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Suprun EV, Khmeleva SA, Duskaev IF, Ptitsyn KG, Kurbatov LK, Shershov VE, Kuznetsova VE, Lapa SA, Chudinov AV, Radko SP. Combining recombinase polymerase amplification with tyrosine modified 2'-deoxyuridine-5'-triphosphate for direct voltammetric detection of double-stranded DNA: Application to potato pathogen Dickeya solani. Talanta 2024; 273:125841. [PMID: 38460421 DOI: 10.1016/j.talanta.2024.125841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/11/2024]
Abstract
The approach based on a combination of isothermal recombinase polymerase amplification (RPA), 2'-deoxyuridine-5'-triphosphate modified with tyrosine aromatic group (dUTP-Y1), and direct voltammetric detection of RPA product carrying electroactive labels was successfully applied to the potato pathogen Dickeya solani. The artificial nucleotide dUTP-Y1 demonstrated a good compatibility with RPA, enabling by targeting a section of D. solani genome with a unique sequence to produce the full-size modified products at high levels of substitution of dTTP by dUTP-Y1 (up to 80-90 %) in the reaction mixture. The optimized procedure of square wave voltammetry allowed to reliably detect the product generated by RPA at 80 % substitution of dTTP by dUTP-Y1 (dsDNA-Y1) in microliter sample volumes on the surface of disposable carbon screen printed electrodes at the potential of about 0.6 V. The calibration curve for the amplicon detection was linear in coordinates 'Ip, A vs. Log (c, M)' within the 0.05-1 μM concentration range. The limit of detection for dsDNA-Y1 was estimated as 8 nM. The sensitivity of the established electrochemical approach allowed to detect amplicons generated in a single standard 50 μL RPA reaction after their purification with silica-coated magnetic beads. The overall detectability of D. solani with the suggested combination of RPA and voltammetric registration of dsDNA-Y1 can be as low as a few copies of bacterial genome per standard reaction. In total, amplification, purification, and electrochemical detection take about 120-150 min. Considering the potential of direct electrochemical analysis for miniaturization, as well as compliance with low-cost and low-power requirements, the findings provide grounds for future development of microfluidic devices integrating isothermal amplification, amplicon purification and detection based on the tyrosine modified nucleotide for the purpose of 'on-site' detection of various pathogens.
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Affiliation(s)
- Elena V Suprun
- Chemistry Faculty of M.V. Lomonosov Moscow State University, Lenin Hills, 1/3, Moscow, 119991, Russia; Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow, 119121, Russia.
| | - Svetlana A Khmeleva
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow, 119121, Russia
| | - Insaf F Duskaev
- Chemistry Faculty of M.V. Lomonosov Moscow State University, Lenin Hills, 1/3, Moscow, 119991, Russia; Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow, 119121, Russia
| | - Konstantin G Ptitsyn
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow, 119121, Russia
| | - Leonid K Kurbatov
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow, 119121, Russia
| | - Valeriy E Shershov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street, 32, Moscow, 119991, Russia
| | - Viktoriya E Kuznetsova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street, 32, Moscow, 119991, Russia
| | - Sergey A Lapa
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street, 32, Moscow, 119991, Russia
| | - Alexander V Chudinov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street, 32, Moscow, 119991, Russia
| | - Sergey P Radko
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow, 119121, Russia
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Burkin KM, Ivanov AV, Zherdev AV, Dzantiev BB, Safenkova IV. A Critical Study on DNA Probes Attached to Microplate for CRISPR/Cas12 Trans-Cleavage Activity. BIOSENSORS 2023; 13:824. [PMID: 37622910 PMCID: PMC10452489 DOI: 10.3390/bios13080824] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/03/2023] [Accepted: 08/15/2023] [Indexed: 08/26/2023]
Abstract
CRISPR/Cas12-based biosensors are emerging tools for diagnostics. However, their application of heterogeneous formats needs the efficient detection of Cas12 activity. We investigated DNA probes attached to the microplate surface and cleaved by Cas12a. Single-stranded (ss) DNA probes (19 variants) and combined probes with double-stranded (ds) and ssDNA parts (eight variants) were compared. The cleavage efficiency of dsDNA-probes demonstrated a bell-shaped dependence on their length, with a cleavage maximum of 50%. On the other hand, the cleavage efficiency of ssDNA probes increased monotonously, reaching 70%. The most effective ssDNA probes were integrated with fluorescein, antibodies, and peroxidase conjugates as reporters for fluorescent, lateral flow, and chemiluminescent detection. Long ssDNA probes (120-145 nt) proved the best for detecting Cas12a trans-activity for all of the tested variants. We proposed a test system for the detection of the nucleocapsid (N) gene of SARS-CoV-2 based on Cas12 and the ssDNA-probe attached to the microplate surface; its fluorescent limit of detection was 0.86 nM. Being united with pre-amplification using recombinase polymerase, the system reached a detection limit of 0.01 fM, thus confirming the effectiveness of the chosen ssDNA probe for Cas12-based biosensors.
