1
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Zhao Y, Wan Z, Zhang M, Li B, Zhang X, Tian W, Li YY, Zhang C. Multiplex competitive annealing mediated isothermal amplification with high fidelity DNA polymerase (HiFi-CAMP). Talanta 2024; 280:126698. [PMID: 39142130 DOI: 10.1016/j.talanta.2024.126698] [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: 04/01/2024] [Revised: 08/08/2024] [Accepted: 08/09/2024] [Indexed: 08/16/2024]
Abstract
Various isothermal amplification methods have been developed for point-of-care testing (POCT) of various infectious diseases. Here, we proposed a novel isothermal amplification method, named as 5'-half complementary primers mediated isothermal amplification (HCPA). Because of the similarity of our method to the previous method competitive annealing mediated isothermal amplification (CAMP) in primer design, we also use the name CAMP for our method. We demonstrated that CAMP is mediated by both a linear isothermal amplification pattern and a loop-mediated isothermal amplification pattern. To improve the specificity and enable multiplex detection, we further developed HiFi-CAMP method that uses a small amount of high-fidelity DNA polymerase to cut HFman probe to release fluorescent signal. The HiFi-CAMP method was demonstrated to have a good specificity and sensitivity, and fast amplification speed in detection of three human respiratory viruses, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), respiratory syncytial virus A (RSV-A) and influenza A viruses (IAV). When compared with gold standard RT-qPCR assays, the HiFi-CAMP assays showed sensitivities of 90.0 %, 71.4 % and 78.1 %, specificities of 100 %, 100 % and 95.5 %, and consistencies of 93.0 %, 93.3 % and 88.2 % for SARS-CoV-2, RSV-A and IAV, respectively. Furthermore, a duplex HiFi-CAMP assay was also developed to simultaneously detect RSV-A and SARS-CoV-2. The HiFi-CAMP will provide a promising candidate for POCT diagnosis in resource-limited settings.
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Affiliation(s)
- Yongjuan Zhao
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Zhenzhou Wan
- Medical Laboratory of Taizhou Fourth People's Hospital, Taizhou, 225300, China
| | - Min Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Bing Li
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Xiaoling Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Weimin Tian
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Yu-Ye Li
- Department of Dermatology and Venereology, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, China
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.
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2
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Bodulev OL, Zakharov MD, Sakharov IY. Chemiluminescent plate assay of microRNA-155 coupled with catalytic hairpin assembly with oligonucleotide release (CHAOR). Talanta 2024; 270:125525. [PMID: 38091747 DOI: 10.1016/j.talanta.2023.125525] [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: 10/31/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 01/27/2024]
Abstract
A heterogeneous sensitive microRNA-155 assay based on a new isothermal amplification method, called catalytic hairpin assembly with oligonucleotide release (CHAOR), was developed. The principle of CHAOR was studied by non-denaturing electrophoresis. To detect the amplification product, a polyperoxidase-streptavidin conjugate (molar ratio 1:80) and an enhanced chemiluminescence reaction were used, which made it possible to increase assay sensitivity. The detection limit of microRNA-155 assay was 0.4 pM. The coefficient of variation of the chemiluminescent signal, formed upon the heterogeneous determination of miRNA-155, was less than 12 % within the working range. The efficiency of CHAOR as an amplification method was similar to that of traditional CHA, as miRNA-155 assays based on CHAOR and CHA had similar analytical parameters. In addition, the proposed assay was highly specific. Contrary to traditional CHA, CHAOR, one of whose products is a single-stranded oligonucleotide, can be used in analytical methods based on cascade amplification.
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Affiliation(s)
- Oleg L Bodulev
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory, bldg.1, Moscow, 119991, Russia
| | - Maxim D Zakharov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory, bldg.1, Moscow, 119991, Russia
| | - Ivan Yu Sakharov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory, bldg.1, Moscow, 119991, Russia.
