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Safenkova IV, Samokhvalov AV, Serebrennikova KV, Eremin SA, Zherdev AV, Dzantiev BB. DNA Probes for Cas12a-Based Assay with Fluorescence Anisotropy Enhanced Due to Anchors and Salts. BIOSENSORS 2023; 13:1034. [PMID: 38131794 PMCID: PMC10741848 DOI: 10.3390/bios13121034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023]
Abstract
CRISPR/Cas12a is a potent biosensing tool known for its high specificity in DNA analysis. Cas12a recognizes the target DNA and acquires nuclease activity toward single-stranded DNA (ssDNA) probes. We present a straightforward and versatile approach to transforming common Cas12a-cleavable DNA probes into enhancing tools for fluorescence anisotropy (FA) measurements. Our study involved investigating 13 ssDNA probes with linear and hairpin structures, each featuring fluorescein at one end and a rotation-slowing tool (anchor) at the other. All anchors induced FA changes compared to fluorescein, ranging from 24 to 110 mr. Significant FA increases (up to 180 mr) were obtained by adding divalent metal salts (Mg2+, Ca2+, Ba2+), which influenced the rigidity and compactness of the DNA probes. The specific Cas12a-based recognition of double-stranded DNA (dsDNA) fragments of the bacterial phytopathogen Erwinia amylovora allowed us to determine the optimal set (probe structure, anchor, concentration of divalent ion) for FA-based detection. The best sensitivity was obtained using a hairpin structure with dC10 in the loop and streptavidin located near the fluorescein at the stem in the presence of 100 mM Mg2+. The detection limit of the dsDNA target was equal to 0.8 pM, which was eight times more sensitive compared to the common fluorescence-based method. The enhancing set ensured detection of single cells of E. amylovora per reaction in an analysis based on CRISPR/Cas12a with recombinase polymerase amplification. Our approach is universal and easy to implement. Combining FA with Cas12a offers enhanced sensitivity and signal reliability and could be applied to different DNA and RNA analytes.
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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, Moscow 119071, Russia; (I.V.S.); (A.V.S.); (K.V.S.); (S.A.E.); (A.V.Z.)
| | - Alexey V. Samokhvalov
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (I.V.S.); (A.V.S.); (K.V.S.); (S.A.E.); (A.V.Z.)
| | - Kseniya V. Serebrennikova
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (I.V.S.); (A.V.S.); (K.V.S.); (S.A.E.); (A.V.Z.)
| | - Sergei A. Eremin
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (I.V.S.); (A.V.S.); (K.V.S.); (S.A.E.); (A.V.Z.)
- Faculty of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Anatoly V. Zherdev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (I.V.S.); (A.V.S.); (K.V.S.); (S.A.E.); (A.V.Z.)
| | - Boris B. Dzantiev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (I.V.S.); (A.V.S.); (K.V.S.); (S.A.E.); (A.V.Z.)
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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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Yang Y, Wang D, Lü P, Ma S, Chen K. Research progress on nucleic acid detection and genome editing of CRISPR/Cas12 system. Mol Biol Rep 2023; 50:3723-3738. [PMID: 36648696 PMCID: PMC9843688 DOI: 10.1007/s11033-023-08240-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 01/03/2023] [Indexed: 01/18/2023]
Abstract
PURPOSE This work characterizes the applications of CRISPR/Cas12 system, including nucleic acid detection, animal, plant and microbial genome editing. METHODS The literature on CRISPR/Cas12 system was collected and reviewed. RESULTS CRISPR/Cas system is an acquired immune system derived from bacteria and archaea, which has become the most popular technology around the world because of its outstanding contribution in genome editing. Type V CRISPR/Cas systems are distinguished by a single RNA-guided RuvC nuclease domain with single effector molecule. Cas12a, the first reported type V CRISPR/Cas system, targets double-stranded DNA (dsDNA) adjacent to PAM sequences and trans-cleaves single-stranded DNA (ssDNA). We present the applications of CRISPR/Cas12 system for nucleic acid detection and genome editing in animals, plants and microorganisms. Furthermore, this review also summarizes the applications of other Cas12 proteins, such as Cas12b, Cas12c, Cas12d, and so on, which further widen the application prospects of CRISPR/Cas12 system. CONCLUSIONS Knowledge of the applications of CRISPR/Cas12 system is necessary for improving the understanding of the functional diversity of CRISPR/Cas12 system and also provides significant references for further research and utilization of CRISPR/Cas12 in other new fields.
