of structural and bio-physicochemical characteristics for binding residue recognition. We comprehensively evaluate GraphBind on DNA/RNA benchmark datasets. The results demonstrate the superior performance of GraphBind than state-of-the-art methods. Moreover, GraphBind is extended to other ligand-binding residue prediction to verify its generalization capability. Web server of GraphBind is freely available at http://www.csbio.sjtu.edu.cn/bioinf/GraphBind/.

DNA Nanosieve-Based Regenerative Electrochemical Biosensor Utilizing Nucleic Acid Flexibility for Accurate Allele Typing in Clinical Samples

ACS Sensors ◽  
2021 ◽  
Vol 6 (3) ◽  
pp. 1348-1356
Author(s):  
Jin-Yuan Chen ◽  
Liang-Yong Yang ◽  
Zhou-Jie Liu ◽  
Qing-Xia Wei ◽  
Ying Zhang ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Electrochemical Biosensor ◽  
Clinical Samples

scholarly journals CRISPR is a useful biological tool for detecting nucleic acid of SARS-CoV-2 in human clinical samples

2021 ◽  
pp. 111772
Author(s):  
Md. Rashidur Rahman ◽  
Md. Amjad Hossain ◽  
Md. Mozibullah ◽  
Fateh Al Mujib ◽  
Afrina Afrose ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Clinical Samples ◽  
Biological Tool

Nucleic acid related compounds. 40. Synthesis and biological activities of 5-alkynyluracil nucleosides

1983 ◽  
Vol 26 (5) ◽  
pp. 661-666 ◽  
Author(s):  
Erik De Clercq ◽  
Johan Descamps ◽  
Jan Balzarini ◽  
Jerzy Giziewicz ◽  
Philip J. Barr ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Biological Activities ◽  
Related Compounds

scholarly journals Imidazole: Having Versatile Biological Activities

2013 ◽  
Vol 2013 ◽  
pp. 1-12 ◽  
Author(s):  
Amita Verma ◽  
Sunil Joshi ◽  
Deepika Singh
Keyword(s):  
Natural Products ◽  
Nucleic Acid ◽  
Biological Activities ◽  
Imidazole Ring ◽  
Heterocyclic Ring ◽  
Heterocyclic Chemistry ◽  
The Past ◽  
Poorly Soluble ◽  
Anti Hiv ◽  
Imidazole Compounds

Imidazoles have occupied a unique position in heterocyclic chemistry, and its derivatives have attracted considerable interests in recent years for their versatile properties in chemistry and pharmacology. Imidazole is nitrogen-containing heterocyclic ring which possesses biological and pharmaceutical importance. Thus, imidazole compounds have been an interesting source for researchers for more than a century. The imidazole ring is a constituent of several important natural products, including purine, histamine, histidine, and nucleic acid. Being a polar and ionisable aromatic compound, it improves pharmacokinetic characteristics of lead molecules and thus is used as a remedy to optimize solubility and bioavailability parameters of proposed poorly soluble lead molecules. There are several methods used for the synthesis of imidazole-containing compounds, and also their various structure reactions offer enormous scope in the field of medicinal chemistry. The imidazole derivatives possess extensive spectrum of biological activities such as antibacterial, anticancer, antitubercular, antifungal, analgesic, and anti-HIV activities. This paper aims to review the biological activities of imidazole during the past years.

scholarly journals Comparative performance and cycle threshold values of 10 nucleic acid amplification tests for SARS-CoV-2 on clinical samples

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0252757
Author(s):  
Miyuki Mizoguchi ◽  
Sohei Harada ◽  
Koh Okamoto ◽  
Yoshimi Higurashi ◽  
Mahoko Ikeda ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Diagnostic Performance ◽  
Nucleic Acid Amplification ◽  
Clinical Samples ◽  
Nucleic Acid Amplification Tests ◽  
Cycle Threshold ◽  
E Gene ◽  
Viral Copy Number ◽  
Gene Test ◽  
Positive Results

