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Wu M, Hu S, Zhu Y, Cong F, Liu S. Simultaneous Detection of Three Subgroups of Avian Leukosis Virus Using the Nanoparticle-Assisted PCR Assay. Viruses 2023; 16:15. [PMID: 38275950 PMCID: PMC10819818 DOI: 10.3390/v16010015] [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: 08/30/2023] [Revised: 10/28/2023] [Accepted: 11/02/2023] [Indexed: 01/27/2024] Open
Abstract
Nanoparticle-assisted polymerase chain reaction (nanoPCR) is a novel method for the rapid detection of pathogens. A sensitive and specific multiple nanoPCR assay was developed for simultaneous detection of avian leucosis virus (ALV) subgroups A, B and J. In this study, three pairs of primers were designed, based on the conserved region of the gp85 gene. An exploration of the optimal primer concentration and annealing temperature were carried out, for better performance of the nanoPCR assay. According to the results, the multiple nanoPCR assay amplified 336 pb, 625 bp and 167 bp fragments of ALV-A, -B and -J, respectively, and showed no cross-reactivity with irrelevant pathogens, suggesting the excellent specificity of the assay. The constructed standard DNA templates were used to estimate the limit of detection. As shown by the results, the detection limit of the nanoPCR assay was nearly 10 copies/μL. To further evaluate the detection ability of the assay, 186 clinical samples were detected using the nanoPCR assay, among which, 14 samples were confirmed as ALV positive; the results were further confirmed by sequencing. In conclusion, a highly specific and sensitive nanoPCR assay was successfully developed, which could be a useful tool for clinical diagnosis as well as for the discrimination of ALV-A, -B and -J.
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Affiliation(s)
- Miaoli Wu
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150026, China;
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou 510633, China;
| | - Shuaiqi Hu
- College of Animal Science, Anhui Science and Technology University and Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, Fengyang 233100, China;
| | - Yujun Zhu
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou 510633, China;
| | - Feng Cong
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou 510633, China;
| | - Shengwang Liu
- Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150026, China;
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2
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Jiang X, Yang M, Liu J. Capping Gold Nanoparticles to Achieve a Protein-like Surface for Loop-Mediated Isothermal Amplification Acceleration and Ultrasensitive DNA Detection. ACS APPLIED MATERIALS & INTERFACES 2022; 14:27666-27674. [PMID: 35687651 DOI: 10.1021/acsami.2c06061] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is a popular DNA amplification method. Gold nanoparticles (AuNPs) were reported to enhance the efficiency of LAMP, although the underlying mechanism remained elusive. Since AuNPs strongly adsorb a range of ligands, preadsorbed ligands cannot be easily displaced. In this work, we systematically investigated the effect of surface-modified AuNPs on LAMP by varying the order of mixing of AuNPs with each reagent in the LAMP system (Mg2+, template DNA, dNTPs, primers, and polymerase). Mixing the AuNPs with the primers delayed the LAMP based on SYBR green I fluorescence. While other orders of mixing had little effect, all accelerated the reaction. We then tested other common ligands including polymers (polyethylene glycol and polyvinylpyrrolidone), inorganic ions (Br-), proteins, glutathione (GSH), and DNA (A15) on AuNP-LAMP. The boosted AuNP performance on LAMP was most obvious when the AuNPs formed a protein-like surface. Finally, using GSH-capped AuNPs, a detection limit of around 100 copies/μL-1 of target DNA was achieved. This work has identified a ligand-capped AuNP strategy to boost LAMP and yielded a higher sensitivity in DNA sensing, which also deepens our understanding of AuNP-assisted LAMP.
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Affiliation(s)
- Xingxing Jiang
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Minghui Yang
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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3
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Qin T, Wang J, Cui SJ. Development of a nanoparticle-assisted PCR assay to distinguish canine coronaviruses I and II. J Vet Diagn Invest 2021; 33:104-107. [PMID: 33350347 DOI: 10.1177/1040638720974114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Nanoparticle-assisted PCR (nanoPCR) is a novel method for the simple, rapid, and specific detection of viruses. We developed a nanoPCR method to detect and differentiate canine coronavirus I (CCoV I) and II (CCoV II). Primer pairs were designed against the M gene conserved region of CCoV I and CCoV II, producing specific fragments of 239 bp (CCoV I) and 105 bp (CCoV II). We optimized the annealing temperature and primer concentrations for the CCoV nanoPCR assay and assessed its sensitivity and specificity. Under optimized nanoPCR reaction conditions, the detection limits were 6.47 × 101 copies/μL for CCoV I and 6.91 × 102 copies/μL for CCoV II. No fragments were amplified using other canine viruses as templates. The sensitivity of the nanoPCR assay was 100-fold higher than that of a conventional RT-PCR assay. Among 60 clinical samples collected from Beijing, China, the assay detected 12% positive for CCoV I and 48% positive for CCoV II. Our nanoPCR method is an effective method to rapidly detect CCoV I and CCoV II alone, or as a mixed infection, in dogs.