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Affiliation(s)
| | | | | | | | - Irina V. Safenkova
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (K.M.B.); (A.V.I.); (A.V.Z.); (B.B.D.)
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Ivanov AV, Safenkova IV, Zherdev AV, Wan Y, Dzantiev BB. Comparison of Single-Stranded DNA Probes Conjugated with Magnetic Particles for Trans-Cleavage in Cas12a-Based Biosensors. BIOSENSORS 2023; 13:700. [PMID: 37504099 PMCID: PMC10376970 DOI: 10.3390/bios13070700] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/29/2023]
Abstract
Biosensors based on endonuclease Cas12 provide high specificity in pathogen detection. Sensitive detection using Cas12-based assays can be achieved using trans-cleaved DNA probes attached to simply separated carriers, such as magnetic particles (MPs). The aim of this work was to compare polyA, polyC, and polyT single-stranded (ss) DNA with different lengths (from 10 to 145 nt) as trans-target probes were immobilized on streptavidin-covered MPs. Each ssDNA probe was labeled using fluorescein (5') and biotin (3'). To compare the probes, we used guide RNAs that were programmed for the recognition of two bacterial pathogens: Dickeya solani (causing blackleg and soft rot) and Erwinia amylovora (causing fire blight). The Cas12 was activated by targeting double-stranded DNA fragments of D. solani or E. amylovora and cleaved the MP-ssDNA conjugates. The considered probes demonstrated basically different dependencies in terms of cleavage efficiency. PolyC was the most effective probe when compared to polyA or polyT probes of the same length. The minimal acceptable length for the cleavage follows the row: polyC < polyT < polyA. The efficiencies of polyC and polyT probes with optimal length were proven for the DNA targets' detection of D. solani and E. amylovora. The regularities found can be used in Cas12a-based detection of viruses, bacteria, and other DNA/RNA-containing analytes.
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Affiliation(s)
- Aleksandr V Ivanov
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Irina V Safenkova
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Anatoly V Zherdev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Yi Wan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Hainan University, Haikou 570228, China
| | - Boris B Dzantiev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
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Ivanov AV, Safenkova IV, Biketov SF, Zherdev AV, Dzantiev BB. Engineering of DNA Structures Attached to Magnetic Particles for Effective Trans- and Cis-Cleavage in Cas12-Based Biosensors. Int J Mol Sci 2023; 24:ijms24054484. [PMID: 36901914 PMCID: PMC10003267 DOI: 10.3390/ijms24054484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/15/2023] [Accepted: 02/22/2023] [Indexed: 03/12/2023] Open
Abstract
Sequence-specific endonuclease Cas12-based biosensors have rapidly evolved as a strong tool to detect nucleic acids. Magnetic particles (MPs) with attached DNA structures could be used as a universal platform to manipulate the DNA-cleavage activity of Cas12. Here, we propose nanostructures of trans- and cis-DNA targets immobilized on the MPs. The main advantage of the nanostructures is a rigid double-stranded DNA adaptor that distances the cleavage site from the MP surface to ensure maximum Cas12 activity. Adaptors with different lengths were compared by detecting the cleavage by fluorescence and gel electrophoresis of the released DNA fragments. The length-dependent effects for cleavage on the MPs' surface were found both for cis- and trans-targets. For trans-DNA targets with a cleavable 15-dT tail, the results showed that the optimal range of the adaptor length was 120-300 bp. For cis-targets, we varied the length and location of the adaptor (at the PAM or spacer ends) to estimate the effect of the MP's surface on the PAM-recognition process or R-loop formation. The sequential arrangement of an adaptor, PAM, and a spacer was preferred and required the minimum adaptor length of 3 bp. Thus, with cis-cleavage, the cleavage site can be located closer to the surface of the MPs than with trans-cleavage. The findings provide solutions for efficient Cas12-based biosensors using surface-attached DNA structures.