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3
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Garafutdinov RR, Kupova OY, Sakhabutdinova AR. Influence of Nucleotide Context on Non-Specific Amplification of DNA with Bst exo - DNA Polymerase. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:53-64. [PMID: 38467545 DOI: 10.1134/s0006297924010036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/30/2023] [Accepted: 12/02/2023] [Indexed: 03/13/2024]
Abstract
Isothermal nucleic acids amplification that requires DNA polymerases with strand-displacement activity gained more attention in the last two decades. Among the DNA polymerases with strand-displacement activity, Bst exo- is the most widely used. However, it tends to carry out nonspecific DNA synthesis through multimerization. In this study, the effect of nucleotide sequence on the Bst exo- binding with DNA and on the efficiency of multimerization initiation, are reported. Preference for binding of the "closed" form of Bst exo- to the purine-rich DNA sequences, especially those containing dG at the 3'-end of the growing chain was revealed using molecular docking of the single-stranded trinucleotides (sst) and trinucleotide duplexes (dst). The data obtained in silico were confirmed in the experiments using oligonucleotide templates that differ in the structure of the 3'- and 5'-terminal motifs. It has been shown that templates with the oligopurine 3'-terminal fragment and oligopyrimidine 5'-terminal part contribute to the earlier start of multimerization. The results can be used for design of nucleotide sequences suitable for reliable isothermal amplification. To avoid multimerization, DNA templates and primers containing terminal dA and/or dG nucleotides should be excluded.
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Affiliation(s)
- Ravil R Garafutdinov
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, Ufa, 450054, Russia.
| | - Olga Yu Kupova
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, Ufa, 450054, Russia
| | - Assol R Sakhabutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, Ufa, 450054, Russia
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4
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Du J, He JS, Wang R, Wu J, Yu X. Ultrasensitive reporter DNA sensors built on nucleic acid amplification techniques: Application in the detection of trace amount of protein. Biosens Bioelectron 2024; 243:115761. [PMID: 37864901 DOI: 10.1016/j.bios.2023.115761] [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: 08/26/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/23/2023]
Abstract
The detection of protein is of great significance for the study of biological physiological function, early diagnosis of diseases and drug research. However, the sensitivity of traditional protein detection methods for detecting trace amount of proteins was relatively low. By integrating sensitive nucleic acid amplification techniques (NAAT) with protein detection methods, the detection limit of protein detection methods can be substantially improved. The DNA that can specifically bind to protein targets and convert protein signals into DNA signals is collectively referred to reporter DNA. Various NAATs have been used to establish NAAT-based reporter DNA sensors. And according to whether enzymes are involved in the amplification process, the NAAT-based reporter DNA sensors can be divided into two types: enzyme-assisted NAAT-based reporter DNA sensors and enzyme-free NAAT-based reporter DNA sensors. In this review, we will introduce the principles and applications of two types of NAAT-based reporter DNA sensors for detecting protein targets. Finally, the main challenges and application prospects of NAAT-based reporter DNA sensors are discussed.
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Affiliation(s)
- Jungang Du
- College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311215, China
| | - Jin-Song He
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Rui Wang
- Human Phenome Institute, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200438, China.
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311215, China.
| | - Xiaoping Yu
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China.