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Affiliation(s)
- Tong Qin
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,Beijing Observation Station for Veterinary Drug and Veterinary Biotechnology, Ministry of Agriculture, Beijing, China
| | - Jing Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,Beijing Observation Station for Veterinary Drug and Veterinary Biotechnology, Ministry of Agriculture, Beijing, China
| | - Shang-Jin Cui
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,Beijing Observation Station for Veterinary Drug and Veterinary Biotechnology, Ministry of Agriculture, Beijing, China
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4
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Li S, Wang Z, Wang Y, Song M, Lu G, Dang N, Yin H, Qu Y, Deng Y. Effects of graphene oxide on PCR amplification for microbial community survey. BMC Microbiol 2020; 20:278. [PMID: 32917142 PMCID: PMC7488489 DOI: 10.1186/s12866-020-01965-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 09/02/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Graphene oxide (GO) has been suggested as an efficient assistant additive to eliminate non-specific amplification of the polymerase chain reaction (PCR). Although many studies have focused on exploring its molecular mechanism, the practice of GO on the quantitation of microbial community has not been implemented yet. In this study, GO was added in PCR system to explore the changes on removing typical amplification errors, such as chimera and mismatches on two kinds of mock communities (an evenly mixed and a staggered mock communities) and environmental samples. RESULTS High-throughput sequencing of bacterial and fungal communities, based on 16S rRNA genes and internal transcribed spacers (ITS) respectively, showed that GO could significantly increase large segmental error (chimeric sequence) in PCR procedure while had no specific effect on point error (mismatched sequence). Besides, GO reduced the α-diversity of community, and changed the composition of fungal community more obviously than bacterial community. CONCLUSIONS Our study provides the first quantitative data on microbial community level to prove the negative effect of GO, and also indicates that there may be a more complex interaction between GO and comprehensive DNA fragments in PCR process.
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Affiliation(s)
- Shuzhen Li
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technolog, Dalian, 116024, China
| | - Zhujun Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuanyuan Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Maoyong Song
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Guangxin Lu
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, 810016, China
| | - Ning Dang
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, 810016, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
| | - Yuanyuan Qu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technolog, Dalian, 116024, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China. .,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
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5
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Gao CH, Mortimer M, Zhang M, Holden PA, Cai P, Wu S, Xin Y, Wu Y, Huang Q. Impact of metal oxide nanoparticles on in vitro DNA amplification. PeerJ 2019; 7:e7228. [PMID: 31293839 PMCID: PMC6599668 DOI: 10.7717/peerj.7228] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/31/2019] [Indexed: 11/20/2022] Open
Abstract
Polymerase chain reaction (PCR) is used as an in vitro model system of DNA replication to assess the genotoxicity of nanoparticles (NPs). Prior results showed that several types of NPs inhibited PCR efficiency and increased amplicon error frequency. In this study, we examined the effects of various metal oxide NPs on inhibiting PCR, using high- vs. low-fidelity DNA polymerases; we also examined NP-induced DNA mutation bias at the single nucleotide level. The effects of seven major types of metal oxide NPs (Fe2O3, ZnO, CeO2, Fe3O4, Al2O3, CuO, and TiO2) on PCR replication via a low-fidelity DNA polymerase (Ex Taq) and a high-fidelity DNA polymerase (Phusion) were tested. The successfully amplified PCR products were subsequently sequenced using high-throughput amplicon sequencing. Using consistent proportions of NPs and DNA, we found that the effects of NPs on PCR yield differed depending on the DNA polymerase. Specifically, the efficiency of the high-fidelity DNA polymerase (Phusion) was significantly inhibited by NPs during PCR; such inhibition was not evident in reactions with Ex Taq. Amplicon sequencing showed that the overall error rate of NP-amended PCR was not significantly different from that of PCR without NPs (p > 0.05), and NPs did not introduce single nucleotide polymorphisms during PCR. Thus, overall, NPs inhibited PCR amplification in a DNA polymerase-specific manner, but mutations were not introduced in the process.
