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Santos DJAD, Oliveira TRD, Araújo GMD, Pott-Junior H, Melendez ME, Sabino EC, Leite OD, Faria RC. An electrochemical genomagnetic assay for detection of SARS-CoV-2 and Influenza A viruses in saliva. Biosens Bioelectron 2024; 255:116210. [PMID: 38537427 DOI: 10.1016/j.bios.2024.116210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/28/2024] [Accepted: 03/11/2024] [Indexed: 04/15/2024]
Abstract
Viral respiratory infections represent a major threat to the population's health globally. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19 disease and in some cases the symptoms can be confused with Influenza disease caused by the Influenza A viruses. A simple, fast, and selective assay capable of identifying the etiological agent and differentiating the diseases is essential to provide the correct clinical management to the patient. Herein, we described the development of a genomagnetic assay for the selective capture of viral RNA from SARS-CoV-2 and Influenza A viruses in saliva samples and employing a simple disposable electrochemical device for gene detection and quantification. The proposed method showed excellent performance detecting RNA of SARS-CoV-2 and Influenza A viruses, with a limit of detection (LoD) and limit of quantification (LoQ) of 5.0 fmol L-1 and 8.6 fmol L-1 for SARS-CoV-2, and 1.0 fmol L-1 and 108.9 fmol L-1 for Influenza, respectively. The genomagnetic assay was employed to evaluate the presence of the viruses in 36 saliva samples and the results presented similar responses to those obtained by the real-time reverse transcription-polymerase chain reaction (RT-PCR), demonstrating the reliability and capability of a method as an alternative for the diagnosis of COVID-19 and Influenza with point-of-care capabilities.
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Affiliation(s)
| | | | | | - Henrique Pott-Junior
- Department of Medicine, Federal University of São Carlos, São Carlos, SP, 13565-905, Brazil
| | | | - Ester Cerdeira Sabino
- Institute of Tropical Medicine, Faculty of Medicine, University of São Paulo, São Paulo, SP, 05403-000, Brazil
| | - Oldair Donizeti Leite
- Department of Chemistry, Federal University of São Carlos, São Carlos, SP, 13565-905, Brazil; Federal Technological University of Paraná, Campus Medianeira, Medianeira, PR, 85884-000, Brazil.
| | - Ronaldo Censi Faria
- Department of Chemistry, Federal University of São Carlos, São Carlos, SP, 13565-905, Brazil.
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2
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Yang Y, Wang Z, Xie H, Hu Y, Liu H. A SAW-Based Programmable Controlled RNA Detecting Device: Rapid In Situ Cytolysis-RNA Capture-RNA Release-PCR in One Mini Chamber. Adv Sci (Weinh) 2024:e2309744. [PMID: 38773709 DOI: 10.1002/advs.202309744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/19/2024] [Indexed: 05/24/2024]
Abstract
Viral RNA detection is crucial in preventing and treating early infectious diseases. Traditional methods of RNA detection require a large amount of equipment and technical personnel. In this study, proposed a programmable controlled surface acoustic wave (SAW)-based RNA detecting device has been proposed. The proposed device can perform the entire viral RNA detection process, including cell lysis by cell-microparticle collision through SAW-induced liquid whirling, RNA capture by SAW-suspended magnetic beads, RNA elution through SAW-induced high streaming force, and PCR thermal cycling through SAW-generated heat. The device has completed all RNA detection steps in one mini chamber, requiring only 489 µl reagents for RNA extraction, much smaller than the amount used in manual RNA extraction (2065 µl). The experimental results have shown that PCR results from the device are comparable to those achieved via commercial qPCR instrumental detection. This work has demonstrated the potential of SAW-based lab-on-a-chip devices for point-of-care testing and provided a novel approach for rapidly detecting infectious diseases.
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Affiliation(s)
- Yupeng Yang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518000, P. R. China
- University of Jinan, Jinan, 250022, P. R. China
| | - Zenan Wang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518000, P. R. China
| | - Hetao Xie
- University of Jinan, Jinan, 250022, P. R. China
| | - Ying Hu
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518000, P. R. China
| | - Hong Liu
- University of Jinan, Jinan, 250022, P. R. China
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3
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He W, Li X, Li X, Guo M, Zhang M, Hu R, Li M, Ding S, Yan Y. Split activator of CRISPR/Cas12a for direct and sensitive detection of microRNA. Anal Chim Acta 2024; 1303:342477. [PMID: 38609257 DOI: 10.1016/j.aca.2024.342477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/29/2024] [Accepted: 03/13/2024] [Indexed: 04/14/2024]
Abstract
CRISPR/Cas12a-based nucleic acid assays have been increasingly used for molecular diagnostics. However, most current CRISPR/Cas12a-based RNA assays require the conversion of RNA into DNA by preamplification strategies, which increases the complexity of detection. Here, we found certain chimeric DNA-RNA hybrid single strands could activate the trans-cleavage activity of Cas12a, and then discovered the activating effect of split ssDNA and RNA when they are present simultaneously. As proof of concept, split nucleic acid-activated Cas12a (SNA-Cas12a) strategy was developed for direct detection of miR-155. By adding a short ssDNA to the proximal end of the crRNA spacer sequence, we realized the direct detection of RNA targets using Cas12a. With the assistance of ssDNA, we extended the limitation that CRISPR/Cas12a cannot be activated by RNA targets. In addition, by taking advantage of the programmability of crRNA, the length of its binding to DNA and RNA was optimized to achieve the optimal efficiency in activating Cas12a. The SNA-Cas12a method enabled sensitive miR-155 detection at pM level. This method was simple, rapid, and specific. Thus, we proposed a new Cas12a-based RNA detection strategy that expanded the application of CRISPR/Cas12a.
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Affiliation(s)
- Wen He
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Xinyu Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Xinmin Li
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, 400021, PR China
| | - Minghui Guo
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Mengxuan Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Ruiwei Hu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Menghan Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yurong Yan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
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4
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Moço ACR, Gomide JAL, Flauzino JMR, Brussasco JG, Luz LFG, Soares MMCN, Madurro JM, Brito-Madurro AG. Fentogram electrochemical detection of HIV RNA based on graphene quantum dots and gold nanoparticles. J Pharm Biomed Anal 2024; 242:116025. [PMID: 38422670 DOI: 10.1016/j.jpba.2024.116025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/29/2024] [Accepted: 02/07/2024] [Indexed: 03/02/2024]
Abstract
This work reports the construction of an HIV-specific genosensor through the modification of carbon screen-printed electrodes (CSPE) with graphene quantum dots decorated with L-cysteine and gold nanoparticles (cys-GQDs/AuNps). Cys-GQDs were characterized by FT-IR and UV-vis spectra and electronic properties of the modified electrodes were evaluated by cyclic voltammetry and electrochemical impedance spectroscopy. The modification of the electrode surface with cys-GQDs and AuNps increased the electrochemical performance of the electrode, improving the electron transfer of the anionic redox probe [Fe(CN)6]3-/4- on the electrochemical platform. When compared to the bare surface, the modified electrode showed a 1.7 times increase in effective electrode area and a 29 times decrease in charge transfer resistance. The genosensor response was performed by differential pulse voltammetry, monitoring the current response of the anionic redox probe, confirmed with real genomic RNA samples, making it possible to detect 1 fg/mL. In addition, the genosensor maintained its response for 60 days at room temperature. This new genosensor platform for early detection of HIV, based on the modification of the electrode surface with cys-GQDs and AuNps, discriminates between HIV-negative and positive samples, showing a low detection limit, as well as good specificity and stability, which are relevant properties for commercial application of biosensors.
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Affiliation(s)
- Anna C R Moço
- Institute of Biotechnology, Federal University of Uberlândia, 38405-319 Uberlândia, Minas Gerais, Brazil
| | - José A L Gomide
- Institute of Biotechnology, Federal University of Uberlândia, 38405-319 Uberlândia, Minas Gerais, Brazil
| | - Jose M R Flauzino
- Institute of Biotechnology, Federal University of Uberlândia, 38405-319 Uberlândia, Minas Gerais, Brazil
| | - Jéssica G Brussasco
- Institute of Biotechnology, Federal University of Uberlândia, 38405-319 Uberlândia, Minas Gerais, Brazil
| | - Luiz F G Luz
- Institute of Biotechnology, Federal University of Uberlândia, 38405-319 Uberlândia, Minas Gerais, Brazil
| | - Márcia M C N Soares
- Adolfo Lutz Institute, Regional Laboratory, 15061-020 São José do Rio Preto, São Paulo, Brazil
| | - João M Madurro
- Institute of Chemistry, Federal University of Uberlândia, 38400-902 Uberlândia, Minas Gerais, Brazil
| | - Ana G Brito-Madurro
- Institute of Biotechnology, Federal University of Uberlândia, 38405-319 Uberlândia, Minas Gerais, Brazil.
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5
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Li X, Wang H, Qi X, Ji Y, Li F, Chen X, Li K, Li L. PCR Independent Strategy-Based Biosensors for RNA Detection. Biosensors (Basel) 2024; 14:200. [PMID: 38667193 PMCID: PMC11048163 DOI: 10.3390/bios14040200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024]
Abstract
RNA is an important information and functional molecule. It can respond to the regulation of life processes and is also a key molecule in gene expression and regulation. Therefore, RNA detection technology has been widely used in many fields, especially in disease diagnosis, medical research, genetic engineering and other fields. However, the current RT-qPCR for RNA detection is complex, costly and requires the support of professional technicians, resulting in it not having great potential for rapid application in the field. PCR-free techniques are the most attractive alternative. They are a low-cost, simple operation method and do not require the support of large instruments, providing a new concept for the development of new RNA detection methods. This article reviews current PCR-free methods, overviews reported RNA biosensors based on electrochemistry, SPR, microfluidics, nanomaterials and CRISPR, and discusses their challenges and future research prospects in RNA detection.
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Affiliation(s)
- Xinran Li
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (X.Q.); (F.L.)
| | - Haoqian Wang
- Development Center of Science and Technology, Ministry of Agriculture and Rural Affairs, Beijing 100176, China;
| | - Xin Qi
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (X.Q.); (F.L.)
| | - Yi Ji
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China;
| | - Fukai Li
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (X.Q.); (F.L.)
| | - Xiaoyun Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China;
| | - Kai Li
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (X.Q.); (F.L.)
| | - Liang Li
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (X.Q.); (F.L.)
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6
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Zhao Y, Zhang J, Ma N, Kong J, Zhang X. Vitamin B 12-catalyzed electro-polymerization for ultrasensitive RNA detection. Bioelectrochemistry 2024; 155:108578. [PMID: 37742523 DOI: 10.1016/j.bioelechem.2023.108578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/14/2023] [Accepted: 09/19/2023] [Indexed: 09/26/2023]
Abstract
Vitamin B12 being a natural catalyst in atom transfer radical polymerization (ATRP), has the advantages of mild reaction conditions, good biocompatibility and high catalytic efficiency. In this report, an electrochemical biosensor of the lung cancer biomarker microRNA-21 (miRNA-21) is designed for early screening of lung cancer with high sensitivity at the femtomolar level. In this approach, hairpin DNA with N3 end group was first attached to the electrode surface. When miRNA-21 was present and paired with hairpin DNA, the N3 group released and attached to the ATRP initiator through "click reaction". Through eATRP, a large number of FerrocenylMethyl Methacrylate (FcMMA) monomers polymerized into long chains for signal amplification. These long chains had a distinct electrical signal in the square wave voltammetry (SWV), which can detect RNA with high sensitivity. The limit of detection (LOD) goes down to 1.010 fM after ATRP polymerization, which is lower than that of the majority of other ultra-sensitive RNA electrochemical assays. Results also show that the vitamin B12-based electrochemical biosensor is highly selective and suitable for RNA detection in complex biological samples.