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Affiliation(s)
- Aleksandr V. Ivanov
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Irina V. Safenkova
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
- Correspondence: ; Tel./Fax: +7-495-954-2804
| | - Sergey F. Biketov
- State Research Center for Applied Microbiology & Biotechnology, 142279 Obolensk, Moscow Region, Russia
| | - Anatoly V. Zherdev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Boris B. Dzantiev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
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Tang W, Yang D, Ma J, Chen J, Xie Y, Sun H, Zhang C. Development of a dual RT-RPA detection for Sweet potato feathery mottle virus and Sweet potato chlorotic stuntvirus. Mol Cell Probes 2022; 65:101846. [PMID: 35840109 DOI: 10.1016/j.mcp.2022.101846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/08/2022] [Accepted: 07/08/2022] [Indexed: 11/26/2022]
Abstract
The disease co-infected by Sweet potato feathery mottle virus (SPFMV) and Sweet potato chlorotic stunt virus (SPCSV) is devastating in sweet potato, as it would give rise to the serious losses in both production and quality. Consequently, it is conducive for preventing and controlling this disease to detect these two viruses accurately and timely. Here we developed and optimized a dual reverse transcription recombinase polymerase amplification (RT-RPA) for rapid and accurate detection of SPFMV and SPCSV. Four special primers were designed based on the conserved sequences of SPFMV and SPCSV, respectively. The sensitivity of dual RT-RPA for SPFMV and SPCSV was 10-4 ng/μL at the optimal conditions in which the primer ratio between SPFMV and SPCSV was 2:1, and the reaction incubated for 25 min at a temperature of 39 °C. Both 61 sweet potato samples and 5 morning glory samples collected from China were tested using the dual RT-RPA successfully. Therefore, the dual RT-RPA is a reliable, rapid, sensitive method to detect these two viruses in sweet potato. It is the RT-RPA that was used for detection of SPFMV and SPCSV simultaneously firstly. This dual RT-RPA, as a convenient and powerful tool, will be useful to diagnose SPFMV and SPCSV.
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Affiliation(s)
- Wei Tang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai Area, Key Laboratory of Biology and Genetic Improvement of Sweet Potato, Ministry of Agriculture, Jiangsu Xuzhou Sweet Potato Research Center, Xuzhou, 221131, Jiangsu, China
| | - Dongjing Yang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai Area, Key Laboratory of Biology and Genetic Improvement of Sweet Potato, Ministry of Agriculture, Jiangsu Xuzhou Sweet Potato Research Center, Xuzhou, 221131, Jiangsu, China
| | - Jukui Ma
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai Area, Key Laboratory of Biology and Genetic Improvement of Sweet Potato, Ministry of Agriculture, Jiangsu Xuzhou Sweet Potato Research Center, Xuzhou, 221131, Jiangsu, China
| | - Jingwei Chen
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai Area, Key Laboratory of Biology and Genetic Improvement of Sweet Potato, Ministry of Agriculture, Jiangsu Xuzhou Sweet Potato Research Center, Xuzhou, 221131, Jiangsu, China
| | - Yiping Xie
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai Area, Key Laboratory of Biology and Genetic Improvement of Sweet Potato, Ministry of Agriculture, Jiangsu Xuzhou Sweet Potato Research Center, Xuzhou, 221131, Jiangsu, China
| | - Houjun Sun
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai Area, Key Laboratory of Biology and Genetic Improvement of Sweet Potato, Ministry of Agriculture, Jiangsu Xuzhou Sweet Potato Research Center, Xuzhou, 221131, Jiangsu, China.
| | - Chengling Zhang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai Area, Key Laboratory of Biology and Genetic Improvement of Sweet Potato, Ministry of Agriculture, Jiangsu Xuzhou Sweet Potato Research Center, Xuzhou, 221131, Jiangsu, China.