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Affiliation(s)
- Chun-Hui Gao
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Monika Mortimer
- Bren School of Environmental Science and Management, Earth Research Institute and University of California Center for the Environmental Implications of Nanotechnology (UC CEIN), University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Ming Zhang
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Patricia A Holden
- Bren School of Environmental Science and Management, Earth Research Institute and University of California Center for the Environmental Implications of Nanotechnology (UC CEIN), University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Peng Cai
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Shan Wu
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Yuexing Xin
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Yichao Wu
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
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6
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Lee SH, Park SM, Kim BN, Kwon OS, Rho WY, Jun BH. Emerging ultrafast nucleic acid amplification technologies for next-generation molecular diagnostics. Biosens Bioelectron 2019; 141:111448. [PMID: 31252258 DOI: 10.1016/j.bios.2019.111448] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/31/2019] [Accepted: 06/17/2019] [Indexed: 02/07/2023]
Abstract
Over the last decade, nucleic acid amplification tests (NAATs) including polymerase chain reaction (PCR) were an indispensable methodology for diagnosing cancers, viral and bacterial infections owing to their high sensitivity and specificity. Because the NAATs can recognize and discriminate even a few copies of nucleic acid (NA) and species-specific NA sequences, NAATs have become the gold standard in a wide range of applications. However, limitations of NAAT approaches have recently become more apparent by reason of their lengthy run time, large reaction volume, and complex protocol. To meet the current demands of clinicians and biomedical researchers, new NAATs have developed to achieve ultrafast sample-to-answer protocols for the point-of-care testing (POCT). In this review, ultrafast NA-POCT platforms are discussed, outlining their NA amplification principles as well as delineating recent advances in ultrafast NAAT applications. The main focus is to provide an overview of NA-POCT platforms in regard to sample preparation of NA, NA amplification, NA detection process, interpretation of the analysis, and evaluation of the platform design. Increasing importance will be given to innovative, ultrafast amplification methods and tools which incorporate artificial intelligence (AI)-associated data analysis processes and mobile-healthcare networks. The future prospects of NA POCT platforms are promising as they allow absolute quantitation of NA in individuals which is essential to precision medicine.
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Affiliation(s)
- Sang Hun Lee
- Department of Bioengineering, University of California Berkeley, CA, USA
| | | | - Brian N Kim
- Department of Electrical and Computer Engineering, University of Central Florida, FL, USA
| | - Oh Seok Kwon
- Infectious Disease Research Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon, South Korea
| | - Won-Yep Rho
- School of International Engineering and Science, Chonbuk National University, Jeonju, South Korea
| | - Bong-Hyun Jun
- Department of Bioscience and Biotechnology, Konkuk University, South Korea.
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7
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Zhu Y, Wang GH, Cui YD, Cui SJ. Establishment of a nanoparticle-assisted RT-PCR assay to distinguish field strains and attenuated strains of porcine epidemic diarrhea virus. Arch Virol 2016; 161:2543-7. [PMID: 27287433 PMCID: PMC7087100 DOI: 10.1007/s00705-016-2918-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 05/31/2016] [Indexed: 11/26/2022]
Abstract
Porcine epidemic diarrhea virus (PEDV) can cause serious disease and even death in neonatal piglets, resulting in serious damage to the swine industry worldwide. Open reading frame 3 (ORF3) is the only accessory gene in the PEDV genome. Previous studies have indicated that PEDV vaccine strains have a partial deletion in ORF3. In this study, a nanoparticle-assisted polymerase chain reaction (nanoparticle-assisted RT-PCR) assay targeting the ORF3 of PEDV was developed to distinguish PEDV field strains from attenuated strains by using a specific pair of primers. The PCR products of field strains and attenuated strains were 264 bp and 215 bp in length, respectively. The sensitivity and specificity of this assay were also assessed. The nanoparticle-assisted RT-PCR assay was 10-100 times more sensitive than the conventional RT-PCR assay, with no cross-reactions when amplifying porcine pseudorabies virus (PRV), porcine circovirus type 2 (PCV2), classical swine fever virus (CSFV), porcine parvovirus (PPV), porcine reproductive and respiratory syndrome virus (PRRSV), porcine rotavirus (RV), and porcine transmissible gastroenteritis virus (TGEV). The nanoparticle-assisted RT-PCR assay we describe here can be used to distinguish field strains from vaccine strains of PEDV, and it shows promise for reducing economic loss due to PEDV infection.