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Affiliation(s)
- Yu Zhao
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu 210094, PR China
| | - Jian Zhang
- Nanjing Lishui District Hospital of Traditional Chinese Medicine, Nanjing 211200, PR China; Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210028, PR China
| | - Nan Ma
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu 210094, PR China
| | - Jinming Kong
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu 210094, PR China.
| | - Xueji Zhang
- School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, Guangdong 518060, PR China
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7
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Zheng F, Kawabe Y, Kamihira M. RNA Aptamer-Mediated Gene Activation Systems for Inducible Transgene Expression in Animal Cells. ACS Synth Biol 2024; 13:230-241. [PMID: 38073086 DOI: 10.1021/acssynbio.3c00472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
RNA expression analyses can be used to obtain various information from inside cells, such as physical conditions, the chemical environment, and endogenous signals. For detecting RNA, the system regulating intracellular gene expression has the potential for monitoring RNA expression levels in real time within living cells. Synthetic biology provides powerful tools for detecting and analyzing RNA inside cells. Here, we devised an RNA aptamer-mediated gene activation system, RAMGA, to induce RNA-triggered gene expression activation by employing an inducible complex formation strategy grounded in synthetic biology. This methodology connects DNA-binding domains and transactivators through target RNA using RNA-binding domains, including phage coat proteins. MS2 bacteriophage coat protein fused with a transcriptional activator and PP7 bacteriophage coat protein fused with the tetracycline repressor (tetR) can be bridged by target RNA encoding MS2 and PP7 stem-loops, resulting in transcriptional activation. We generated recombinant CHO cells containing an inducible GFP expression module governed by a minimal promoter with a tetR-responsive element. Cells carrying the trigger RNA exhibited robust reporter gene expression, whereas cells lacking it exhibited no expression. GFP expression was upregulated over 200-fold compared with that in cells without a target RNA expression vector. Moreover, this system can detect the expression of mRNA tagged with aptamer tags and modulate reporter gene expression based on the target mRNA level without affecting the expression of the original mRNA-encoding gene. The RNA-triggered gene expression systems developed in this study have potential as a new platform for establishing gene circuits, evaluating endogenous gene expression, and developing novel RNA detectors.
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Affiliation(s)
- Feiyang Zheng
- Department of Chemical Engineering, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yoshinori Kawabe
- Department of Chemical Engineering, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Masamichi Kamihira
- Department of Chemical Engineering, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
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Wang Y, Wang W, Lu X, Chen T, Wang Y, Wen Y, Hu J, Song J, Wang X. Novel RNA genosensor based on highly stable gold nanoparticles decorated phosphorene nanohybrid with graphene for highly sensitive and low-cost electrochemical detection of coconut cadang-cadang viroid. Mikrochim Acta 2023; 191:52. [PMID: 38147136 DOI: 10.1007/s00604-023-06130-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/28/2023] [Indexed: 12/27/2023]
Abstract
Coconut cadang-cadang viroid (CCCVd) is an infectious single-stranded RNA (ssRNA) pathogen, which leads directly to the death of a large number of coconut palm trees and heavy economic loss to coconut farmers. Herein, a novel electrochemical impedance RNA genosensor is presented based on highly stable gold nanoparticles (AuNPs) decorated phosphorene (BP) nanohybrid with graphene (Gr) for highly sensitive, low-cost, and label-free detection of CCCVd. BP-AuNPs are environmentally friendly prepared by ultrasonic-assisted liquid-phase exfoliation of black phosphorus, accompanying direct reduction of chloroauric acid. Gr/BP-AuNPs are facilely prepared by the in situ growth of AuNPs onto the BP surface and its nanohybrid with Gr to improve environmental stability of BP. Gr/BP-AuNP-based RNA genosensor is fabricated by immobilizing the thiol-functionalized single-stranded DNA (ssDNA) oligonucleotide probe onto the surface of Gr/BP-AuNP-modified glassy carbon electrode via gold-thiol interactions, which served as an electrochemical genosensing platform for the label-free impedance detection of CCCVd by hybridization between the functionalized ssDNA probe and the complementary CCCVd ssRNA sequence in a wide linear range from 1.0 × 10-11 to 1.0 × 10-7 M with a low limit of detection of 2.8 × 10-12 M. This work supplies an experimental support and theoretical direction for the fabrication of RNA biosensors based on graphene-like materials and potential application for a specific diagnosis of plant RNA viral disease in Arecaceae planting industry.
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Affiliation(s)
- Yutang Wang
- Department of Biochemistry and Molecular Biology, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
- Institute of Functional Materials and Agricultural Applied Chemistry, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Wenqi Wang
- Institute of Functional Materials and Agricultural Applied Chemistry, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Xinyu Lu
- Institute of Functional Materials and Agricultural Applied Chemistry, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Tao Chen
- Institute of Functional Materials and Agricultural Applied Chemistry, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Yihua Wang
- Department of Biochemistry and Molecular Biology, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China.
| | - Yangping Wen
- Institute of Functional Materials and Agricultural Applied Chemistry, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China.
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China.
| | - Jiaqi Hu
- Institute of Functional Materials and Agricultural Applied Chemistry, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Jianbo Song
- Department of Biochemistry and Molecular Biology, College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Xiaoqiang Wang
- Institute of Functional Materials and Agricultural Applied Chemistry, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
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Chang S, Liu L, Mu C, Wen F, Xiang J, Zhai K, Wang B, Wu L, Nie A, Shu Y, Xue T, Liu Z. An Ultrasensitive SPR biosensor for RNA detection based on robust GeP 5 nanosheets. J Colloid Interface Sci 2023; 651:938-947. [PMID: 37579668 DOI: 10.1016/j.jcis.2023.08.064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 07/20/2023] [Accepted: 08/10/2023] [Indexed: 08/16/2023]
Abstract
Ultrasensitive and rapid detection of biomarkers is among the upmost priorities in promoting healthcare advancements. Improved sensitivity of photonic sensors based on two-dimensional (2D) materials have brought exciting prospects for achieving real-time and label-free biosensing at dilute target concentrations. Here, we report a high-sensitivity surface plasmon resonance (SPR) RNA sensor using metallic 2D GeP5 nanosheets as the sensing material. Theoretical evaluations revealed that the presence of GeP5 nanosheets can greatly enhance the plasmonic electric field of the Au film thereby boosting sensing sensitivity, and that optimal sensitivity (146° RIU-1) can be achieved with 3-nm-thick GeP5. By functionalizing GeP5 nanosheets with specific cDNA probes, detection of SARS-CoV-2 RNA sequences were achieved using the GeP5-based SPR sensor, with high sensitivity down to a detection limit of 10 aM and excellent selectivity. This work demonstrates the immense potential of GeP5-based SPR sensors for advanced biosensing applications and paves the way for utilizing GeP5 nanosheets in novel sensor devices.
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Affiliation(s)
- Shaopeng Chang
- Center for High Pressure Science, State Key Lab of Metastable Materials Science and Technology, Yanshan University, Qinhuangdao 066004, China
| | - Lixuan Liu
- Institute of Quantum Materials and Devices, School of Electronics and Information Engineering, Tiangong University, Tianjin 300387, China.
| | - Congpu Mu
- Center for High Pressure Science, State Key Lab of Metastable Materials Science and Technology, Yanshan University, Qinhuangdao 066004, China
| | - Fusheng Wen
- Center for High Pressure Science, State Key Lab of Metastable Materials Science and Technology, Yanshan University, Qinhuangdao 066004, China
| | - Jianyong Xiang
- Center for High Pressure Science, State Key Lab of Metastable Materials Science and Technology, Yanshan University, Qinhuangdao 066004, China
| | - Kun Zhai
- Center for High Pressure Science, State Key Lab of Metastable Materials Science and Technology, Yanshan University, Qinhuangdao 066004, China
| | - Bochong Wang
- Center for High Pressure Science, State Key Lab of Metastable Materials Science and Technology, Yanshan University, Qinhuangdao 066004, China
| | - Leiming Wu
- Guangdong Provincial Key Laboratory of Information Photonics Technology, School of Information Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Anmin Nie
- Center for High Pressure Science, State Key Lab of Metastable Materials Science and Technology, Yanshan University, Qinhuangdao 066004, China
| | - Yu Shu
- Center for High Pressure Science, State Key Lab of Metastable Materials Science and Technology, Yanshan University, Qinhuangdao 066004, China.
| | - Tianyu Xue
- Center for High Pressure Science, State Key Lab of Metastable Materials Science and Technology, Yanshan University, Qinhuangdao 066004, China.
| | - Zhongyuan Liu
- Center for High Pressure Science, State Key Lab of Metastable Materials Science and Technology, Yanshan University, Qinhuangdao 066004, China
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10
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Pauly MD, Weis-Torres S, Hayden TM, Ganova-Raeva LM, Kamili S. Development of simple, rapid, and sensitive methods for detection of hepatitis C virus RNA from whole blood using reverse transcription loop-mediated isothermal amplification. J Clin Microbiol 2023; 61:e0077123. [PMID: 37933990 PMCID: PMC10662345 DOI: 10.1128/jcm.00771-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/19/2023] [Indexed: 11/08/2023] Open
Abstract
Hepatitis C virus (HCV) infection is an underdiagnosed global health problem. Diagnosis of current HCV infections typically requires testing for HCV RNA using high-complexity laboratory tests. Methods for the detection of HCV RNA that are simple, inexpensive, rapid, and compatible with use outside of a laboratory setting are very important in order to improve access to hepatitis C diagnostic testing and facilitate accelerated linkage to care. We developed and evaluated three simple workflows for extracting HCV RNA from small volumes of whole blood for use in a sensitive, pan-genotypic RT-LAMP assay. The water workflow uses osmotic stress to release HCV RNA and has a limit of detection of 4.3 log10(IU/mL) (95% CI 4.0-4.9). The heat workflow uses a heating step to release HCV RNA and has a limit of detection of 4.2 log10(IU/mL) (95% CI 3.8-5.1). The bead workflow, which uses chemical lysis of the sample and a streamlined paramagnetic solid phase reversible immobilization bead procedure for nucleic acid purification, has a limit of detection of 2.8 log10(IU/mL) (95% CI 2.5-3.4). When used to test whole blood spiked with HCV RNA-positive plasma samples in which most HCV levels were below 5.0 log10(IU/mL), the water, heat, and bead workflows detected HCV RNA in 69%, 75%, and 94% of samples, respectively. These workflows are compatible with visual lateral flow dipsticks, and each takes less than 60 min from sample to result. Each workflow can be performed with minimal and inexpensive equipment. With further procedural simplifications, these workflows may form the basis of assays for the point-of-care diagnosis of HCV infections.
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Affiliation(s)
- Matthew D. Pauly
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, USA, Atlanta, Georgia
| | - Sabrina Weis-Torres
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, USA, Atlanta, Georgia
| | - Tonya M. Hayden
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, USA, Atlanta, Georgia
| | - Lilia M. Ganova-Raeva
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, USA, Atlanta, Georgia
| | - Saleem Kamili
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, USA, Atlanta, Georgia
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11
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Kimchi O, Larsen BB, Dunkley ORS, te Velthuis AJ, Myhrvold C. RNA structure modulates Cas13 activity and enables mismatch detection. bioRxiv 2023:2023.10.05.560533. [PMID: 37987004 PMCID: PMC10659300 DOI: 10.1101/2023.10.05.560533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The RNA-targeting CRISPR nuclease Cas13 has emerged as a powerful tool for applications ranging from nucleic acid detection to transcriptome engineering and RNA imaging1-6. Cas13 is activated by the hybridization of a CRISPR RNA (crRNA) to a complementary single-stranded RNA (ssRNA) protospacer in a target RNA1,7. Though Cas13 is not activated by double-stranded RNA (dsRNA) in vitro, it paradoxically demonstrates robust RNA targeting in environments where the vast majority of RNAs are highly structured2,8. Understanding Cas13's mechanism of binding and activation will be key to improving its ability to detect and perturb RNA; however, the mechanism by which Cas13 binds structured RNAs remains unknown9. Here, we systematically probe the mechanism of LwaCas13a activation in response to RNA structure perturbations using a massively multiplexed screen. We find that there are two distinct sequence-independent modes by which secondary structure affects Cas13 activity: structure in the protospacer region competes with the crRNA and can be disrupted via a strand-displacement mechanism, while structure in the region 3' to the protospacer has an allosteric inhibitory effect. We leverage the kinetic nature of the strand displacement process to improve Cas13-based RNA detection, enhancing mismatch discrimination by up to 50-fold and enabling sequence-agnostic mutation identification at low (<1%) allele frequencies. Our work sets a new standard for CRISPR-based nucleic acid detection and will enable intelligent and secondary-structure-guided target selection while also expanding the range of RNAs available for targeting with Cas13.
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Affiliation(s)
- Ofer Kimchi
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, 08544, USA
| | - Benjamin B. Larsen
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, 08544, USA
| | - Owen R. S. Dunkley
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, 08544, USA
| | | | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, 08544, USA
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, 08544, USA
- Omenn-Darling Bioengineering Institute, Princeton University, Princeton, New Jersey, 08544, USA
- Department of Chemistry, Princeton University, Princeton, New Jersey, 08544, USA
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12
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Xu C, Yu J, Ning X, Xu M, He S, Wu J, Pu K. Semiconducting Polymer Nanospherical Nucleic Acid Probe for Transcriptomic Imaging of Cancer Chemo-Immunotherapy. Adv Mater 2023; 35:e2306739. [PMID: 37660291 DOI: 10.1002/adma.202306739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/27/2023] [Indexed: 09/04/2023]
Abstract
Real-time in vivo imaging of RNA can enhance the understanding of physio-pathological processes. However, most nucleic acid-based sensors have poor resistance to nucleases and limited photophysical properties, making them suboptimal for this purpose. To address this, a semiconducting polymer nanospherical nucleic acid probe (SENSE) for transcriptomic imaging of cancer immunity in living mice is developed. SENSE comprises a semiconducting polymer (SP) backbone covalently linked with recognition DNA strands, which are complemented by dye-labeled signal DNA strands. Upon detection of targeted T lymphocyte transcript (Gzmb: granzyme B), the signal strands are released, leading to a fluorescence enhancement correlated to transcript levels with superb sensitivity. The always-on fluorescence of the SP core also serves as an internal reference for tracking SENSE uptake in tumors. Thus, SENSE has the dual-signal channel that enables ratiometric imaging of Gzmb transcripts in the tumor of living mice for evaluating chemo-immunotherapy; moreover, it has demonstrated sensitivity and specificity comparable to flow cytometry and quantitative polymerase chain reaction, yet offering a faster and simpler means of T cell detection in resected tumors. Therefore, SENSE represents a promising tool for in vivo RNA imaging.