Background A number of nucleic acid amplification tests (NAATs) for SARS-CoV-2 with different reagents have been approved for clinical use in Japan. These include research kits approved under emergency use authorization through simplified process to stabilize the supply of the reagents. Although these research kits have been increasingly used in clinical practice, limited data is available for the diagnostic performance in clinical settings. Methods We compared sensitivity, specificity, and cycle threshold (Ct) values obtained by NAATs using 10 kits approved in Japan including eight kits those receiving emergency use authorization using 69 frozen-stored clinical samples including 23 positive samples with various Ct values and 46 negative samples. Results Viral copy number of the frozen-stored samples determined with LightMix E-gene test ranged from 0.6 to 84521.1 copies/μL. While no false-positive results were obtained by any of these tests (specificity: 100% [95% CI, 88.9%-100%]), sensitivity of the nine tests ranged from 68.2% [95% CI, 45.1%-86.1%] to 95.5% [95% CI, 77.2%-99.9%] using LightMix E-gene test as the gold standard. All tests showed positive results for all samples with ≥100 copies/μL. Significant difference of Ct values even among tests amplifying the same genetic region (N1-CDC, N2) was also observed. Conclusion Difference in the diagnostic performance was observed among NAATs approved in Japan. Regarding diagnostic kits for emerging infectious diseases, a system is needed to ensure both rapidity of reagent supply and accuracy of diagnosis. Ct values, which are sometimes regarded as a marker of infectivity, are not interchangeable when obtained by different assays.

scholarly journals MicroRNAs Regulated by the LPS/TLR2 Immune Axis as Bona Fide Biomarkers for Diagnosis of Acute Leptospirosis

mSphere ◽  
2020 ◽  
Vol 5 (4) ◽  
Author(s):  
Charles Solomon Akino Mercy ◽  
Natarajaseenivasan Suriya Muthukumaran ◽  
Prema Velusamy ◽  
Palanisamy Bothammal ◽  
Krishnamoorthi Sumaiya ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Early Diagnosis ◽  
Infectious Diseases ◽  
Cellular Response ◽  
Biological Activities ◽  
Mapk Signaling ◽  
Functional Enrichment ◽  
Clinical Samples ◽  
Systemic Complications

ABSTRACT Leptospirosis remains a significant human health issue due to its systemic complications. Therefore, biomarkers that are more effective are urgently needed for the early diagnosis of leptospirosis. MicroRNAs (miRNAs) are evolutionarily conserved regulatory RNAs that have shown the potential to be used as biomarkers for diagnosis, prognosis, and therapy of infectious diseases. In this study, we performed an unbiased screen using the miRNome miRNA array to identify circulating miRNAs with the potential to serve as authentic biomarkers for early diagnosis of leptospirosis. Because leptospiral lipopolysaccharide (LPS) is the predominant leptospiral antigen and plays a vital role in immunological and biological activities, we used LPS treated and untreated in vitro (THP1 cells) and in vivo (BALB/c mice) surrogate models to identify the LPS-specific miRNAs. Differential expression analysis revealed 18 miRNAs to be associated strongly with LPS stimulation in THP1 cells. Of these, three (miR-let-7b-5p, miR-144-3p, and miR-21-5p) were observed to be present at increased levels in vivo. The identified miRNAs were validated for their biomarker potential using serum samples from leptospirosis-negative patients and patients with confirmed cases of leptospirosis. Identified miRNAs were able to discriminate the acute leptospiral infection from other febrile diseases with a test sensitivity and specificity of 93.2% and 88.19%, respectively. Gene functional enrichment and protein-protein interaction (PPI) network analysis revealed that the identified miRNAs play important roles in disease signal transduction, signaling by interleukins, the stress-activated protein kinase signaling cascade, the mitogen-activated protein kinase (MAPK) signaling pathway, and the cellular response to a transforming growth factor β (TGF-β) stimulus with a notable interconnection between these biological processes. IMPORTANCE Here, we used miRNAs that are differentially regulated by the LPS/TLR2 immune axis to devise a miRNA-based diagnosis for leptospirosis. The study established the role of the circulating stable miRNAs (miR-21-5p, miR-144-3p, and miR-let-7b-5p) as an early diagnostic marker for leptospirosis. These miRNAs can be used to diagnose acute leptospirosis and also to differentiate leptospiral infection from other bacterial and spirochetal infections, as proved by the use of human clinical samples. Thus, our findings indicate that miRNAs can play a crucial role in the diagnosis of infectious diseases, like leptospirosis, that are generally misdiagnosed.

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