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Affiliation(s)
- Yu Zhu
- Institute of Animal Science(IAS), Chinese Academy of Agricultural Sciences(CAAS), Yuanmingyuan West Road 2, Hai Dian District, Beijing, 100193, China
- College of Animal Science and Technology, HLJ August First Land Reclamation University, Daqing, 163319, China
| | - Gui-Hua Wang
- Animal Medical Center DBN Technology Group, Beijing, 100195, China
| | - Yu-Dong Cui
- College of Animal Science and Technology, HLJ August First Land Reclamation University, Daqing, 163319, China.
| | - Shang-Jin Cui
- Institute of Animal Science(IAS), Chinese Academy of Agricultural Sciences(CAAS), Yuanmingyuan West Road 2, Hai Dian District, Beijing, 100193, China.
- College of Animal Science and Technology, HLJ August First Land Reclamation University, Daqing, 163319, China.
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8
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Rehman A, Sarwar Y, Raza ZA, Hussain SZ, Mustafa T, Khan WS, Ghauri MA, Haque A, Hussain I. Metal nanoparticle assisted polymerase chain reaction for strain typing of Salmonella Typhi. Analyst 2016; 140:7366-72. [PMID: 26381602 DOI: 10.1039/c5an01286d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Salmonella enterica serotype Typhi (S. Typhi) is the causative agent of typhoid fever and remains a major health threat in most of the developing countries. The prompt diagnosis of typhoid directly from the patient's blood requires high level of sensitivity and specificity. Some of us were the first to report PCR based diagnosis of typhoid. This approach has since then been reported by many scientists using different genomic targets. Since the number of bacteria circulating in the blood of a patient can be as low as 0.3 cfu ml(-1), there is always a room for improvement in diagnostic PCR. In the present study, the role of different types of nanoparticles was investigated to improve the existing PCR based methods for diagnosis and strain typing of S. Typhi (targeting Variable Number of Tandem Repeats [VNTR]) by using optimized PCR systems. Three different types of nanoparticles were used i.e., citrate stabilized gold nanoparticles, rhamnolipid stabilized gold and silver nanoparticles, and magnetic iron oxide nanoparticles. The non-specific amplification was significantly reduced in VNTR typing when gold and silver nanoparticles were used in an appropriate concentration. More importantly, the addition of nanoparticles decreased the non-specificity to a significant level in the case of multiplex PCR thus further validating the reliability of PCR for the diagnosis of typhoid.
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Affiliation(s)
- Asma Rehman
- Nanobiotech Group, National Institute for Biotechnology & Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Pakistan
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9
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Kambli P, Kelkar-Mane V. Nanosized Fe3O4 an efficient PCR yield enhancer-Comparative study with Au, Ag nanoparticles. Colloids Surf B Biointerfaces 2016; 141:546-552. [PMID: 26896662 DOI: 10.1016/j.colsurfb.2016.02.024] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 01/28/2016] [Accepted: 02/09/2016] [Indexed: 12/28/2022]
Abstract
Nanomaterials-assisted PCR is a promising field of nanobiotechnology that amalgamates nanomaterials into the conventional PCR system to achieve better amplification of desired product. With literature documenting the variable effects of these nanomaterials on the PCR yield and amplification; it was thought worthwhile to compare the PCR enhancing efficiency of three transition metal nanoparticles in form of stable colloidal suspensions at varying concentrations.The nanoparticles(NPs) of silver, gold and magnetite were chemically synthesized by reducing their respective salts and characterized using UV-vis spectroscopy. Their morphology was assessed using nanoparticle tracking system and AFM. The effect of these nanofluids on amplification of 800 bp prokaryotic DNA template with 30% GC content was studied using conventional thermal cycler. The reaction kinetics for all the three nanofluids yielded a Gaussian curve of amplification with varying concentrations. The ammonium salt of oleic acid coated magnetite (Fe3O4) nanoparticles at a concentration of 0.72 × 10(-2)nM and average size of 33 nm demonstrated highest amplification efficiency of 190% as compared to the citrate stabilized AgNP-25 nm (45%) and AuNP-15.19 nm (134%) using a conventional PCR system. The major reasons that allow Fe3O4 NPs outperform the other 2 transition metal NP's seem to be attributed to its heat conduction property as well as effective adsorption of PCR components onto the ammonium salt of oleic acid coated magnetite nanofluids. The data from our study offers valuable information for the application of ferrofluids as economically, efficient and effective alternative for nanomaterial-assisted PCR yield enhancers.