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Affiliation(s)
- Cheng Xu
- School of Chemistry Chemical Engineering and Biotechnology, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore
| | - Jie Yu
- School of Chemistry Chemical Engineering and Biotechnology, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore
| | - Xiaoyu Ning
- School of Chemistry Chemical Engineering and Biotechnology, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore
| | - Mengke Xu
- School of Chemistry Chemical Engineering and Biotechnology, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore
| | - Shasha He
- School of Chemistry Chemical Engineering and Biotechnology, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore
| | - Jiayan Wu
- School of Chemistry Chemical Engineering and Biotechnology, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore
| | - Kanyi Pu
- School of Chemistry Chemical Engineering and Biotechnology, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore, 636921, Singapore
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13
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Yu Z, Pan L, Ma X, Li T, Wang F, Yang D, Li M, Wang P. Detection of SARS-CoV-2 RNA with a plasmonic chiral biosensor. Biosens Bioelectron 2023; 237:115526. [PMID: 37453279 DOI: 10.1016/j.bios.2023.115526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023]
Abstract
The detection of SARS-CoV-2 infection is crucial for effective prevention and surveillance of COVID-19. In this study, we report the development of a novel detection assay named CENSOR that enables sensitive and specific detection of SARS-CoV-2 RNA using a plasmonic chiral biosensor in combination with CRISPR-Cas13a. The chiral biosensor was designed by assembling gold nanorods (AuNR) into three-dimensional plasmonic architectures of controllable chirality on a DNA origami template. This modular assembly mode enhances the flexibility and adaptability of the sensor, thereby improving its universality as a sensing platform. In the presence of SARS-CoV-2 RNA, the CRISPR-Cas13a enzyme triggers collateral cleavage of RNA molecules, resulting in a differential chiral signal readout by the biosensor compared to when there are no RNA targets present. Notably, even subtle variations in the concentration of SARS-CoV-2 RNA can provoke significant changes in chiral signals after preamplification of RNA targets (calculated LOD: 0.133 aM), which establishes the foundation for quantitative detection. Furthermore, CENSOR demonstrated high sensitivity and accuracy in detecting SARS-CoV-2 RNA from clinical samples, suggesting its potential application in clinical settings for viral detection beyond SARS-CoV-2.
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Affiliation(s)
- Zhicai Yu
- Department of Laboratory Medicine, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Li Pan
- Department of Laboratory Medicine, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xiaowei Ma
- Department of Laboratory Medicine, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Tianming Li
- Department of Laboratory Medicine, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Fukai Wang
- Department of Laboratory Medicine, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Donglei Yang
- Department of Laboratory Medicine, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Min Li
- Department of Laboratory Medicine, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
| | - Pengfei Wang
- Department of Laboratory Medicine, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
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14
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Musto C, Tamba M, Calzolari M, Rossi A, Grisendi A, Marzani K, Bonilauri P, Delogu M. Detection of West Nile and Usutu Virus RNA in Autumn Season in Wild Avian Hosts in Northern Italy. Viruses 2023; 15:1771. [PMID: 37632113 PMCID: PMC10458002 DOI: 10.3390/v15081771] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
West Nile (WNV) and Usutu (USUV) viruses are two mosquito-borne viruses belonging to the family Flaviviridae and genus Flavivirus. The natural transmission cycle of WNV and USUV involves mosquitoes and birds, while mammals are thought to be accidental hosts. The goal of this study was to report-in the context of "off-season monitoring" and passive surveillance-the detection of WNV and USUV RNA in wild birds. To this end, we analyzed biological samples of wild birds in Northern Italy, from October to May, hence outside of the regional monitoring period (June-September). The virological investigations for the detection of USUV and WNV RNA were performed using real-time PCR on frozen samples of the brain, myocardium, kidney, and spleen. In a total sample of 164 wild birds belonging to 27 different species, sequences of both viruses were detected: four birds (2.44%) were positive for WNV and five (3.05%) for USUV. Off-season infections of WNV and especially USUV are still widely discussed and only a few studies have been published to date. To the best of our knowledge, this study is the first report on the detection of USUV RNA until December 22nd. Although further studies are required, our results confirm the viral circulation out-of-season of Flavivirus in wild birds, suggesting reconsidering the epidemiological monitoring period based on each individual climate zone and taking into consideration global warming which will play an important role in the epidemiology of vector-borne diseases.
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Affiliation(s)
- Carmela Musto
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Bologna, Italy;
| | - Marco Tamba
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia-Romagna, 25124 Brescia, Italy; (M.T.); (M.C.); (A.R.); (A.G.); (K.M.); (P.B.)
| | - Mattia Calzolari
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia-Romagna, 25124 Brescia, Italy; (M.T.); (M.C.); (A.R.); (A.G.); (K.M.); (P.B.)
| | - Arianna Rossi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia-Romagna, 25124 Brescia, Italy; (M.T.); (M.C.); (A.R.); (A.G.); (K.M.); (P.B.)
| | - Annalisa Grisendi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia-Romagna, 25124 Brescia, Italy; (M.T.); (M.C.); (A.R.); (A.G.); (K.M.); (P.B.)
| | - Katia Marzani
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia-Romagna, 25124 Brescia, Italy; (M.T.); (M.C.); (A.R.); (A.G.); (K.M.); (P.B.)
| | - Paolo Bonilauri
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia-Romagna, 25124 Brescia, Italy; (M.T.); (M.C.); (A.R.); (A.G.); (K.M.); (P.B.)
| | - Mauro Delogu
- Department of Veterinary Medical Sciences, University of Bologna, 40064 Bologna, Italy;
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15
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Wang S, Li H, Dong K, Shu W, Zhang J, Zhang J, Zhao R, Wei S, Feng D, Xiao X, Zhang W. A universal and specific RNA biosensor via DNA circuit-mediated PAM-independent CRISPR/Cas12a and PolyA-rolling circle amplification. Biosens Bioelectron 2023; 226:115139. [PMID: 36774734 DOI: 10.1016/j.bios.2023.115139] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023]
Abstract
Point of care testing (POCT) has important clinical significance for the diagnosis and prognosis evaluation of diseases. At present, the biosensor based on CRISPR/Cas12a has become a powerful diagnostic tool due to its high sensitivity. However, CRISPR/Cas12a requires PAM sequence to recognize target double strand and only can recognize specific sequence, so it is not universal. The current RNA detection techniques either lack consideration for specificity and universality, are expensive and difficult, or both. Therefore, it is crucial to create a CRISPR/Cas12a-based RNA detection system that is easy to use, cheap, specific, and universal in order to further its use in molecular diagnostics. Here, we established a DNA circuit-mediated PAM-independent CRISPR/Cas12a coupled PolyA-rolling circle amplification for RNA detection biosensor, namely DCPRBiosensor. The DCPRBiosensor not only functions as a simple, inexpensive, and highly sensitive RNA detection sensor, but it also boasts innovative specificity and universality features. More importantly, DCPRBiosensor removes the PAM restriction of CRISPR/Cas12a. The DCPRBiosensor's detection limit reached 100 aM and it had a linear relationship between 100 aM and 10 pM. We detected four piRNAs to verify the universality and stability of DCPRBiosensor. Then, we verified that DCPRBiosensor has good discrimination ability for single-base mismatch. Finally, we successfully detected piRNA in DLD-1 and HCT-116 cells and urine mixed samples within 4.5 h. In conclusion, we believe that DCPRBiosensor will have a substantial impact on both the development of CRISPR/as12a's applications and the investigation of the clinical value of piRNA.
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Affiliation(s)
- Sidan Wang
- Queen Mary School, Nanchang University, Nanchang, 330006, China
| | - Haojia Li
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Kejun Dong
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Wan Shu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Jiarui Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Jun Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Rong Zhao
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Sitian Wei
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Dilu Feng
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China.
| | - Xianjin Xiao
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Wei Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China.
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16
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Feng ZY, Yun YF, Li X, Zhang J. Impact of Divalent Metal Ions on Regulation of Trans-cleavage Activity of CRISPR-Cas13a: A Combined Experimental and Computational Study. Chembiochem 2023; 24:e202300034. [PMID: 37040174 DOI: 10.1002/cbic.202300034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 04/02/2023] [Accepted: 04/11/2023] [Indexed: 04/12/2023]
Abstract
CRISPR-LbuCas13a has emerged as a revolutionary tool for in vitro diagnosis. Similar to other Cas effectors, LbuCas13a requires Mg2+ to maintain its nuclease activity. However, the effect of other divalent metal ions on its trans-cleavage activity remains less explored. Herein, we addressed this issue by combined experimental and molecular dynamics simulation analysis. In vitro studies showed that both Mn2+ and Ca2+ could replace Mg2+ as cofactors of LbuCas13a. In contrast, Ni2+, Zn2+, Cu2+ or Fe2+ inhibits the cis- and trans-cleavage activity, while Pb2+ does not affect. Importantly, molecular dynamics simulations confirmed that calcium, magnesium and manganese hydrated ions have strong affinity to nucleotide bases, thus stabilizing the conformation of crRNA repeat region and enhancing the trans-cleavage activity. Finally, we showed that combination of Mg2+ and Mn2+ can further enhance the trans-cleavage activity to allow amplified RNA detection, revealing its potential advantage for in vitro diagnosis.
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Affiliation(s)
| | | | - Xiang Li
- Nanjing University, Chemistry, CHINA
| | - Jingjing Zhang
- Nanjing university, Department of Chemistry, Xianlin Road 163, 210023, Nanjing, CHINA
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17
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Dong Z, Gao D, Li Y, An K, Ni J, Meng L, Wu H. Self-assembled DNA nanoparticles enable cascade circuits for m RNA detection and imaging in living cells. Anal Chim Acta 2023; 1249:340934. [PMID: 36868769 DOI: 10.1016/j.aca.2023.340934] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/08/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023]
Abstract
Fluorescence molecular probes have been regarded as a valuable tool for RNA detection and imaging. However, the pivotal challenge is how to develop an efficient fluorescence imaging platform for accurate identification of RNA molecules with low expression in complicated physiological environments. Herein, we construct the DNA nanoparticles to glutathione (GSH)-responsive controllable release of hairpin reactants for catalytic hairpin assembly (CHA)-hybridization chain reaction (HCR) cascade circuits, which enables the analysis and imaging of low-abundance target mRNA in living cells. The aptamer-tethered DNA nanoparticles are constructed via the self-assembly of single-stranded DNAs (ssDNAs), exhibiting sufficient stability, cell-specific penetration, and precise controllability. Moreover, the in-depth integration of different DNA cascade circuits shows the improved sensing performance of DNA nanoparticles in live cell analysis. Therefore, through the combination of multi-amplifiers and programmable DNA nanostructure, the developed strategy enables accurately triggered release of hairpin reactants and further achieves sensitive imaging and quantitative evaluation of survivin mRNA in carcinoma cells, which provides a potential platform to facilitate RNA fluorescence imaging applications in early clinical cancer theranostics.
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Affiliation(s)
- Zhe Dong
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, PR China; State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Debo Gao
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, PR China
| | - Yuancheng Li
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, PR China
| | - Kang An
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, PR China
| | - Jing Ni
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, PR China
| | - Ling Meng
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, PR China
| | - Han Wu
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, PR China.
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18
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Huber LB, Betz K, Marx A. Reverse Transcriptases: From Discovery and Applications to Xenobiology. Chembiochem 2023; 24:e202200521. [PMID: 36354312 DOI: 10.1002/cbic.202200521] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/09/2022] [Indexed: 11/12/2022]
Abstract
Reverse transcriptases are DNA polymerases that can use RNA as a template for DNA synthesis. They thus catalyze the reverse of transcription. Although discovered in 1970, reverse transcriptases are still of great interest and are constantly being further developed for numerous modern research approaches. They are frequently used in biotechnological and molecular diagnostic applications. In this review, we describe the discovery of these fascinating enzymes and summarize research results and applications ranging from molecular cloning, direct virus detection, and modern sequencing methods to xenobiology.