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5
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Akhmetzianova LU, Davletkulov TM, Sakhabutdinova AR, Chemeris AV, Gubaydullin IM, Garafutdinov RR. LAMPrimers iQ: New primer design software for loop-mediated isothermal amplification (LAMP). Anal Biochem 2024; 684:115376. [PMID: 37924966 DOI: 10.1016/j.ab.2023.115376] [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: 08/01/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/06/2023]
Abstract
Nucleic acids amplification is a widely used technique utilized for different manipulations with DNA and RNA. Although, polymerase chain reaction (PCR) remains the most popular amplification method, isothermal approaches are gained more attention last decades. Among these, loop-mediated isothermal amplification (LAMP) became an excellent alternative to PCR. LAMP requires an increased number of primers and, therefore, is considered a highly specific amplification reaction compared to PCR. LAMP primers design is still a non-trivial task, and all niceties should be taken into account during their selection. Here, we report on a new program called LAMPrimers iQ destined for high-quality LAMP primers design. LAMPrimers iQ is based on an original algorithm considering rigorous criteria for primers selection. Unlike alternative programs, LAMPrimers iQ can process long DNA or RNA sequences, and completely avoid primers that can form homo- and heterodimers. The quality of the primers designed was checked using SARS-CoV-2 coronavirus RNA as a model target. It was shown that primers selected with LAMPrimers iQ provide higher specificity and reliable detection of viral RNA compared to those obtained by alternative programs. The program is available at https://github.com/Restily/LAMPrimers-iQ.
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Affiliation(s)
- Liana U Akhmetzianova
- Institute of Petrochemistry and Catalysis, Ufa Federal Research Center, Russian Academy of Sciences, 450075, prosp. Oktyabrya, 141, Ufa, Bashkortostan, Russian Federation; Ufa State Petroleum Technological University, 450064, st. Cosmonauts, 1, Ufa, Bashkortostan, Russian Federation.
| | - Timur M Davletkulov
- Ufa State Petroleum Technological University, 450064, st. Cosmonauts, 1, Ufa, Bashkortostan, Russian Federation.
| | - Assol R Sakhabutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, 450054, prosp. Oktyabrya, 71, Ufa, Bashkortostan, Russian Federation.
| | - Alexey V Chemeris
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, 450054, prosp. Oktyabrya, 71, Ufa, Bashkortostan, Russian Federation.
| | - Irek M Gubaydullin
- Institute of Petrochemistry and Catalysis, Ufa Federal Research Center, Russian Academy of Sciences, 450075, prosp. Oktyabrya, 141, Ufa, Bashkortostan, Russian Federation; Ufa State Petroleum Technological University, 450064, st. Cosmonauts, 1, Ufa, Bashkortostan, Russian Federation.
| | - Ravil R Garafutdinov
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, 450054, prosp. Oktyabrya, 71, Ufa, Bashkortostan, Russian Federation.
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6
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Fang Y, Yang Y, Yao Z, Lei X, Dong Z, Zhang M, Yao R, Tian B. On-Particle Hyperbranched Rolling Circle Amplification-Scaffolded Magnetic Nanoactuator Assembly for Ferromagnetic Resonance Detection of MicroRNA. ACS Sens 2023; 8:4792-4800. [PMID: 38073137 DOI: 10.1021/acssensors.3c01967] [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] [Indexed: 12/23/2023]
Abstract
Inspired by natural molecular machines, scientists are devoted to designing nanomachines that can navigate in aqueous solutions, sense their microenvironment, actuate, and respond. Among different strategies, magnetically driven nanoactuators can easily be operated remotely in liquids and thus are valuable in biosensing. Here we report a magnetic nanoactuator swarm with rotating-magnetic-field-controlled conformational changes for reaction acceleration and target quantification. By grafting nucleic acid amplification primers, magnetic nanoparticle (MNP) actuators can assemble and be fixed with a flexible DNA scaffold generated by surface-localized hyperbranched rolling circle amplification in response to the presence of a target microRNA, osa-miR156. Net magnetic anisotropy changes of the system induced by the MNP assembly can be measured by ferromagnetic resonance spectroscopy as shifts in the resonance field. With a total assay time of ca. 120 min, the proposed biosensor offers a limit of detection of 6 fM with a dynamic detection range spanning 5 orders of magnitude. The specificity of the system is validated by testing different microRNAs and salmon sperm DNA. Endogenous microRNAs extracted from Oryza sativa leaves are tested with both quantitative reverse transcription-PCR and our approach, showing comparable performances with a Pearson correlation coefficient >0.9 (n = 20).