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Ivanov AV, Safenkova IV, Zherdev AV, Dzantiev BB. DIRECT 2: A novel platform for a CRISPR-Cas12-based assay comprising universal DNA-IgG probe and a direct lateral flow test. Biosens Bioelectron 2022; 208:114227. [PMID: 35390717 DOI: 10.1016/j.bios.2022.114227] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/17/2022] [Accepted: 03/25/2022] [Indexed: 12/14/2022]
Abstract
CRISPR-Cas12-based biosensors are a promising tool for the detection of nucleic acids. After dsDNA-target-activated Cas12 cleaves the ssDNA probe, a lateral flow test (LFT) is applied for rapid, simple, and out-of-laboratory detection of the cleaved probe. However, most of the existing approaches of LFT detection have disadvantages related to inverted test/control zones in which the assay result depends not only on the cleavage of the probe but also on the second factor: the binding of the non-cleaved probe in the control zone. We proposed a novel platform for the detection of trans-cleaved DNA using a universal DNA-IgG probe and LFT with the sequential direct location of test and control zones. The advantage of the platform consists of the assay result depending only on the cleaved probe. For this, we designed a composite probe that comprise two parts: the DNA part (biotinylated dsDNA connected to ssDNA with fluorescein) (FAM), and the antibody part (mouse anti-FAM IgG). The Cas12, with guide RNA, was activated by the dsDNA-target. The activated Cas12 cleaved the probe, releasing the ssDNA-FAM-IgG reporter that was detected by the LFT. The sandwich LFT was proposed with anti-mouse IgG adsorbed in the test zone and on the surface of gold nanoparticles. We called the platform with direct location zones and direct analyte-signal dependence the DNA-Immunoglobulin Reporter Endonuclease Cleavage Test (DIRECT2). Therefore, this proof-of-concept study demonstrated that the combination of the proposed DNA-IgG probe and direct LFT opens new opportunities for CRISPR-Cas12 activity detection and its bioanalytical applications.
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Affiliation(s)
- Aleksandr V Ivanov
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071, Moscow, Russia
| | - Irina V Safenkova
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071, Moscow, Russia
| | - Anatoly V Zherdev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071, Moscow, Russia
| | - Boris B Dzantiev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071, Moscow, Russia.
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Mohammad-Razdari A, Rousseau D, Bakhshipour A, Taylor S, Poveda J, Kiani H. Recent advances in E-monitoring of plant diseases. Biosens Bioelectron 2022; 201:113953. [PMID: 34998118 DOI: 10.1016/j.bios.2021.113953] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 12/20/2021] [Accepted: 12/30/2021] [Indexed: 02/09/2023]
Abstract
Infectious plant diseases are caused by pathogenic microorganisms, such as fungi, oomycetes, bacteria, viruses, phytoplasma, and nematodes. Plant diseases have a significant effect on the plant quality and yield and they can destroy the entire plant if they are not controlled in time. To minimize disease-related losses, it is essential to identify and control pathogens in the early stages. Plant disease control is thus a fundamental challenge both for global food security and sustainable agriculture. Conventional methods for plant diseases control have given place to electronic control (E-monitoring) due to their lack of portability, being time consuming, need for a specialized user, etc. E-monitoring using electronic nose (e-nose), biosensors, wearable sensors, and 'electronic eyes' has attracted increasing attention in recent years. Detection, identification, and quantification of pathogens based on electronic sensors (E-sensors) are both convenient and practical and may be used in combination with conventional methods. This paper discusses recent advances made in E-sensors as component parts in combination with wearable sensors, in electronic sensing systems to control and detect viruses, bacteria, pathogens and fungi. In addition, future challenges using sensors to manage plant diseases are investigated.