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Affiliation(s)
- Luisa B Huber
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78464, Konstanz, Germany
| | - Karin Betz
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78464, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78464, Konstanz, Germany
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19
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Yu Z, Xu J, She Q. Harnessing the LdCsm RNA Detection Platform for Efficient microRNA Detection. Int J Mol Sci 2023; 24:ijms24032857. [PMID: 36769177 PMCID: PMC9918065 DOI: 10.3390/ijms24032857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/24/2023] [Accepted: 01/27/2023] [Indexed: 02/05/2023] Open
Abstract
In cancer diagnosis, diverse microRNAs (miRNAs) are used as biomarkers for carcinogenesis of distinctive human cancers. Thus, the detection of these miRNAs and their quantification are very important in prevention of cancer diseases in human beings. However, efficient RNA detection often requires RT-PCR, which is very complex for miRNAs. Recently, the development of CRISPR-based nucleic acid detection tools has brought new promises to efficient miRNA detection. Three CRISPR systems can be explored for miRNA detection, including type III, V, and VI, among which type III (CRISPR-Cas10) systems have a unique property as they recognize RNA directly and cleave DNA collaterally. In particular, a unique type III-A Csm system encoded by Lactobacillus delbrueckii subsp. bulgaricus (LdCsm) exhibits robust target RNA-activated DNase activity, which makes it a promising candidate for developing efficient miRNA diagnostic tools. Herein, LdCsm was tested for RNA detection using fluorescence-quenched DNA reporters. We found that the system is capable of specific detection of miR-155, a microRNA implicated in the carcinogenesis of human breast cancer. The RNA detection system was then improved by various approaches including assay conditions and modification of the 5'-repeat tag of LdCsm crRNAs. Due to its robustness, the resulting LdCsm detection platform has the potential to be further developed as a better point-of-care miRNA diagnostics relative to other CRISPR-based RNA detection tools.
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Affiliation(s)
| | | | - Qunxin She
- Correspondence: ; Tel.: +86-532-58631522
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20
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Sun JR, Yang LZ, Dai YL, Wu H, Li S, Xu YF, Huang Y, Wu H, Shen Z, Zou C, Chen LL. Using sno-lncRNAs as potential markers for Prader-Willi syndrome diagnosis. RNA Biol 2023; 20:419-430. [PMID: 37405372 DOI: 10.1080/15476286.2023.2230406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023] Open
Abstract
The genetic disorder Prader-Willi syndrome (PWS) is mainly caused by the loss of multiple paternally expressed genes in chromosome 15q11-q13 (the PWS region). Early diagnosis of PWS is essential for timely treatment, leading to effectively easing some clinical symptoms. Molecular approaches for PWS diagnosis at the DNA level are available, but the diagnosis of PWS at the RNA level has been limited. Here, we show that a cluster of paternally transcribed snoRNA-ended long noncoding RNAs (sno-lncRNAs, sno-lncRNA1-5) derived from the SNORD116 locus in the PWS region can serve as diagnostic markers. In particular, quantification analysis has revealed that 6,000 copies of sno-lncRNA3 are present in 1 μL whole blood samples from non-PWS individuals. sno-lncRNA3 is absent in all examined whole blood samples of 8 PWS individuals compared to 42 non-PWS individuals and dried blood samples of 35 PWS individuals compared to 24 non-PWS individuals. Further developing a new CRISPR-MhdCas13c system for RNA detection with a sensitivity of 10 molecules per μL has ensured sno-lncRNA3 detection in non-PWS, but not PWS individuals. Together, we suggest that the absence of sno-lncRNA3 represents a potential marker for PWS diagnosis that can be detected by both RT-qPCR and CRISPR-MhdCas13c systems with only microlitre amount of blood samples. Such an RNA-based sensitive and convenient approach may facilitate the early detection of PWS.
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Affiliation(s)
- Jiu-Ru Sun
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Liang-Zhong Yang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Shanghai, China
| | - Yang-Li Dai
- Department of Endocrinology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Huang Wu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Shanghai, China
- Department of Blood Transfusion, Daping Hospital ArmyMedical University, Chongqing, China
| | - Siqi Li
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Shanghai, China
| | - Yi-Feng Xu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Shanghai, China
| | - Youkui Huang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Shanghai, China
| | - Hao Wu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Shanghai, China
| | - Zheng Shen
- Department of Endocrinology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chaochun Zou
- Department of Endocrinology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ling-Ling Chen
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Shanghai, China
- New Cornerstone Science Laboratory, Shenzhen, China
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21
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Qin S, Chen X, Xu Z, Li T, Zhao S, Hu R, Zhu J, Li Y, Yang Y, Liu M. Telomere G-triplex lights up Thioflavin T for RNA detection: new wine in an old bottle. Anal Bioanal Chem 2022; 414:6149-6156. [PMID: 35725832 PMCID: PMC9208972 DOI: 10.1007/s00216-022-04180-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/06/2022] [Accepted: 06/13/2022] [Indexed: 02/07/2023]
Abstract
Few reports are found working on the features and functions of the human telomere G-triplex (ht-G3) though the telomere G-quadruplex has been intensely studied and widely implemented to develop various biosensors. We herein report that ht-G3 lights up Thioflavin T (ThT) and establish a sensitive biosensing platform for RNA detection by introducing a target recycling strategy. An optimal condition was selected out for ht-G3 to promote ThT to generate a strong fluorescence. Accordingly, an ht-G3-based molecular beacon was successfully designed against the corresponding RNA sequence of the SARS-CoV-2 N-gene. The sensitivity for the non-amplified RNA target achieves 0.01 nM, improved 100 times over the conventional ThT–based method. We believe this ht-G3/ThT–based label-free strategy could be widely applied for RNA detection.
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Affiliation(s)
- Shanshan Qin
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology - Wuhan National Laboratory for Optoelectronics, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Xuliang Chen
- Department of Cardiovascular Surgery, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Zhichen Xu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology - Wuhan National Laboratory for Optoelectronics, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Tao Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology - Wuhan National Laboratory for Optoelectronics, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Shuhong Zhao
- University of Chinese Academy of Sciences, Beijing, 10049, China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Rui Hu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology - Wuhan National Laboratory for Optoelectronics, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Jiang Zhu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology - Wuhan National Laboratory for Optoelectronics, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Ying Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology - Wuhan National Laboratory for Optoelectronics, Chinese Academy of Sciences, Wuhan, 430071, China.
- University of Chinese Academy of Sciences, Beijing, 10049, China.
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology - Wuhan National Laboratory for Optoelectronics, Chinese Academy of Sciences, Wuhan, 430071, China.
- University of Chinese Academy of Sciences, Beijing, 10049, China.
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology - Wuhan National Laboratory for Optoelectronics, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
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22
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Kevill JL, Pellett C, Farkas K, Brown MR, Bassano I, Denise H, McDonald JE, Malham SK, Porter J, Warren J, Evens NP, Paterson S, Singer AC, Jones DL. A comparison of precipitation and filtration-based SARS-CoV-2 recovery methods and the influence of temperature, turbidity, and surfactant load in urban wastewater. Sci Total Environ 2022; 808:151916. [PMID: 34826466 PMCID: PMC8610557 DOI: 10.1016/j.scitotenv.2021.151916] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/09/2021] [Accepted: 11/19/2021] [Indexed: 05/09/2023]
Abstract
Wastewater-based epidemiology (WBE) has become a complimentary surveillance tool during the SARS-CoV-2 pandemic. Viral concentration methods from wastewater are still being optimised and compared, whilst viral recovery under different wastewater characteristics and storage temperatures remains poorly understood. Using urban wastewater samples, we tested three viral concentration methods; polyethylene glycol precipitation (PEG), ammonium sulphate precipitation (AS), and CP select™ InnovaPrep® (IP) ultrafiltration. We found no major difference in SARS-CoV-2 and faecal indicator virus (crAssphage) recovery from wastewater samples (n = 46) using these methods, PEG slightly (albeit non-significantly), outperformed AS and IP for SARS-CoV-2 detection, as a higher genome copies per litre (gc/l) was recorded for a larger proportion of samples. Next generation sequencing of 8 paired samples revealed non-significant differences in the quality of data between AS and IP, though IP data quality was slightly better and less variable. A controlled experiment assessed the impact of wastewater suspended solids (turbidity; 0-400 NTU), surfactant load (0-200 mg/l), and storage temperature (5-20 °C) on viral recovery using the AS and IP methods. SARS-CoV-2 recoveries were >20% with AS and <10% with IP in turbid samples, whilst viral recoveries for samples with additional surfactant were between 0-18% for AS and 0-5% for IP. Turbidity and sample storage temperature combined had no significant effect on SARS-CoV-2 recovery (p > 0.05), whilst surfactant and storage temperature combined were significant negative correlates (p < 0.001 and p < 0.05, respectively). In conclusion, our results show that choice of methodology had small effect on viral recovery of SARS-CoV-2 and crAssphage in wastewater samples within this study. In contrast, sample turbidity, storage temperature, and surfactant load did affect viral recovery, highlighting the need for careful consideration of the viral concentration methodology used when working with wastewater samples.
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Affiliation(s)
- Jessica L Kevill
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK.
| | - Cameron Pellett
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Kata Farkas
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey LL59 5AB, UK
| | - Mathew R Brown
- Joint Biosecurity Centre, Department of Health and Social Care, London WC1B 4DA, UK; School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Irene Bassano
- Joint Biosecurity Centre, Department of Health and Social Care, London WC1B 4DA, UK; Department of Infectious Disease, Imperial College London, London SW7 2AZ, UK
| | - Hubert Denise
- Joint Biosecurity Centre, Department of Health and Social Care, London WC1B 4DA, UK
| | - James E McDonald
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Shelagh K Malham
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey LL59 5AB, UK
| | - Jonathan Porter
- Environment Agency National Laboratory Service, Exeter, Devon EX6 8PE, UK
| | - Jonathan Warren
- Environment Agency National Laboratory Service, Exeter, Devon EX6 8PE, UK
| | - Nicholas P Evens
- Environment Agency National Laboratory Service, Exeter, Devon EX6 8PE, UK
| | - Steve Paterson
- Centre of Genomics Research & NERC Environmental Omics Facility, University of Liverpool, Liverpool L69 7ZB, UK
| | | | - Davey L Jones
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; Food Futures Institute, Murdoch University, 90 South Street, Murdoch, WA 6105, Australia
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23
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Jiao C, Beisel CL. Reprogramming TracrRNAs for Multiplexed RNA Detection. Methods Mol Biol 2022; 2518:217-235. [PMID: 35666448 DOI: 10.1007/978-1-0716-2421-0_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
CRISPR-based detection and recording technologies are gaining increasing attention in disease surveillance and prevention. In this chapter, we describe how our recent discovery of noncanonical crRNAs inspired the engineering of reprogrammed tracrRNAs and led to a powerful platform for multiplexed RNA detection. We provide detailed protocols regarding how to design reprogrammed tracrRNA and carry out assays in vitro and in vivo.
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Affiliation(s)
- Chunlei Jiao
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Würzburg, Germany
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Würzburg, Germany.
- Medical Faculty, University of Würzburg, Würzburg, Germany.
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24
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Dubé M, Kaufmann DE. Single-Cell Multiparametric Analysis of Rare HIV-Infected Cells Identified by Duplexed RNAflow-FISH. Methods Mol Biol 2022; 2407:291-313. [PMID: 34985672 DOI: 10.1007/978-1-0716-1871-4_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
HIV-infected cells are difficult to characterize in vivo because of their great paucity and their diversity. This chapter describes a duplexed flow cytometry method that enables detection, quantification and phenotyping of these rare cells at single-cell resolution. Primary CD4+ T cells are enriched from PBMCs, stained for surface and intracellular proteins and then subjected to fluorescent in situ hybridization to label viral RNA before acquisition on a flow cytometer. Technical and analytical advices are provided to improve the quality of the data. This flow cytometric RNA fluorescent in situ hybridization (RNAflow-FISH) procedure can be applied to the characterization of both HIV-infected cells from viremic people living with HIV and reactivated viral reservoirs from virally suppressed individuals on therapy.
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Affiliation(s)
- Mathieu Dubé
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Daniel E Kaufmann
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada.
- Université de Montréal, Montreal, QC, Canada.