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Affiliation(s)
- Yuan Fang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, China
- Department of Biomedical Engineering, School of Basic Medical Sciences, Central South University, Changsha 410013, China
| | - Yulin Yang
- Department of Biomedical Engineering, School of Basic Medical Sciences, Central South University, Changsha 410013, China
| | - Ziyang Yao
- Department of Biomedical Engineering, School of Basic Medical Sciences, Central South University, Changsha 410013, China
| | - Xi Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, China
| | - Zhuxin Dong
- Department of Biomedical Engineering, School of Basic Medical Sciences, Central South University, Changsha 410013, China
- Furong Laboratory, Changsha 410008, China
| | - Meng Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, China
- Shenzhen Research Institute, Hunan University, Shenzhen 518000, China
| | - Ruifeng Yao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha 410082, China
- Shenzhen Research Institute, Hunan University, Shenzhen 518000, China
| | - Bo Tian
- Department of Biomedical Engineering, School of Basic Medical Sciences, Central South University, Changsha 410013, China
- Furong Laboratory, Changsha 410008, China
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7
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Yang T, Luo Z, Wang Y, Li L, Xu Y, Lin X. Hydrogel Digital LAMP with Suppressed Nonspecific Amplification for Rapid Diagnostics of Fungal Disease in Fresh Fruits. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:18636-18644. [PMID: 37975529 DOI: 10.1021/acs.jafc.3c06141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Fungal disease, mainly caused by Alternaria alternata infection, can generate severe economic losses and health hazards. However, rapid nucleic acid test without nonspecific reaction still remains challenging. Here, we reported the hydrogel digital loop-mediated isothermal amplification (HdLAMP) with suppressed nonspecific amplification for rapid diagnosis of fungi in fresh fruits. The introduction of hydrogel offered a simple platform to achieve absolute quantification. By breaking the 3'end G-C anchor, the nonspecific amplification of primers could be suppressed, while the specific positive reaction in HdLAMP was not affected. This method could be applied for A. alternata detection in 9 min with excellent performances in speed, specificity, reproducibility, sensitivity, and detection limit down to a single copy. Finally, the real diseased jujubes during postharvest storage were successfully diagnosed as an A. alternata infection. HdLAMP promotes the molecular diagnosis of fungal diseases and broadens the application of hydrogels in the agricultural and food industry.
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Affiliation(s)
- Tao Yang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Zisheng Luo
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
- Ningbo Innovation Center, Zhejiang University, Ningbo 315100, China
| | - Yiru Wang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Li Li
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
- Ningbo Innovation Center, Zhejiang University, Ningbo 315100, China
| | - Yanqun Xu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
- Ningbo Innovation Center, Zhejiang University, Ningbo 315100, China
| | - Xingyu Lin
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
- State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou 310058, China
- Ningbo Innovation Center, Zhejiang University, Ningbo 315100, China
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8
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Song Z, Hu K, Rao J, Cheng B, Xu L, An R, Liang X. Unexpected Mechanism and Inhibition Effect for Nonspecific Amplification Involving Dynamic Binding of Primers with Background DNA. Anal Chem 2023; 95:16819-16829. [PMID: 37922263 DOI: 10.1021/acs.analchem.3c02274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2023]
Abstract
Nonspecific amplification is a serious issue in DNA detection as it can lead to false-positive results and reduce specificity. It is very important to well understand its mechanism through sequencing nonspecific products. Here, an approach is developed using a nanopore sequencing technique after acquiring the long repetitive sequence of DNA products from nonspecific amplification. Based on the sequencing results, a new mechanism of nonspecific amplification designated as dynamic mismatched primer binding (DMPB) with the background DNA (bgDNA) is proposed. Unexpectedly, our findings show that the primers (∼20 nt) can bind to bgDNA for primer extension when only 6-11 fully matched (9-14 mismatched) base pairs are formed. After the single-stranded DNAs (ssDNAs) attached to the first primer are produced, more interestingly, with the aid of DNA polymerase, the other primer can bind to these ssDNAs in the case that the fully matched base pairs formed between them are even shorter than 6 bp. As a result, perfect "seeds" for polymerase chain reaction with information on both primers are produced so that exponential nonspecific amplification can occur. The DMPB mechanism can explain nonspecific amplification in other approaches as well. Finally, a mini-hairpin DNA is used to effectively inhibit nonspecific amplification by preventing the formation of an unexpected primer-bgDNA complex.