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Affiliation(s)
- Yanhua Yang
- School of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu Province, People's Republic of China.
| | - Dandan Wang
- School of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu Province, People's Republic of China
| | - Peng Lü
- School of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu Province, People's Republic of China
| | - Shangshang Ma
- School of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu Province, People's Republic of China
| | - Keping Chen
- School of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu Province, People's Republic of China
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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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Wang J, Wang Y, Liu H, Hu X, Zhang M, Liu X, Ye H, Zeng H. An ultra-sensitive test strip combining with RPA and CRISPR/Cas12a system for the rapid detection of GM crops. Food Control 2023. [DOI: 10.1016/j.foodcont.2022.109383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Kang X, Lei C, Shi J, Liu X, Ren W, Liu C. A versatile CRISPR/Cas12a-based biosensing platform coupled with a target-protected transcription strategy. Biosens Bioelectron 2023; 219:114801. [PMID: 36270083 DOI: 10.1016/j.bios.2022.114801] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/21/2022] [Accepted: 10/08/2022] [Indexed: 11/05/2022]
Abstract
Besides the critical role in gene editing, CRISPR/Cas system also brings a new signal amplification mechanism to the development of next generation biosensing technologies. Herein, we have developed a versatile CRISPR/Cas12a sensing platform by combining a target protection-based transcription amplification strategy with the Cas12a-based signal amplification mechanism, which allows for the sensitive detection of both nucleic acid and non-nucleic acid targets. In this design, a rationally designed transcription template sequence is able to avoid Exonuclease I (Exo I) degradation only in the existence of the target-mediated binding events including either nucleic acid hybridization or protein-based affinity interactions. This target binding-induced protection effect can facilitate the subsequent transcription amplification to generate crRNA and activate the subsequent Cas12a trans-cleavage signal amplification mechanism to yield target dosage-responsive fluorescence signal. In contrast, if the target is absent, the protection-free transcription template will be completely digested by Exo I, thus no fluorescence response is produced. This new strategy well eliminates the T7 polymerase-associated non-specific transcription background and realizes the sensitive detection of various kinds of biomolecules including microRNA, protein, as well as exosome, broadening the application scenarios of CRISPR/Cas system in the field of bioanalysis and biosensing.
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Affiliation(s)
- Xinyue Kang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, Shaanxi Province, PR China
| | - Chao Lei
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, Shaanxi Province, PR China
| | - Jingjing Shi
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, Shaanxi Province, PR China
| | - Xiaoling Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, Shaanxi Province, PR China.
| | - Wei Ren
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, Shaanxi Province, PR China
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, Shaanxi Province, PR China.
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Recent advances on CRISPR/Cas system-enabled portable detection devices for on-site agri-food safety assay. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.09.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Zhang X, Yang Y, Cao J, Qi Z, Li G. Point-of-care CRISPR/Cas biosensing technology: A promising tool for preventing the possible COVID-19 resurgence caused by contaminated cold-chain food and packaging. FOOD FRONTIERS 2022; 4:FFT2176. [PMID: 36712576 PMCID: PMC9874772 DOI: 10.1002/fft2.176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/1912] [Revised: 12/12/1912] [Accepted: 12/12/1912] [Indexed: 02/01/2023] Open
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused great public health concern and has been a global threat due to its high transmissibility and morbidity. Although the SARS-CoV-2 transmission mainly relies on the person-to-person route through the respiratory droplets, the possible transmission through the contaminated cold-chain food and packaging to humans has raised widespread concerns. This review discussed the possibility of SARS-CoV-2 transmission via the contaminated cold-chain food and packaging by tracing the occurrence, the survival of SARS-CoV-2 in the contaminated cold-chain food and packaging, as well as the transmission and outbreaks related to the contaminated cold-chain food and packaging. Rapid, accurate, and reliable diagnostics of SARS-CoV-2 is of great importance for preventing and controlling the COVID-19 resurgence. Therefore, we summarized the recent advances on the emerging clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system-based biosensing technology that is promising and powerful for preventing the possible COVID-19 resurgence caused by the contaminated cold-chain food and packaging during the COVID-19 pandemic, including CRISPR/Cas system-based biosensors and their integration with portable devices (e.g., smartphone, lateral flow assays, microfluidic chips, and nanopores). Impressively, this review not only provided an insight on the possibility of SARS-CoV-2 transmission through the food supply chain, but also proposed the future opportunities and challenges on the development of CRISPR/Cas system-based detection methods for the diagnosis of SARS-CoV-2.
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Affiliation(s)
- Xianlong Zhang
- Food safety and Quality Control Innovation team, Department of Food Science and EngineeringSchool of Food and Biological Engineering, Shaanxi University of Science and TechnologyXi'an710021China
| | - Yan Yang
- Food safety and Quality Control Innovation team, Department of Food Science and EngineeringSchool of Food and Biological Engineering, Shaanxi University of Science and TechnologyXi'an710021China
| | - Juanjuan Cao
- Food safety and Quality Control Innovation team, Department of Food Science and EngineeringSchool of Food and Biological Engineering, Shaanxi University of Science and TechnologyXi'an710021China
| | - Zihe Qi
- Food safety and Quality Control Innovation team, Department of Food Science and EngineeringSchool of Food and Biological Engineering, Shaanxi University of Science and TechnologyXi'an710021China
| | - Guoliang Li
- Food safety and Quality Control Innovation team, Department of Food Science and EngineeringSchool of Food and Biological Engineering, Shaanxi University of Science and TechnologyXi'an710021China
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