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25
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Di Maria F, La Rosa G, Bonato T, Pivato A, Piazza R, Mancini P, Bonanno Ferraro G, Veneri C, Iaconelli M, Beccaloni E, Scaini F, Bonadonna L, Vicenza T, Suffredini E. An innovative approach for the non-invasive surveillance of communities and early detection of SARS-CoV-2 via solid waste analysis. Sci Total Environ 2021; 801:149743. [PMID: 34467913 PMCID: PMC8372477 DOI: 10.1016/j.scitotenv.2021.149743] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 08/11/2021] [Accepted: 08/14/2021] [Indexed: 05/11/2023]
Abstract
The diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection requires the detection of viral RNA by reverse transcription-polymerase chain reaction (RT-qPCR) performed mainly using nasopharyngeal swabs. However, this procedure requires separate analysis per each individual, performed in advanced centralized laboratory facilities with specialized medical personnel. In this study, an alternative approach termed "solid waste-based surveillance (SWBS)" was explored, in order to investigate SARS-CoV-2 infection in small communities through the indirect sampling of saliva left on waste. Sampling was performed at 20 different sites in Italy during the second peak of COVID-19. Three swabs were positive for SARS-CoV-2 using a published RT-qPCR protocol targeting the non-structural protein 14 region, and the viral load ranged 4.8 × 103-4.0 × 106 genome copies/swab. Amino acid substitutions already reported in SARS-CoV-2 sequences circulating in Italy (A222V and P521S) were detected in two positive samples. These findings confirmed the effectiveness of SWBS for non-invasive and dynamic SARS-CoV-2 surveillance.
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Affiliation(s)
- F Di Maria
- LAR Laboratory, Department of Engineering, University of Perugia, Perugia, Italy.
| | - G La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - T Bonato
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Venice, Italy
| | - A Pivato
- Department of Civil, Environmental and Architectural Engineering, University of Padua, Italy
| | - R Piazza
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Venice, Italy
| | - P Mancini
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - G Bonanno Ferraro
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - C Veneri
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - M Iaconelli
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - E Beccaloni
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - F Scaini
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - L Bonadonna
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - T Vicenza
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - E Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
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26
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Liu L, Ye K, Jia Z, Xue T, Nie A, Xiang J, Mu C, Wang B, Wen F, Zhai K, Zhao Z, Gong Y, Liu Z, Tian Y. High-sensitivity and versatile plasmonic biosensor based on grain boundaries in polycrystalline 1L WS 2 films. Biosens Bioelectron 2021; 194:113596. [PMID: 34500226 DOI: 10.1016/j.bios.2021.113596] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 12/19/2022]
Abstract
Structural defects play an important role in exploitation of two-dimensional layered materials (2DLMs) for advanced biosensors with the increasingly high sensitivity and low detection limit. Grain boundaries (GBs), as an important type of structural defect in polycrystalline 2DLM films, potentially provide sufficient active defect sites for the immobilization of bioreceptor units via chemical functionalization. In this work, we report the selective functionalization of high-density GBs with complementary DNA receptors, via gold nanoparticle (AuNP) linkers, in wafer-scale polycrystalline monolayer (1L) W(Mo)S2 films as versatile plasmonic biosensing platforms. The large surface area and GB-rich nature of the polycrystalline 1L WS2 film enabled the immobilization of bioreceptors in high surface density with spatial uniformity, while the AuNPs perform not only as bioreceptor linkers, but also promote detection sensitivity through surface plasmon resonance enhancement effect. Therefore, the presented biosensor demonstrated highly sensitive and selective sub-femto-molar detection of representative RNA sequences from the novel coronavirus (RdRp, ORF1ad and E). This work demonstrates the immense potential of AuNP-decorated GB-rich 2DLMs in the design of ultra-sensitive biosensing platforms for the detection of biological targets beyond RNA, bringing new opportunities for novel healthcare technologies.
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27
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Tabara K, Watanabe K, Shigeto H, Yamamura S, Kishi T, Kitamatsu M, Ohtsuki T. Fluorophore-PNA-Quencher/Quencher-DNA probe for mi RNA detection. Bioorg Med Chem Lett 2021; 51:128359. [PMID: 34534675 DOI: 10.1016/j.bmcl.2021.128359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/26/2021] [Accepted: 09/09/2021] [Indexed: 10/20/2022]
Abstract
Micro RNAs (miRNAs) are involved in a variety of biological functions and are attracting attention as diagnostic and prognostic markers for various diseases. Highly sensitive RNA detection methods are required to determine miRNA expression levels and intracellular localization. In this study, we designed new double-stranded peptide nucleic acid (PNA)/DNA probes consisting of a fluorophore-PNA-quencher (fPq) and a quencher-DNA (qD) for miR-221 detection. We optimized the fPq structure, PNA-DNA hybrid length, and hybrid position. The resultant fPq-2/qD-6b probe was a 6-bp hybrid probe with a 10-base fPq and a 6-base qD. The signal-to-background ratios of the probes showed that fPq-2/qD-6b had a higher target sensitivity than fPq (PNA beacon)-type and fP/qD-type probes. The results of the detection limit and target specificity indicate that the fPq/qD probe is promising for RNA detection in both cells and cell extracts as well as for miRNA diagnosis.
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Affiliation(s)
- Kentaro Tabara
- Department of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, Japan
| | - Kazunori Watanabe
- Department of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, Japan
| | - Hajime Shigeto
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology, 2217-14 Hayashi-cho, Takamatsu, Kagawa 761-0395, Japan
| | - Shohei Yamamura
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology, 2217-14 Hayashi-cho, Takamatsu, Kagawa 761-0395, Japan
| | - Takamasa Kishi
- Department of Applied Chemistry, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Mizuki Kitamatsu
- Department of Applied Chemistry, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Takashi Ohtsuki
- Department of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, Japan.
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28
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Gutiérrez-Gálvez L, García-Mendiola T, Gutiérrez-Sánchez C, Guerrero-Esteban T, García-Diego C, Buendía I, García-Bermejo ML, Pariente F, Lorenzo E. Carbon nanodot-based electrogenerated chemiluminescence biosensor for miRNA-21 detection. Mikrochim Acta 2021; 188:398. [PMID: 34716815 PMCID: PMC8557186 DOI: 10.1007/s00604-021-05038-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/25/2021] [Indexed: 11/30/2022]
Abstract
A simple carbon nanodot–based electrogenerated chemiluminescence biosensor is described for sensitive and selective detection of microRNA-21 (miRNA-21), a biomarker of several pathologies including cardiovascular diseases (CVDs). The photoluminescent carbon nanodots (CNDs) were obtained using a new synthesis method, simply by treating tiger nut milk in a microwave reactor. The synthesis is environmentally friendly, simple, and efficient. The optical properties and morphological characteristics of the CNDs were exhaustively investigated, confirming that they have oxygen and nitrogen functional groups on their surfaces and exhibit excitation-dependent fluorescence emission, as well as photostability. They act as co-reactant agents in the anodic electrochemiluminescence (ECL) of [Ru(bpy)3]2+, producing different signals for the probe (single-stranded DNA) and the hybridized target (double-stranded DNA). These results paved the way for the development of a sensitive ECL biosensor for the detection of miRNA-21. This was developed by immobilization of a thiolated oligonucleotide, fully complementary to the miRNA-21 sequence, on the disposable gold electrode. The target miRNA-21 was hybridized with the probe on the electrode surface, and the hybridization was detected by the enhancement of the [Ru(bpy)3]2+/DNA ECL signal using CNDs. The biosensor shows a linear response to miRNA-21 concentration up to 100.0 pM with a detection limit of 0.721 fM. The method does not require complex labeling steps, and has a rapid response. It was successfully used to detect miRNA-21 directly in serum samples from heart failure patients without previous RNA extraction neither amplification process.
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Affiliation(s)
- Laura Gutiérrez-Gálvez
- Department of Analytical Chemistry and Instrumental Analysis, Universidad Autónoma de Madrid, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain
| | - Tania García-Mendiola
- Department of Analytical Chemistry and Instrumental Analysis, Universidad Autónoma de Madrid, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain. .,Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain. .,IMDEA Nanociencia, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain.
| | - Cristina Gutiérrez-Sánchez
- Department of Analytical Chemistry and Instrumental Analysis, Universidad Autónoma de Madrid, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain.
| | - Tamara Guerrero-Esteban
- Department of Analytical Chemistry and Instrumental Analysis, Universidad Autónoma de Madrid, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain
| | - Cristina García-Diego
- Instituto de Catálisis y Petroleoquímica, Consejo Superior de Investigaciones Científicas, C/Marie Curie 2, 28049, Madrid, Spain
| | - Irene Buendía
- Biomarkers and Therapeutic Targets Group and Core Facility, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Spanish Renal Research Network (REDinREN), Madrid, Spain
| | - M Laura García-Bermejo
- Biomarkers and Therapeutic Targets Group and Core Facility, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Spanish Renal Research Network (REDinREN), Madrid, Spain
| | - Félix Pariente
- Department of Analytical Chemistry and Instrumental Analysis, Universidad Autónoma de Madrid, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain.,Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain
| | - Encarnación Lorenzo
- Department of Analytical Chemistry and Instrumental Analysis, Universidad Autónoma de Madrid, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain.,Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain.,IMDEA Nanociencia, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain
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29
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Zhang S, Chen J, Liu D, Hu B, Luo G, Huang Z. A novel microfluidic RNA chip for direct, single-nucleotide specific, rapid and partially-degraded RNA detection. Talanta 2021; 239:122974. [PMID: 34920889 DOI: 10.1016/j.talanta.2021.122974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 10/20/2022]
Abstract
Direct RNA detection is critical for providing the RNA insights into gene expression profiling, noncoding RNAs, RNA-associated diseases and pathogens, without reverse transcription. However, classical RNA analysis usually requires RT-PCR, which can cause bias amplification and quantitation errors. To address this challenge, herein we report a microfluidic RNA chip (the microchip prototype) for direct RNA detection, which is primarily based on RNA extension and labeling with DNA polymerase. This detection strategy is of high specificity (discriminating against single-nucleotide differences), rapidity, accuracy, nuclease resistance, and reusability. Further, we have successfully detected disease-associated RNAs in clinical samples, demonstrating its great potentials in biomedical research and clinical diagnosis.
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Affiliation(s)
- Shun Zhang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, PR China; SeNA Research Institute and Szostak-CDHT Large Nucleic Acids Institute, Chengdu, Sichuan, PR China
| | - Jiuyi Chen
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, PR China
| | - Dan Liu
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, PR China
| | - Bei Hu
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, PR China
| | - Guangcheng Luo
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, PR China
| | - Zhen Huang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, PR China; SeNA Research Institute and Szostak-CDHT Large Nucleic Acids Institute, Chengdu, Sichuan, PR China.
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30
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Bogiel T, Rzepka M, Depka D. Reliable Diagnostics of SARS-CoV-2 Infections Using One- and Two-Gene Molecular Tests for a Viral RNA Detection-Results Questioning Previous Observations. Diagnostics (Basel) 2021; 11:diagnostics11101839. [PMID: 34679537 PMCID: PMC8534906 DOI: 10.3390/diagnostics11101839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/02/2021] [Accepted: 10/03/2021] [Indexed: 12/18/2022] Open
Abstract
SARS-CoV-2 is a new virus from the Coronaviridae family and its rapid spread is now the most important medical problem worldwide. Currently used tests vary in the number and selection of SARS-CoV-2 target genes. Meanwhile, the choice of the appropriate target gene may be important in terms of a reliable detection of a viral RNA. As some researchers questioned the sensitivity of the monogenic VIASURE SARS-CoV-2 S gene Real Time PCR Detection Kit (CerTest Biotec, Zaragoza, Spain) in mid-2020, the aim of the study was to evaluate the usefulness of this kit, used along with the BD MAX™ System (Becton Dickinson, East Rutherford, NJ, USA), and compare the results with two-gene Bosphore Novel Coronavirus (2019-nCoV) Detection Kit v1 (Anatolia Diagnostics and Biotechnology Products Inc., Istanbul, Turkey). Both tests were carried out on 306 nasopharyngeal/oropharyngeal swabs. The consistent results (72 positive and 225 negative results found simultaneously in both kits) were obtained for 297 (97.1%) samples altogether, while discrepancies between the results of the evaluated tests were observed for nine (2.9%) specimens. There were no statistically significant differences between the method used and the frequency of positive results. Both tests, targeted at detecting one and two genes, are effective in SARS-CoV-2 RNA detection.