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Affiliation(s)
- Ziting Song
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Kunling Hu
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Jun Rao
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Bingxiao Cheng
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Liyuan Xu
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Ran An
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Xingguo Liang
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
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9
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Lin C, Chen F, Huang D, Li W, He C, Tang Y, Li X, Liu C, Han L, Yang Y, Zhu Y, Chen R, Shi Y, Xia C, Yan Z, Du H, Huang L. A universal all-in-one RPA-Cas12a strategy with de novo autodesigner and its application in on-site ultrasensitive detection of DNA and RNA viruses. Biosens Bioelectron 2023; 239:115609. [PMID: 37611446 DOI: 10.1016/j.bios.2023.115609] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/23/2023] [Accepted: 08/16/2023] [Indexed: 08/25/2023]
Abstract
Revolutionary all-in-one RPA-CRISPR assays are rapidly becoming the most sought-after tools for point-of-care testing (POCT) due to their high sensitivity and ease of use. Despite the availability of one-pot methods for specific targets, the development of more efficient methods for new targets remains a significant challenge. In this study, we present a rapid and universal approach to establishing an all-in-one RPA-Cas12a method CORDSv2 based on rational balancing amplification and Cas12a cleavage, which achieves ultrasensitive detection of several targets, including SARS-CoV-2, ASFV, HPV16, and HPV18. CORDSv2 demonstrates a limit of detection (LOD) of 0.6 cp/μL and 100% sensitivity for SARS-CoV-2, comparable to qPCR. Combining with our portable device(hippo-CORDS), it has a visual detection LOD of 6 cp/μL and a sensitivity up to 100% for SARS-CoV-2 and 97% for Ct<35 ASFV samples, surpassing most one-pot visual methods. To simplify and accelerate the process for new targets, we also develop a de novo autodesigner by which the optimal couples of primers and crRNA can be selected rapidly. As a universal all-in-one RPA-CRISPR method for on-site testing, CORDSv2 becomes an attractive choice for rapid and accurate diagnosis in resource-limited settings.
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Affiliation(s)
- Cailing Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Feng Chen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Dongchao Huang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Wenyan Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Changsheng He
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China; Experimental Animal Center, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Yingjun Tang
- WENS Foodstuff Group Co., Ltd., Yunfu, 527400, China
| | - Xueping Li
- Guangzhou Yoyoung Bio-tech Company, Guangzhou, 510300, China
| | - Can Liu
- Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan, 528000, China; School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 515150, China
| | - Liya Han
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Yunpeng Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Yongchong Zhu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Ruikang Chen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Yuanju Shi
- Guangzhou Yoyoung Bio-tech Company, Guangzhou, 510300, China
| | - Chenglai Xia
- Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan, 528000, China; School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 515150, China
| | - Zhibin Yan
- Guangdong Provincial Key Laboratory of Optical Information Materials and Technology & Institute of Electronic Paper Displays, South China Academy of Advanced Optoelectronics, South China Normal University, Guangzhou, 510006, PR China
| | - Hongli Du
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Lizhen Huang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China; Fangrui Institute of Innovative Drugs, South China University of Technology, Guangzhou, 510006, China.