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Affiliation(s)
- Ayat Mohammad-Razdari
- Department of Mechanical Engineering of Biosystems, Shahrekord University, 8818634141, Shahrekord, Iran.
| | - David Rousseau
- Angevin de Recherche en Ingénierie des Systèmes (LARIS), UMR INRAe IRHS, Université d'Angers, France
| | - Adel Bakhshipour
- Department of Biosystems Engineering, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | - Stephen Taylor
- Mass Spectrometry and Instrumentation Group, Department of Electrical Engineering and Electronics, University of Liverpool, Liverpool, L69 3GJ, UK.
| | - Jorge Poveda
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Universidad Pública de Navarra (UPNA), Campus Arrosadía, Pamplona, Spain
| | - Hassan Kiani
- Department of Biosystems Engineering, Science and Research Branch, Islamic Azad University, Tehran, Iran
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Ivanov AV, Safenkova IV, Zherdev AV, Dzantiev BB. The Potential Use of Isothermal Amplification Assays for In-Field Diagnostics of Plant Pathogens. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112424. [PMID: 34834787 PMCID: PMC8621059 DOI: 10.3390/plants10112424] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 11/02/2021] [Accepted: 11/05/2021] [Indexed: 05/27/2023]
Abstract
Rapid, sensitive, and timely diagnostics are essential for protecting plants from pathogens. Commonly, PCR techniques are used in laboratories for highly sensitive detection of DNA/RNA from viral, viroid, bacterial, and fungal pathogens of plants. However, using PCR-based methods for in-field diagnostics is a challenge and sometimes nearly impossible. With the advent of isothermal amplification methods, which provide amplification of nucleic acids at a certain temperature and do not require thermocyclic equipment, going beyond the laboratory has become a reality for molecular diagnostics. The amplification stage ceases to be limited by time and instruments. Challenges to solve involve finding suitable approaches for rapid and user-friendly plant preparation and detection of amplicons after amplification. Here, we summarize approaches for in-field diagnostics of phytopathogens based on different types of isothermal amplification and discuss their advantages and disadvantages. In this review, we consider a combination of isothermal amplification methods with extraction and detection methods compatible with in-field phytodiagnostics. Molecular diagnostics in out-of-lab conditions are of particular importance for protecting against viral, bacterial, and fungal phytopathogens in order to quickly prevent and control the spread of disease. We believe that the development of rapid, sensitive, and equipment-free nucleic acid detection methods is the future of phytodiagnostics, and its benefits are already visible.
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Ivanov AV, Safenkova IV, Zherdev AV, Dzantiev BB. Recombinase Polymerase Amplification Assay with and without Nuclease-Dependent-Labeled Oligonucleotide Probe. Int J Mol Sci 2021; 22:11885. [PMID: 34769313 PMCID: PMC8584857 DOI: 10.3390/ijms222111885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 01/18/2023] Open
Abstract
The combination of recombinase polymerase amplification (RPA) and lateral flow test (LFT) is a strong diagnostic tool for rapid pathogen detection in resource-limited conditions. Here, we compared two methods generating labeled RPA amplicons following their detection by LFT: (1) the basic one with primers modified with different tags at the terminals and (2) the nuclease-dependent one with the primers and labeled oligonucleotide probe for nuclease digestion that was recommended for the high specificity of the assay. Using both methods, we developed an RPA-LFT assay for the detection of worldwide distributed phytopathogen-alfalfa mosaic virus (AMV). A forward primer modified with fluorescein and a reverse primer with biotin and fluorescein-labeled oligonucleotide probe were designed and verified by RPA. Both labeling approaches and their related assays were characterized using the in vitro-transcribed mRNA of AMV and reverse transcription reaction. The results demonstrated that the RPA-LFT assay based on primers-labeling detected 103 copies of RNA in reaction during 30 min and had a half-maximal binding concentration 22 times lower than probe-dependent RPA-LFT. The developed RPA-LFT was successfully applied for the detection of AMV-infected plants. The results can be the main reason for choosing simple labeling with primers for RPA-LFT for the detection of other pathogens.
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Affiliation(s)
| | | | | | - Boris B. Dzantiev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia; (A.V.I.); (I.V.S.); (A.V.Z.)