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Liu L, Wang Z, Wang Y, Luan J, Morrissey JJ, Naik RR, Singamaneni S. Plasmonically Enhanced CRISPR/Cas13a-Based Bioassay for Amplification-Free Detection of Cancer-Associated RNA. Adv Healthc Mater 2021; 10:e2100956. [PMID: 34369102 PMCID: PMC8542602 DOI: 10.1002/adhm.202100956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/25/2021] [Indexed: 12/15/2022]
Abstract
Novel methods that enable sensitive, accurate and rapid detection of RNA would not only benefit fundamental biological studies but also serve as diagnostic tools for various pathological conditions, including bacterial and viral infections and cancer. Although highly sensitive, existing methods for RNA detection involve long turn-around time and extensive capital equipment. Here, an ultrasensitive and amplification-free RNA quantification method is demonstrated by integrating CRISPR-Cas13a system with an ultrabright fluorescent nanolabel, plasmonic fluor. This plasmonically enhanced CRISPR-powered assay exhibits nearly 1000-fold lower limit-of-detection compared to conventional assay relying on enzymatic reporters. Using a xenograft tumor mouse model, it is demonstrated that this novel bioassay can be used for ultrasensitive and quantitative monitoring of cancer biomarker (lncRNA H19). The novel biodetection approach described here provides a rapid, ultrasensitive, and amplification-free strategy that can be broadly employed for detection of various RNA biomarkers, even in resource-limited settings.
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Affiliation(s)
- Lin Liu
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. Louis, St Louis, MO, 63130, USA
| | - Zheyu Wang
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. Louis, St Louis, MO, 63130, USA
| | - Yixuan Wang
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. Louis, St Louis, MO, 63130, USA
| | - Jingyi Luan
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. Louis, St Louis, MO, 63130, USA
| | - Jeremiah J. Morrissey
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO, 63110, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Rajesh R. Naik
- 711 Human Performance Wing, Air Force Research Laboratory, Wright Patterson Air Force Base, Dayton, OH, 45433, USA
| | - Srikanth Singamaneni
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. Louis, St Louis, MO, 63130, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
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Diaz LM, Johnson BE, Jenkins DM. Real-time optical analysis of a colorimetric LAMP assay for SARS-CoV-2 in saliva with a handheld instrument improves accuracy compared with endpoint assessment. J Biomol Tech 2021; 32:158-171. [PMID: 35027873 PMCID: PMC8730521 DOI: 10.7171/jbt.21-3203-011] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Controlling the course of the Coronavirus Disease 2019 (COVID-19) pandemic will require widespread deployment of consistent and accurate diagnostic testing of the novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Ideally, tests should detect a minimum viral load, be minimally invasive, and provide a rapid and simple readout. Current Food and Drug Administration (FDA)-approved RT-qPCR-based standard diagnostic approaches require invasive nasopharyngeal swabs and involve laboratory-based analyses that can delay results. Recently, a loop-mediated isothermal nucleic acid amplification (LAMP) test that utilizes colorimetric readout received FDA approval. This approach utilizes a pH indicator dye to detect drop in pH from nucleotide hydrolysis during nucleic acid amplification. This method has only been approved for use with RNA extracted from clinical specimens collected via nasopharyngeal swabs. In this study, we developed a quantitative LAMP-based strategy to detect SARS-CoV-2 RNA in saliva. Our detection system distinguished positive from negative sample types using a handheld instrument that monitors optical changes throughout the LAMP reaction. We used this system in a streamlined LAMP testing protocol that could be completed in less than 2 h to directly detect inactivated SARS-CoV-2 in minimally processed saliva that bypassed RNA extraction, with a limit of detection (LOD) of 50 genomes/reaction. The quantitative method correctly detected virus in 100% of contrived clinical samples spiked with inactivated SARS-CoV-2 at either 1× (50 genomes/reaction) or 2× (100 genomes/reaction) of the LOD. Importantly, the quantitative method was based on dynamic optical changes during the reaction and was able to correctly classify samples that were misclassified by endpoint observation of color.
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Affiliation(s)
- Lena M. Diaz
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawaiï i at Mãnoa, Honolulu, HI, USA
| | - Brandon E. Johnson
- Center for Biomedical Research, The Queen’s Medical Center, Honolulu, HI, USA
| | - Daniel M. Jenkins
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawaiï i at Mãnoa, Honolulu, HI, USA
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Carter JG, Orueta Iturbe L, Duprey JHA, Carter IR, Southern CD, Rana M, Whalley CM, Bosworth A, Beggs AD, Hicks MR, Tucker JHR, Dafforn TR. Ultrarapid detection of SARS-CoV-2 RNA using a reverse transcription-free exponential amplification reaction, RTF-EXPAR. Proc Natl Acad Sci U S A 2021; 118:e2100347118. [PMID: 34400545 DOI: 10.1073/pnas.2100347118] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
We report a rapid COVID-19 assay that gives a sample-to-signal time of under 10 min. The current gold-standard COVID-19 assay uses PCR, where strands of DNA are copied (amplified) many times to generate a read-out signal. However, as the virus genome is RNA, first conversion into DNA is required using reverse transcription (RT) before amplification. While just as sensitive, our assay is faster because 1) we have designed a method for generating DNA (the trigger strand) from RNA, bypassing the lengthy RT step, and 2) a quicker amplification process than PCR, called exponential amplification reaction (EXPAR), is used to amplify the trigger. This methodology could ultimately be applied to any RNA-based assay, including the detection of other infectious agents. A rapid isothermal method for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19, is reported. The procedure uses an unprecedented reverse transcription–free (RTF) approach for converting genomic RNA into DNA. This involves the formation of an RNA/DNA heteroduplex whose selective cleavage generates a short DNA trigger strand, which is then rapidly amplified using the exponential amplification reaction (EXPAR). Deploying the RNA-to-DNA conversion and amplification stages of the RTF-EXPAR assay in a single step results in the detection, via a fluorescence read-out, of single figure copy numbers per microliter of SARS-CoV-2 RNA in under 10 min. In direct three-way comparison studies, the assay has been found to be faster than both RT-qPCR and reverse transcription loop-mediated isothermal amplification (RT-LAMP), while being just as sensitive. The assay protocol involves the use of standard laboratory equipment and is readily adaptable for the detection of other RNA-based pathogens.
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Huang K, Demirci F, Meyers BC, Caplan JL. A Novel Method to Map Small RNAs with High Resolution. Bio Protoc 2021; 11:e4128. [PMID: 34541046 DOI: 10.21769/bioprotoc.4128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/20/2021] [Accepted: 05/06/2021] [Indexed: 11/02/2022] Open
Abstract
Analyzing cellular structures and the relative location of molecules is essential for addressing biological questions. Super-resolution microscopy techniques that bypass the light diffraction limit have become increasingly popular to study cellular molecule dynamics in situ. However, the application of super-resolution imaging techniques to detect small RNAs (sRNAs) is limited by the choice of proper fluorophores, autofluorescence of samples, and failure to multiplex. Here, we describe an sRNA-PAINT protocol for the detection of sRNAs at nanometer resolution. The method combines the specificity of locked nucleic acid probes and the low background, precise quantitation, and multiplexable characteristics of DNA Point Accumulation for Imaging in Nanoscale Topography (DNA-PAINT). Using this method, we successfully located sRNA targets that are important for development in maize anthers at sub-20 nm resolution and quantitated their exact copy numbers. Graphic abstract: Multiplexed sRNA-PAINT. Multiple Vetting and Analysis of RNA for In Situ Hybridization (VARNISH) probes with different docking strands (i.e., a, b, …) will be hybridized to samples. The first probe will be imaged with the a* imager. The a* imager will be washed off with buffer C, and then the sample will be imaged with b* imager. The wash and image steps can be repeated sequentially for multiplexing.
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Affiliation(s)
- Kun Huang
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA.,Bio-Imaging Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
| | - Feray Demirci
- FiDoSoft Software Consulting, Redmond, Wisconsin, 98052, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, Missouri, USA.,University of Missouri - Columbia, Division of Plant Sciences, 52 Agriculture Lab, Columbia, Missouri, USA
| | - Jeffrey L Caplan
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA.,Bio-Imaging Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
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Jemeršić L, Lojkić I, Krešić N, Keros T, Zelenika TA, Jurinović L, Skok D, Bata I, Boras J, Habrun B, Brnić D. Investigating the Presence of SARS CoV-2 in Free-Living and Captive Animals. Pathogens 2021; 10:635. [PMID: 34064271 PMCID: PMC8224323 DOI: 10.3390/pathogens10060635] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/17/2021] [Accepted: 05/20/2021] [Indexed: 12/15/2022] Open
Abstract
Due to SARS CoV-2 recombination rates, number of infected people and recent reports of environmental contamination, the possibility of SARS CoV-2 transmission to animals can be expected. We tested samples of dominant free-living and captive wildlife species in Croatia for the presence of anti-SARS CoV-2 antibodies and viral RNA. In total, from June 2020 until February 2021, we tested blood, muscle extract and fecal samples of 422 free-living wild boars (Sus scrofa), red foxes (Vulpes vulpes) and jackals (Canis aureus); blood and cloacal swabs of 111 yellow-legged gulls (Larus michahellis) and fecal samples of 32 zoo animals. A commercially available ELISA (ID.Vet, France) and as a confirmatory test, a surrogate virus neutralization test (sVNT; GenScript, Netherlands) were used. Fecal samples were tested for the presence of viral RNA by a real-time RT-PCR protocol. Fifteen out of 533 (2.8%) positive ELISA results were detected; in wild boars (3.9%), red foxes (2.9%) and jackals (4.6%). However, the positive findings were not confirmed by sVNT. No viral RNA was found. In conclusion, no spillover occurred within the investigated period (second COVID-19 wave). However, further investigation is needed, especially regarding wildlife sample features for serological tests.
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Affiliation(s)
- Lorena Jemeršić
- Virology Department, Croatian Veterinary Institute, Savska Cesta 143, 10000 Zagreb, Croatia; (N.K.); (T.K.); (B.H.); (D.B.)
| | - Ivana Lojkić
- Virology Department, Croatian Veterinary Institute, Savska Cesta 143, 10000 Zagreb, Croatia; (N.K.); (T.K.); (B.H.); (D.B.)
| | - Nina Krešić
- Virology Department, Croatian Veterinary Institute, Savska Cesta 143, 10000 Zagreb, Croatia; (N.K.); (T.K.); (B.H.); (D.B.)
| | - Tomislav Keros
- Virology Department, Croatian Veterinary Institute, Savska Cesta 143, 10000 Zagreb, Croatia; (N.K.); (T.K.); (B.H.); (D.B.)
| | - Tajana Amšel Zelenika
- Poultry Center, Croatian Veterinary Institute, Heinzelova 55, 10000 Zagreb, Croatia; (T.A.Z.); (L.J.)
| | - Luka Jurinović
- Poultry Center, Croatian Veterinary Institute, Heinzelova 55, 10000 Zagreb, Croatia; (T.A.Z.); (L.J.)
| | - Damir Skok
- Zagreb Zoo, Maksimirski Perivoj, 10000 Zagreb, Croatia; (D.S.); (I.B.); (J.B.)
| | - Ingeborg Bata
- Zagreb Zoo, Maksimirski Perivoj, 10000 Zagreb, Croatia; (D.S.); (I.B.); (J.B.)
| | - Jadranko Boras
- Zagreb Zoo, Maksimirski Perivoj, 10000 Zagreb, Croatia; (D.S.); (I.B.); (J.B.)
| | - Boris Habrun
- Virology Department, Croatian Veterinary Institute, Savska Cesta 143, 10000 Zagreb, Croatia; (N.K.); (T.K.); (B.H.); (D.B.)
| | - Dragan Brnić
- Virology Department, Croatian Veterinary Institute, Savska Cesta 143, 10000 Zagreb, Croatia; (N.K.); (T.K.); (B.H.); (D.B.)
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Zhang C, Zheng T, Fan H, Zhang T, Han D. Aligner-Mediated Cleavage-Based Isothermal Amplification for SARS-CoV-2 RNA Detection. ACS Appl Bio Mater 2021; 4:3805-3810. [PMID: 35006810 PMCID: PMC7931623 DOI: 10.1021/acsabm.0c01674] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 02/19/2021] [Indexed: 12/22/2022]
Abstract
Rapid detection of SARS-CoV-2 RNA is critical for reducing the global transmission of COVID-19. Here, we report a simple and versatile assay for detection of SARS-CoV-2 RNA based on aligner-mediated cleavage-based strand displacement amplification (AMC-SDA). The entire amplification procedure takes less than 25 min without professional instruments or requirement of specific target sequences and can reach a limit of detection of attomolar RNA concentration. Using pseudovirus as mimicry of clinical SARS-CoV-2 positive samples, we achieved a diagnostic accuracy of 100% in 10 simulated samples (five positive and five negative). We anticipate that our method will provide a universal platform for rapid and accurate detection of emerging infectious diseases.