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10
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Ordóñez CD, Redrejo-Rodríguez M. DNA Polymerases for Whole Genome Amplification: Considerations and Future Directions. Int J Mol Sci 2023; 24:ijms24119331. [PMID: 37298280 DOI: 10.3390/ijms24119331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
In the same way that specialized DNA polymerases (DNAPs) replicate cellular and viral genomes, only a handful of dedicated proteins from various natural origins as well as engineered versions are appropriate for competent exponential amplification of whole genomes and metagenomes (WGA). Different applications have led to the development of diverse protocols, based on various DNAPs. Isothermal WGA is currently widely used due to the high performance of Φ29 DNA polymerase, but PCR-based methods are also available and can provide competent amplification of certain samples. Replication fidelity and processivity must be considered when selecting a suitable enzyme for WGA. However, other properties, such as thermostability, capacity to couple replication, and double helix unwinding, or the ability to maintain DNA replication opposite to damaged bases, are also very relevant for some applications. In this review, we provide an overview of the different properties of DNAPs widely used in WGA and discuss their limitations and future research directions.
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Affiliation(s)
- Carlos D Ordóñez
- CIC bioGUNE, Bizkaia Science and Technology Park, Building 800, 48160 Derio, Spain
| | - Modesto Redrejo-Rodríguez
- Department of Biochemistry, Universidad Autónoma de Madrid and Instituto de Investigaciones Biomédicas "Alberto Sols", CSIC-UAM, 28029 Madrid, Spain
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11
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CRISPR-Cas12a-assisted elimination of the non-specific signal from non-specific amplification in the Exponential Amplification Reaction. Anal Chim Acta 2023; 1251:340998. [PMID: 36925288 DOI: 10.1016/j.aca.2023.340998] [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: 01/13/2023] [Revised: 02/13/2023] [Accepted: 02/21/2023] [Indexed: 02/24/2023]
Abstract
Non-specific amplification is a major problem in nucleic acid amplification resulting in false-positive results, especially for exponential amplification reactions (EXPAR). Although efforts were made to suppress the influence of non-specific amplification, such as chemical blocking of the template's 3'-ends and sequence-independent weakening of template-template interactions, it is still a common problem in many conventional EXPAR reactions. In this study, we propose a novel strategy to eliminate the non-specific signal from non-specific amplification by integrating the CRISPR-Cas12a system into two-templates EXPAR. An EXPAR-Cas12a strategy named EXPCas was developed, where the Cas12a system acted as a filter to filter out non-specific amplificons in EXPAR, suppressing and eliminating the influence of non-specific amplification. As a result, the signal-to-background ratio was improved from 1.3 to 15.4 using this method. With microRNA-21 (miRNA-21) as a target, the detection can be finished in 40 min with a LOD of 103 fM and no non-specific amplification was observed.
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12
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New method for microRNA detection based on multimerization. Anal Biochem 2023; 664:115049. [PMID: 36639117 DOI: 10.1016/j.ab.2023.115049] [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: 11/16/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/13/2023]
Abstract
Detection of specific microRNA (miRNA) is of great demand due to their essential role in genes regulation, stress response and development of diseases. However, mature miRNAs are small molecules that make it difficult to use routine amplification-based methods. Here, we report an approach for detection of miRNA based on a new type of isothermal amplification, namely, multimerization. The proposed technique is simple and versatile, excludes a reverse transcription step, and requires two conventional primers only and no additional stem-loop or fluorogenic probes. Only mature miRNAs can initiate multimerization, thereby, pri- or pre-miRNA are excluded from analysis, ensuring high accuracy of the assay. The approach was approved on miRNA from common wheat Triticum aestivum; the increase of Tae-miRNA159 level for plants affected by Stagonospora nodorum Berk infection was demonstrated. The obtained results allow to perform quantitative analysis, providing determination of specific targets with high reliability (detection limit of about 20 pM).