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Ivanov AV, Safenkova IV, Zherdev AV, Dzantiev BB. Multiplex Assay of Viruses Integrating Recombinase Polymerase Amplification, Barcode-Anti-Barcode Pairs, Blocking Anti-Primers, and Lateral Flow Assay. Anal Chem 2021; 93:13641-13650. [PMID: 34586776 DOI: 10.1021/acs.analchem.1c03030] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A multiplex assay based on recombinase polymerase amplification (RPA) and lateral flow test (LFT) is a desirable tool for many areas. This multiplex assay could be efficiently realized using single-stranded (ss) DNAs located in separate zones on the test strip and bound complementary ssDNA tags of double-stranded (ds) DNA amplicons. Here, we investigate how to enrich multiplex assay capabilities using ssDNAs. Bifunctional oligonucleotide probes integrating (1) a forward primer for RPA, (2) a C9 spacer to stop polymerase, and (3) a ssDNA tag for binding at test strip are developed. The amplicons have a unique individual ssDNA tag at one end and a universal label of fluorescein introducing through a reverse primer at the other end. A conjugate of gold nanoparticles (GNP) with antibodies to fluorescein is used to detect all amplicons. The remainder of primers after RPA interacting with GNP conjugate was found to be a limiting factor for sensitive and specific multiplex assay. The addition of anti-RPA-primers before the use of test strips was proposed to simply and effectively eliminate remaining primers. This approach was successfully applied for the detection of three priority plant RNA viruses: potato virus Y (PVY), -S (PVS) and potato leafroll virus (PLRV). The total time of the assay is 30 min. The multiplex RPA-LFT detected at least 4 ng of PVY per g of plant leaves, 0.04 ng/g for PVS, and 0.04 ng/g for PLRV. The testing of healthy and infected potato samples showed concordance between the developed assay and reverse transcription-polymerase chain reaction. Thus, the capabilities of the proposed universal modules (ssDNA anchors, bifunctional probes, and blocking anti-primers) for multiplex detection of RNA analytes with high specificity and sensitivity were demonstrated.
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Affiliation(s)
- Alexandr V Ivanov
- Research Centre of Biotechnology of the Russian Academy of Sciences, A.N. Bach Institute of Biochemistry, 119071 Moscow, Russia
| | - Irina V Safenkova
- Research Centre of Biotechnology of the Russian Academy of Sciences, A.N. Bach Institute of Biochemistry, 119071 Moscow, Russia
| | - Anatoly V Zherdev
- Research Centre of Biotechnology of the Russian Academy of Sciences, A.N. Bach Institute of Biochemistry, 119071 Moscow, Russia
| | - Boris B Dzantiev
- Research Centre of Biotechnology of the Russian Academy of Sciences, A.N. Bach Institute of Biochemistry, 119071 Moscow, Russia
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Di Nardo F, Chiarello M, Cavalera S, Baggiani C, Anfossi L. Ten Years of Lateral Flow Immunoassay Technique Applications: Trends, Challenges and Future Perspectives. SENSORS (BASEL, SWITZERLAND) 2021; 21:5185. [PMID: 34372422 PMCID: PMC8348896 DOI: 10.3390/s21155185] [Citation(s) in RCA: 165] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 12/22/2022]
Abstract
The Lateral Flow Immunoassay (LFIA) is by far one of the most successful analytical platforms to perform the on-site detection of target substances. LFIA can be considered as a sort of lab-in-a-hand and, together with other point-of-need tests, has represented a paradigm shift from sample-to-lab to lab-to-sample aiming to improve decision making and turnaround time. The features of LFIAs made them a very attractive tool in clinical diagnostic where they can improve patient care by enabling more prompt diagnosis and treatment decisions. The rapidity, simplicity, relative cost-effectiveness, and the possibility to be used by nonskilled personnel contributed to the wide acceptance of LFIAs. As a consequence, from the detection of molecules, organisms, and (bio)markers for clinical purposes, the LFIA application has been rapidly extended to other fields, including food and feed safety, veterinary medicine, environmental control, and many others. This review aims to provide readers with a 10-years overview of applications, outlining the trends for the main application fields and the relative compounded annual growth rates. Moreover, future perspectives and challenges are discussed.
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Affiliation(s)
- Fabio Di Nardo
- Department of Chemistry, University of Torino, 10125 Torino, Italy; (M.C.); (S.C.); (C.B.); (L.A.)
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