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Affiliation(s)
- Chao Zhang
- Institute of Molecular Medicine (IMM), Shanghai Key
Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes
and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong
University, Shanghai 200127, China
| | - Tingting Zheng
- Institute of Molecular Medicine (IMM), Shanghai Key
Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes
and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong
University, Shanghai 200127, China
| | - Hongliang Fan
- Research Center for Analytical Instrumentation,
Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control
Technology, Zhejiang University, Hangzhou 310058,
China
| | - Tao Zhang
- Research Center for Analytical Instrumentation,
Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control
Technology, Zhejiang University, Hangzhou 310058,
China
| | - Da Han
- Institute of Molecular Medicine (IMM), Shanghai Key
Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes
and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong
University, Shanghai 200127, China
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37
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Hirschhorn JW, Kegl A, Dickerson T, Glen WB Jr, Xu G, Alden J, Nolte FS. Verification and Validation of SARS-CoV-2 Assay Performance on the Abbott m2000 and Alinity m Systems. J Clin Microbiol 2021; 59:e03119-20. [PMID: 33568468 DOI: 10.1128/JCM.03119-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/09/2021] [Indexed: 12/19/2022] Open
Abstract
We verified the analytical performance of the Abbott RealTime SARS-CoV-2 assay on the m2000 system and compared its clinical performance to the CDC 2019-nCoV real-time PCR diagnostic panel and the Thermo Fisher TaqPath RT-PCR COVID-19 kit. We also performed a bridging study comparing the RealTime SARS-CoV-2 assay with the new Abbott Alinity m SARS-CoV-2 assay. A number of standards, reference materials, and commercially available controls were used for the analytical verification to confirm the limit of detection, linearity, and reproducibility. We used nasopharyngeal (NP) swab specimens collected in saline for the clinical verification and bridging studies. Overall, we found 91.2% positive percent agreement (PPA; 95% confidence interval [CI] = 76.2 to 98.14%) and a 100% negative percent agreement (NPA; 95% CI = 97.97 to 100%) between the results of the RealTime SARS-CoV-2 and CDC tests with 217 NP specimens (P = 0.13). We found a PPA of 100% (95% CI = 90.26 to 100%) and an NPA of 95.15% (95% CI = 83.47 to 99.4%) between the results of the RealTime and TaqPath tests with 77 NP specimens (P = 0.24). Finally, we tested 203 NP swab specimens for SARS-CoV-2 on the m2000 on the Alinity m systems. The PPA and NPA were 92.2% (95% CI = 85.3 to 96.59%) and 92% (95% CI = 84.8 to 96.5%), respectively (P = 0.4). Although cycle number (Cn) values obtained for the concordant positive samples were highly correlated (R 2 = 0.95), the Cn values were on average 14.14 higher on the Alinity m system due to the unread cycles with the RealTime SARS-CoV-2 assay.
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38
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Mohr SE, Tattikota SG, Xu J, Zirin J, Hu Y, Perrimon N. Methods and tools for spatial mapping of single-cell RNAseq clusters in Drosophila. Genetics 2021; 217:6156631. [PMID: 33713129 DOI: 10.1093/genetics/iyab019] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/02/2021] [Indexed: 01/26/2023] Open
Abstract
Single-cell RNA sequencing (scRNAseq) experiments provide a powerful means to identify clusters of cells that share common gene expression signatures. A major challenge in scRNAseq studies is to map the clusters to specific anatomical regions along the body and within tissues. Existing data, such as information obtained from large-scale in situ RNA hybridization studies, cell type specific transcriptomics, gene expression reporters, antibody stainings, and fluorescent tagged proteins, can help to map clusters to anatomy. However, in many cases, additional validation is needed to precisely map the spatial location of cells in clusters. Several approaches are available for spatial resolution in Drosophila, including mining of existing datasets, and use of existing or new tools for direct or indirect detection of RNA, or direct detection of proteins. Here, we review available resources and emerging technologies that will facilitate spatial mapping of scRNAseq clusters at high resolution in Drosophila. Importantly, we discuss the need, available approaches, and reagents for multiplexing gene expression detection in situ, as in most cases scRNAseq clusters are defined by the unique coexpression of sets of genes.
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Affiliation(s)
- Stephanie E Mohr
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sudhir Gopal Tattikota
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jun Xu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan Zirin
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Boston, MA 02115, USA
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39
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Alladin-Mustan BS, Liu Y, Li Y, de Almeida DRQ, Yuzik J, Mendes CF, Gibbs JM. Reverse transcription lesion-induced DNA amplification: An instrument-free isothermal method to detect RNA. Anal Chim Acta 2021; 1149:238130. [PMID: 33551053 DOI: 10.1016/j.aca.2020.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 12/01/2020] [Accepted: 12/04/2020] [Indexed: 10/22/2022]
Abstract
One challenge in point-of-care (POC) diagnostics is the lack of room-temperature methods for RNA detection based on enzymatic amplification and visualization steps. Here we perform reverse transcription lesion-induced DNA amplification (RT-LIDA), an isothermal amplification method that only requires T4 DNA ligase. RT-LIDA involves the RNA-templated ligation of DNA primers to form complementary DNA (cDNA) followed by toehold-mediated strand displacement of the cDNA and its exponential amplification via our isothermal ligase chain reaction LIDA. Each step is tuned to proceed at 28 °C, which falls within the range of global room temperatures. Using RT-LIDA, we can detect as little as ∼100 amol target RNA and can distinguish RNA target from total cellular RNA. Finally, we demonstrate that the resulting DNA amplicons can be detected colorimetrically, also at room temperature, by rapid, target-triggered disassembly of DNA-modified gold nanoparticles. This integrated amplification/detection platform requires no heating or visualization instrumentation, which is an important step towards realizing instrument-free POC testing.
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Affiliation(s)
| | - Yuning Liu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6E 2G2
| | - Yimeng Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6E 2G2
| | - Daria R Q de Almeida
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6E 2G2
| | - Jesse Yuzik
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6E 2G2
| | - Camilla F Mendes
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6E 2G2
| | - Julianne M Gibbs
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6E 2G2.
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40
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Liu M, Li H, Jia Y, Mak PI, Martins RP. SARS-CoV-2 RNA Detection with Duplex-Specific Nuclease Signal Amplification. Micromachines (Basel) 2021; 12:197. [PMID: 33672890 PMCID: PMC7918681 DOI: 10.3390/mi12020197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 12/23/2022]
Abstract
The emergence of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a zoonotic pathogen, has led to the outbreak of coronavirus disease 2019 (COVID-19) pandemic and brought serious threats to public health worldwide. The gold standard method for SARS-CoV-2 detection requires both reverse transcription (RT) of the virus RNA to cDNA and then polymerase chain reaction (PCR) for the cDNA amplification, which involves multiple enzymes, multiple reactions and a complicated assay optimization process. Here, we developed a duplex-specific nuclease (DSN)-based signal amplification method for SARS-CoV-2 detection directly from the virus RNA utilizing two specific DNA probes. These specific DNA probes can hybridize to the target RNA at different locations in the nucleocapsid protein gene (N gene) of SARS-CoV-2 to form a DNA/RNA heteroduplex. DSN cleaves the DNA probe to release fluorescence, while leaving the RNA strand intact to be bound to another available probe molecule for further cleavage and fluorescent signal amplification. The optimized DSN amount, incubation temperature and incubation time were investigated in this work. Proof-of-principle SARS-CoV-2 detection was demonstrated with a detection sensitivity of 500 pM virus RNA. This simple, rapid, and direct RNA detection method is expected to provide a complementary method for the detection of viruses mutated at the PCR primer-binding regions for a more precise detection.
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Affiliation(s)
- Meiqing Liu
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau 999078, China; (M.L.); (H.L.); (P.-I.M.); (R.P.M.)
| | - Haoran Li
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau 999078, China; (M.L.); (H.L.); (P.-I.M.); (R.P.M.)
- Faculty of Science and Technology–ECE, University of Macau, Macau 999078, China
| | - Yanwei Jia
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau 999078, China; (M.L.); (H.L.); (P.-I.M.); (R.P.M.)
- Faculty of Science and Technology–ECE, University of Macau, Macau 999078, China
- Faculty of Health Sciences, University of Macau, Macau 999078, China
| | - Pui-In Mak
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau 999078, China; (M.L.); (H.L.); (P.-I.M.); (R.P.M.)
- Faculty of Science and Technology–ECE, University of Macau, Macau 999078, China
| | - Rui P. Martins
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau 999078, China; (M.L.); (H.L.); (P.-I.M.); (R.P.M.)
- Faculty of Science and Technology–ECE, University of Macau, Macau 999078, China
- On Leave from Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
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Barnes WM, Zhang Z, Kermekchiev MB. A Single Amino Acid Change to Taq DNA Polymerase Enables Faster PCR, Reverse Transcription and Strand-Displacement. Front Bioeng Biotechnol 2021; 8:553474. [PMID: 33520948 PMCID: PMC7841393 DOI: 10.3389/fbioe.2020.553474] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 12/22/2020] [Indexed: 11/13/2022] Open
Abstract
A change of an aspartic acid to asparagine of Taq (Thermus aquaticus) DNA polymerase is a gain of function mutation that supports faster PCR: the extension times for PCR amplification can be 2-3 times shorter. Surprising results from negative controls led to the discovery of strand-displacement ability and reverse transcriptase activity of Taq D732N DNA polymerase. We demonstrate that the mutant enzyme can, by itself, catalyze RT-PCR, and RT-LAMP assays. Residue 732 is on the surface of the enzyme, not near the active site.
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Affiliation(s)
- Wayne M Barnes
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, United States.,DNA Polymerase Technology, Inc., St. Louis, MO, United States
| | - Zhian Zhang
- DNA Polymerase Technology, Inc., St. Louis, MO, United States
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42
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Abstract
In situ hybridization is a powerful technique that allows the visualization of specific RNA species in biological samples in exquisite detail. It has been particularly well explored in the field of developmental genetics. The spatial and temporal patterns of RNA expression provide us with critical information on likely gene function during embryonic development, and often inform the decision on whether to attempt further gene manipulation approaches. Furthermore, once a mouse strain with altered gene function has been created, in situ hybridization is a critical tool for revealing how the development of embryos with the mutation differs from that of wild-type embryos, and thus infer the function of the altered gene. Here, a well-tested protocol used to visualize RNA expression in whole-mount mid-gestation mouse embryos ranging from 8.5 to 14.5 days post-coitum (dpc) is described. © 2020 Wiley Periodicals LLC. Basic Protocol 1: RNA probe synthesis Alternate Protocol: Preparation of DNA template by PCR Basic Protocol 2: Embryo dissection Basic Protocol 3: Whole mount in situ hybridization Support Protocol: Generation of embryo powder.
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Affiliation(s)
- Annemiek Beverdam
- School of Medical Sciences, UNSW, Sydney, New South Wales, Australia.,The School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
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43
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Abstract
Understanding RNA expression in space and time is a key initial step in dissecting gene function. The ability to visualize gene expression in whole-tissue or whole-specimen preparations, called in situ hybridization (ISH), was first developed 50 years ago. Two decades later, these protocols were adapted to establish robust methods for whole-mount ISH to murine embryos. The precise protocols vary somewhat between early-gestation and mid-gestation mouse embryos; the protocol presented here is optimal for use with post-implantation stage mouse embryos (stages 5.5-9.5 dpc). Routine uses of whole-mount ISH include documenting the wild-type expression pattern of individual genes and comparison of the expression pattern of signature genes (i.e., those that identify particular cells and tissues within an embryo) between wild-type and mutant embryos as part of a phenotyping experiment. This technique remains a mainstay of developmental biology studies and complements the massively parallel assessment of gene expression from dissociated tissues and cells via RNA-sequencing techniques. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Dissection of post-implantation (5.5-9.5 dpc) murine embryos Basic Protocol 2: Whole-mount in situ hybridization in post-implantation embryos Basic Protocol 3: Visualization of post-WMISH embryos Support Protocol 1: Creation of siliconized glass pipettes Support Protocol 2: Creation of embryo powder.
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Affiliation(s)
- Kristen S Barratt
- Early Mammalian Development Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Ruth M Arkell
- Early Mammalian Development Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
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44
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Abstract
Oligonucleotide-templated reactions (OTRs) between two reactive hybridization probes allow for the detection of a DNA or RNA of interest by exploiting the target molecule as a catalyst of chemical reactions. The product of such a reaction commonly exhibits distinct fluorescence properties and can be detected by the means of fluorescence spectroscopy. The vast majority of OTR systems utilize organic dyes as fluorescent reporters. However, the use of brighter emitters, such as semiconductor quantum dots (QDs), has potential to improve the sensitivity of detection by providing brighter signals and permitting the use of probes at very low concentrations. Here we report an RNA-templated reaction between two fluorescently labeled peptide nucleic acid (PNA)-based probes, which proceeds on the surface of a QD. The QD-bound PNA probe bears a cysteine functionality, while the other PNA is functionalized with an organic dye as a thioester. OTR between these probes proceeds through a transfer of the organic dye to the QD and can be conveniently monitored via fluorescence resonance energy transfer (FRET) from the QD to the Cy5. The reaction was performed in a conventional fluorescence microplate reader and permits the detection of RNA in the picomolar range.