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Fan Q, Xie Z, Wei Y, Zhang Y, Xie Z, Xie L, Huang J, Zeng T, Wang S, Luo S, Li M. Development of a visual multiplex fluorescent LAMP assay for the detection of foot-and-mouth disease, vesicular stomatitis and bluetongue viruses. PLoS One 2022; 17:e0278451. [PMID: 36480573 PMCID: PMC9731490 DOI: 10.1371/journal.pone.0278451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/16/2022] [Indexed: 12/13/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is a nucleic acid amplification technique that can be used to amplify target genes at a constant temperature, and it has several advantages, including convenience, specificity and sensitivity. However, due to the special interpretation methods of this technology for reaction results, all the previously reported LAMP detection methods have been restricted to identifying a single target, which limits the application of this technology. In this study, we modified conventional LAMP to include a quencher-fluorophore composite probe complementary to the F1c segment of the inner primer FIP; upon strand separation, a gain in the visible fluorescent signal was observed. The probes could be labeled with different fluorophores, showing different colors at the corresponding wavelengths. Therefore, this multiplex LAMP (mLAMP) assay can simultaneously detect 1-3 target sequences in a single LAMP reaction tube, and the results are more accurate and intuitive. In this study, we comprehensively demonstrated a single-reaction mLAMP assay for the robust detection of three cattle viruses without nonspecific amplification of other related pathogenic cattle viruses. The detection limit of this mLAMP assay was as low as 526-2477 copies/reaction for the recombinant plasmids. It is expected that this mLAMP assay can be widely used in clinical diagnosis.
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Affiliation(s)
- Qing Fan
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Zhixun Xie
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
- * E-mail:
| | - You Wei
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Yanfang Zhang
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Zhiqin Xie
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Liji Xie
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Jiaoling Huang
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Tingting Zeng
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Sheng Wang
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Sisi Luo
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Meng Li
- Guangxi Key Laboratory of Veterinary Biotechnology, Key Laboratory of China(Guangxi)-ASEAN Cross-Border Animal Disease Prevention and Control, Ministry of Agriculture and Rural Affairs of China, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
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Hu X, Qin W, Yuan R, Zhang L, Wang L, Ding K, Liu R, Huang W, Zhang H, Luo Y. Programmable molecular circuit discriminates multidrug-resistant bacteria. Mater Today Bio 2022; 16:100379. [PMID: 36042850 PMCID: PMC9420371 DOI: 10.1016/j.mtbio.2022.100379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 10/31/2022] Open
Abstract
Recognizing multidrug-resistant (MDR) bacteria with high accuracy and precision from clinical samples has long been a difficulty. For reliable detection of MDR bacteria, we investigated a programmable molecular circuit called the Background-free isothermal circuital kit (BRICK). The BRICK method provides a near-zero background signal by integrating four inherent modules equivalent to the conversion, amplification, separation, and reading modules. Interference elimination is largely owing to a molybdenum disulfide nanosheets-based fluorescence nanoswitch and non-specific suppression mediated by molecular inhibitors. In less than 70 min, an accurate distinction of various MDR bacteria was achieved without bacterial lysis. The BRICK technique detected 6.73 CFU/mL of methicillin-resistant Staphylococcus aureus in clinical samples in a proof-of-concept trial. By simply reprogramming the sequence panel, such a high signal-to-noise characteristic has been proven in the four other superbugs. The proposed BRICK method can provide a universal platform for infection surveillance and environmental management thanks to its superior programmability.