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Affiliation(s)
- Oleksandr Zavoiura
- Division Biophotonics, Federal Institute for Materials Research and Testing (BAM), Berlin, Germany.,Department of Chemistry, Humboldt University of Berlin, Berlin, Germany
| | - Ute Resch-Genger
- Division Biophotonics, Federal Institute for Materials Research and Testing (BAM), Berlin, Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt University of Berlin, Berlin, Germany.
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45
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Yin X, Sun Y, Yang R, Qu L, Li Z. RNA-responsive fluorescent carbon dots for fast and wash-free nucleolus imaging. Spectrochim Acta A Mol Biomol Spectrosc 2020; 237:118381. [PMID: 32334324 DOI: 10.1016/j.saa.2020.118381] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 04/14/2020] [Accepted: 04/14/2020] [Indexed: 06/11/2023]
Abstract
RNA as a carrier of genetic information plays a critical role in various physiological processes. RNA-rich nucleolus is usually employed as an important biomarker for many malignant diseases. Herein, RNA-responsive fluorescent carbon dots (CDs) were synthesized by a simple microwave method. Due to the presence of cationic benzothiazolium groups in the CDs, a "turn-on" fluorescence signal was achieved between CDs and RNA. The CDs exhibit excellent RNA selectivity and a good linear relationship with a detection limit of 0.62 μg/mL. The small particle size, polarity sensitivity and RNA response behavior of CDs realized fast and wash-free nucleolus imaging effectively. Overall, these CDs provide a powerful potential tool for monitoring cell nucleus activity and elucidating RNA dynamics.
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Affiliation(s)
- Xiaohui Yin
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou University, Zhengzhou 450001, China
| | - Yuanqiang Sun
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou University, Zhengzhou 450001, China.
| | - Ran Yang
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou University, Zhengzhou 450001, China
| | - Lingbo Qu
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou University, Zhengzhou 450001, China
| | - Zhaohui Li
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou University, Zhengzhou 450001, China.
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46
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Jiao J, Duan C, Xue L, Liu Y, Sun W, Xiang Y. DNA nanoscaffold-based SARS-CoV-2 detection for COVID-19 diagnosis. Biosens Bioelectron 2020; 167:112479. [PMID: 32763826 PMCID: PMC7387931 DOI: 10.1016/j.bios.2020.112479] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 07/24/2020] [Accepted: 07/25/2020] [Indexed: 12/13/2022]
Abstract
COVID-19 pandemic outbreak is the most astounding scene ever experienced in the 21st century. It has been determined to be caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). With the global pandemic, the lack of efficient rapid and accurate molecular diagnostic testing tools has hindered the public opportunely response to the emerging viral threat. Herein, a DNA nanoscaffold hybrid chain reaction (DNHCR)-based nucleic acid assay strategy is reported for rapid detection of SARS-CoV-2 RNA. In this method, the DNA nanoscaffolds have been first constructed by the self-assembly of long DNA strands and self-quenching probes (H1). Then, the SARS-CoV-2 RNA will initiate the hybridization of H1 and free H2 DNA probes along the nanoscaffold, and an illuminated DNA nanostring is instantly obtained. By taking advantages of the localization design of the H1 probes and the temperature tolerance of the isothermal amplification, the proposed DNHCR method can detect target at short responding time (within 10 min) and mild condition (15 °C–35 °C). Moreover, the reliability of DNHCR method in serum and saliva samples have also been validated. Therefore, DNHCR-based method is expected to provide a simple and faster alternative to the traditional SARS-CoV-2 qRT-PCR assay. A simple and specific method has proposed for the assay of SARS-CoV-2 RNAs. Compared with the qRT-PCR, this new method is rapid (about 10 min) and has a wide temperature range (15°C–35°C). This method can complete the detection in only one step, thereby avoiding possible secondary pollution. This method proposed a trajectory hybrid chain reaction , which can improve the detection efficiency.
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Affiliation(s)
- Jin Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, PR China
| | - Chengjie Duan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, PR China
| | - Lan Xue
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, PR China
| | - Yunfei Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, PR China
| | - Weihao Sun
- Department of Geriatric Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210023, PR China.
| | - Yang Xiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, PR China.
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Maponga TG, Lopes T, Cable R, Pistorius C, Preiser W, Andersson MI. Prevalence and risks of hepatitis E virus infection in blood donors from the Western Cape, South Africa. Vox Sang 2020; 115:695-702. [PMID: 32597542 DOI: 10.1111/vox.12966] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 06/03/2020] [Accepted: 06/03/2020] [Indexed: 01/18/2023]
Abstract
BACKGROUND Transfusion-transmitted hepatitis E virus (HEV) infection is a potential risk to recipients of blood transfusions. Infection with HEV poses a high risk to immunocompromised recipients with an increased likelihood of developing chronic infection. The aims of this study were to determine the prevalence of past and active HEV infections in donors from the Western Cape and to identify the risk factors associated with infection. MATERIALS AND METHODS We prospectively tested 10 250 blood donors for HEV infection. A risk factor sub-study investigated 250 donors who completed a questionnaire, and plasma samples were tested for HEV IgG antibodies and pooled for HEV RNA detection. The demographic and risk factors associated with HEV infection were assessed. The molecular study tested 10 000 individual donations using a commercial assay to detect viraemia. HEV viral load and genotype were also determined. RESULTS The overall anti-HEV IgG seroprevalence was 42·8% (107/250) among donors participating in the risk factor sub-study. The likelihood of past HEV infection was higher with an increase in age. Of the 10 000 donor samples individually tested for HEV RNA, one sample was positive with a viral load of 7·9 x 104 IU/ml and belonged to HEV genotype 3. CONCLUSION We found a high seroprevalence of anti-HEV IgG but a low HEV RNA prevalence among donors in the Western Cape, South Africa. The study provides evidence for a potential risk of HEV contamination in the blood supply in South Africa. A cost-benefit analysis is needed before considering the introduction of routine donor screening in our setting.
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Affiliation(s)
- Tongai G Maponga
- Division of Medical Virology, Faculty of Medicine and Health Sciences, University of Stellenbosch, Cape Town, South Africa
| | - Tatum Lopes
- Division of Medical Virology, Faculty of Medicine and Health Sciences, University of Stellenbosch, Cape Town, South Africa
| | | | | | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, University of Stellenbosch, Cape Town, South Africa.,Tygerberg Business Unit, National Health Laboratory Service, Cape Town, South Africa
| | - Monique I Andersson
- Division of Medical Virology, Faculty of Medicine and Health Sciences, University of Stellenbosch, Cape Town, South Africa.,Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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48
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Zou J, Zhi S, Chen M, Su X, Kang L, Li C, Su X, Zhang S, Ge S, Li W. Heat inactivation decreases the qualitative real-time RT-PCR detection rates of clinical samples with high cycle threshold values in COVID-19. Diagn Microbiol Infect Dis 2020; 98:115109. [PMID: 32593875 PMCID: PMC7289114 DOI: 10.1016/j.diagmicrobio.2020.115109] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 06/07/2020] [Accepted: 06/07/2020] [Indexed: 01/07/2023]
Abstract
SARS-CoV-2 has caused COVID-19 pandemic globally in the beginning of 2020, and qualitative real-time RT-PCR has become the gold standard in diagnosis. As SARSCoV-2 with strong transmissibility and pathogenicity, it has become a professional consensus that clinical samples from suspected patients should be heat inactivated at 56°C for 30 min before further processing. However, previous studies on the effect of inactivation on qualitative real-time RT-PCR were conducted with diluted samples rather than clinical samples. The aim of this study was to investigate whether heat inactivation on clinical samples before detection will affect the accuracy of qualitative real-time RT-PCR detection. All 46 throat swab samples from 46 confirmed inpatients were detected by qualitative real-time RT-PCR directly, as well as after heat inactivation. Heat-Inactivation has significantly influenced the qualitative detection results on clinical samples, especially weakly positive samples. The results indicate the urgency to establish a more suitable protocol for COVID-19 clinical sample's inactivation.
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Affiliation(s)
- Jingbo Zou
- Yongchuan District Center for Disease Control and Prevention of Chongqing, Changjiang Road, Yuzhong District, Chongqing, China.
| | - Shenshen Zhi
- Chongqing University Central Hospital, Chongqing Emergency Medical Center, Jiankang Road, Yuzhong District, Chongqing, China.
| | - Mengyuan Chen
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiang'an Campus of Xiamen University, South Xiang'an Rd., Xiamen, China; State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiang'an Campus of Xiamen University, South Xiang'an Rd., Xiamen, China; School of Public Health, Xiamen University, Xiang'an Campus of Xiamen University, South Xiang'an Rd., Xiamen, China.
| | - Xingyu Su
- Yongchuan Health Center for Women and Children, Renmin Avenue, Yongchuan District, Chongqing, China.
| | - Ling Kang
- Yongchuan District Hospital of traditional Chinese Medicine, Yingbin Avenue, Yongchuan District, Chongqing, China.
| | - Caiyu Li
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiang'an Campus of Xiamen University, South Xiang'an Rd., Xiamen, China; State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiang'an Campus of Xiamen University, South Xiang'an Rd., Xiamen, China; School of Public Health, Xiamen University, Xiang'an Campus of Xiamen University, South Xiang'an Rd., Xiamen, China.
| | - Xiaosong Su
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiang'an Campus of Xiamen University, South Xiang'an Rd., Xiamen, China; State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiang'an Campus of Xiamen University, South Xiang'an Rd., Xiamen, China; School of Public Health, Xiamen University, Xiang'an Campus of Xiamen University, South Xiang'an Rd., Xiamen, China.
| | - Shiyin Zhang
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiang'an Campus of Xiamen University, South Xiang'an Rd., Xiamen, China; State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiang'an Campus of Xiamen University, South Xiang'an Rd., Xiamen, China; School of Public Health, Xiamen University, Xiang'an Campus of Xiamen University, South Xiang'an Rd., Xiamen, China.
| | - Shengxiang Ge
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiang'an Campus of Xiamen University, South Xiang'an Rd., Xiamen, China; State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiang'an Campus of Xiamen University, South Xiang'an Rd., Xiamen, China; School of Public Health, Xiamen University, Xiang'an Campus of Xiamen University, South Xiang'an Rd., Xiamen, China.
| | - Wei Li
- Chongqing University Central Hospital, Chongqing Emergency Medical Center, Jiankang Road, Yuzhong District, Chongqing, China.
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49
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Shivalingam A, Taemaitree L, El-Sagheer AH, Brown T. Squaramides and Ureas: A Flexible Approach to Polymerase-Compatible Nucleic Acid Assembly. Angew Chem Int Ed Engl 2020; 59:11416-11422. [PMID: 32153132 PMCID: PMC7383975 DOI: 10.1002/anie.202000209] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/28/2020] [Indexed: 12/15/2022]
Abstract
Joining oligonucleotides together (ligation) is a powerful means of retrieving information from the nanoscale. To recover this information, the linkages created must be compatible with polymerases. However, enzymatic ligation is restrictive and current chemical ligation methods lack flexibility. Herein, a versatile ligation platform based on the formation of urea and squaramide artificial backbones from minimally modified 3′‐ and 5′‐amino oligonucleotides is described. One‐pot ligation gives a urea linkage with excellent read‐through speed, or a squaramide linkage that is read‐through under selective conditions. The squaramide linkage can be broken and reformed on demand, while stable pre‐activated precursor oligonucleotides expand the scope of the ligation reaction to reagent‐free, mild conditions. The utility of our system is demonstrated by replacing the enzymatically biased RNA‐to‐DNA reverse transcription step of RT‐qPCR with a rapid nucleic‐acid‐template‐dependent DNA chemical ligation system, that allows direct RNA detection.
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Affiliation(s)
- Arun Shivalingam
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Lapatrada Taemaitree
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK.,Department of Science and Mathematics, Suez University, Faculty of Petroleum and Mining Engineering, Suez, 43721, Egypt
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
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50
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Mathengtheng L, Goedhals D, Bester PA, Goedhals J, Burt FJ. Persistence of Crimean-Congo Hemorrhagic Fever Virus RNA. Emerg Infect Dis 2020; 26:385-387. [PMID: 31961316 PMCID: PMC6986852 DOI: 10.3201/eid2602.191460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Crimean-Congo hemorrhagic fever virus (CCHFV) causes severe disease with fatalities. Awareness of potential sources of infection is important to reduce risk to healthcare workers and contacts. We detected CCHFV RNA in formalin-fixed, paraffin-embedded tissues from a spontaneous abortion that were submitted for histology 9 weeks after a suspected CCHFV infection in the mother.
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