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Affiliation(s)
- Xiaolin Hu
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, 174 Shazhengjie, Shapingba District, Chongqing, 400044, China
| | - Weichao Qin
- Department of Clinical Laboratory, Jiangjin Hospital, Chongqing University, 725 Jiangzhou Road, Jiangjin District, Chongqing, 402260, China
| | - Rui Yuan
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, 174 Shazhengjie, Shapingba District, Chongqing, 400044, China
| | - Liangliang Zhang
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, 174 Shazhengjie, Shapingba District, Chongqing, 400044, China
| | - Liangting Wang
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, 174 Shazhengjie, Shapingba District, Chongqing, 400044, China
| | - Ke Ding
- Department of Oncology, Jiangjin Hospital, Chongqing University, 725 Jiangzhou Road, Jiangjin District, Chongqing, 402260, China
| | - Ruining Liu
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, 174 Shazhengjie, Shapingba District, Chongqing, 400044, China
| | - Wanyun Huang
- Life Science Laboratories, Biology Department, University of Massachusetts Amherst, 240 Thatcher Road, Amherst, MA, 01002, USA
| | - Hong Zhang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan, Shandong, 250033, China
| | - Yang Luo
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, 174 Shazhengjie, Shapingba District, Chongqing, 400044, China
- Department of Clinical Laboratory, Jiangjin Hospital, Chongqing University, 725 Jiangzhou Road, Jiangjin District, Chongqing, 402260, China
- Department of Clinical Laboratory, Fuling Hospital, Chongqing University, 2 Gaosuntang Road, Fuling District, Chongqing, 408099, China
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Zhang S, Tang L, Zhang J, Sun W, Liu D, Chen J, Hu B, Huang Z. Single-Atom-Directed Inhibition of De Novo DNA Synthesis in Isothermal Amplifications. Anal Chem 2022; 94:15763-15771. [DOI: 10.1021/acs.analchem.2c03489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Shun Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P. R. China
- SeNA Research Institute and Szostak-CDHT Large Nucleic Acids Institute, Chengdu, Sichuan 610095, China
| | - Ling Tang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P. R. China
| | - Jun Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P. R. China
| | - Wen Sun
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P. R. China
| | - Dan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P. R. China
| | - Jiuyi Chen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P. R. China
| | - Bei Hu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P. R. China
| | - Zhen Huang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P. R. China
- SeNA Research Institute and Szostak-CDHT Large Nucleic Acids Institute, Chengdu, Sichuan 610095, China
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Huang Z, Li J, Zhong H, Tian B. Nucleic acid amplification strategies for volume-amplified magnetic nanoparticle detection assay. Front Bioeng Biotechnol 2022; 10:939807. [PMID: 36032733 PMCID: PMC9399362 DOI: 10.3389/fbioe.2022.939807] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/11/2022] [Indexed: 12/26/2022] Open
Abstract
Magnetic nanoparticles (MNPs) can be quantified based on their magnetic relaxation properties by volumetric magnetic biosensing strategies, for example, alternating current susceptometry. Volume-amplified magnetic nanoparticle detection assays (VAMNDAs) employ analyte-initiated nucleic acid amplification (NAA) reactions to increase the hydrodynamic size of MNP labels for magnetic sensing, achieving attomolar to picomolar detection limits. VAMNDAs offer rapid and user-friendly analysis of nucleic acid targets but present inherence defects determined by the chosen amplification reactions and sensing principles. In this mini-review, we summarize more than 30 VAMNDA publications and classify their detection models for NAA-induced MNP size increases, highlighting the performances of different linear, cascade, and exponential NAA strategies. For some NAA strategies that have not yet been reported in VAMNDA, we predicted their performances based on the reaction kinetics and feasible detection models. Finally, challenges and perspectives are given, which may hopefully inspire and guide future VAMNDA studies.
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Bodulev OL, Sakharov IY. Modern Methods for Assessment of microRNAs. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:425-442. [PMID: 35790375 DOI: 10.1134/s0006297922050042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/21/2022] [Accepted: 03/21/2022] [Indexed: 06/15/2023]
Abstract
The review discusses modern methods for the quantitative and semi-quantitative analysis of miRNAs, which are small non-coding RNAs affecting numerous biological processes such as development, differentiation, metabolism, and immune response. miRNAs are considered as promising biomarkers in the diagnosis of various diseases.
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Affiliation(s)
- Oleg L Bodulev
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991, Russia
| | - Ivan Yu Sakharov
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991, Russia.
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Bodulev OL, Sakharov IY. A Microtiter-Plate Chemiluminescence Method for the Determination of MicroRNA-141 Based on the Application of Catalytic Hairpin Assembly and a Streptavidin–Polyperoxidase Conjugate. JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1134/s1061934822040050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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