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Affiliation(s)
- Priyanka Kambli
- Department of Biotechnology, University of Mumbai, Vidyanagari, Kalina, Santacruz (E), Mumbai-98, India
| | - Varsha Kelkar-Mane
- Department of Biotechnology, University of Mumbai, Vidyanagari, Kalina, Santacruz (E), Mumbai-98, India.
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10
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Wanzhe Y, Jianuan L, Peng L, Jiguo S, Ligong C, Juxiang L. Development of a nano-particle-assisted PCR assay for detection of duck tembusu virus. Lett Appl Microbiol 2015; 62:63-7. [PMID: 26482546 DOI: 10.1111/lam.12509] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 07/10/2015] [Accepted: 09/29/2015] [Indexed: 11/28/2022]
Abstract
UNLABELLED Duck tembusu virus (DTMUV) has caused significant economic losses to the poultry industry in China since the spring of 2010. In this study, a nano-PCR assay targeting E gene of DTMUV was developed and their sensitivities and specificities were investigated. Under the optimized conditions of nano-PCR assay for detection of DTMUV, the nano-PCR assay was 10-fold more sensitive than a conventional PCR assay. The lower detection limit of the nano-PCR assay was 1·8 × 10(2) copies μl(-1) of DTMUV RNA, as no cross-reaction was observed with other viruses. This is the first report to demonstrate the application of a nano-PCR assay for the detection of DTMUV. The sensitive, and specific nano-PCR assay developed in this study can be applied widely in clinical diagnosis and field surveillance of DTMUV-infection. SIGNIFICANCE AND IMPACT OF THE STUDY A nanoparticle-assisted polymerase chain reaction (nano-PCR) assay was developed in this study for the rapid detection of duck tembusu virus (DTMUV) with high sensitivity and specificity. This technique has potential application in both clinical diagnosis and field surveillance of DTMUV-infection.
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Affiliation(s)
- Y Wanzhe
- College of Animal Medicine, Agricultural University of Hebei, Baoding, Hebei, China.,Hebei Engineering and Technology Research Center of Veterinary Biotechnology, Baoding, Hebei, China.,North China Research Center of Animal Epidemic Pathogen Biology, Agriculture Ministry, Baoding, Hebei, China
| | - L Jianuan
- College of Animal Medicine, Agricultural University of Hebei, Baoding, Hebei, China
| | - L Peng
- China Animal Disease Control Center, China Agriculture Ministry, Beijing, China
| | - S Jiguo
- College of Animal Medicine, Agricultural University of Hebei, Baoding, Hebei, China.,Hebei Engineering and Technology Research Center of Veterinary Biotechnology, Baoding, Hebei, China.,North China Research Center of Animal Epidemic Pathogen Biology, Agriculture Ministry, Baoding, Hebei, China
| | - C Ligong
- College of Animal Medicine, Agricultural University of Hebei, Baoding, Hebei, China.,Hebei Engineering and Technology Research Center of Veterinary Biotechnology, Baoding, Hebei, China.,North China Research Center of Animal Epidemic Pathogen Biology, Agriculture Ministry, Baoding, Hebei, China
| | - L Juxiang
- College of Animal Medicine, Agricultural University of Hebei, Baoding, Hebei, China.,Hebei Engineering and Technology Research Center of Veterinary Biotechnology, Baoding, Hebei, China.,North China Research Center of Animal Epidemic Pathogen Biology, Agriculture Ministry, Baoding, Hebei, China
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11
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Liu Q, Su J, Li Z, Wang F, Wang Y, Li G, Hua Z. Improvement of rolling circle amplification efficiency with gold nanoparticles. ACTA ACUST UNITED AC 2015. [DOI: 10.1179/1432891715z.0000000002008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Affiliation(s)
- Q. Liu
- Key Laboratory of Food Nutrition and Safety(Tianjin University of Science & Technology), Ministry of Education, Tianjin 300457, China
| | - J. Su
- Key Laboratory of Food Nutrition and Safety(Tianjin University of Science & Technology), Ministry of Education, Tianjin 300457, China
| | - Z. Li
- China National Japonica Rice Research Center, Tianjin 300457, China
| | - F. Wang
- Key Laboratory of Food Nutrition and Safety(Tianjin University of Science & Technology), Ministry of Education, Tianjin 300457, China
- China National Japonica Rice Research Center, Tianjin 300457, China
| | - Y. Wang
- Key Laboratory of Food Nutrition and Safety(Tianjin University of Science & Technology), Ministry of Education, Tianjin 300457, China
| | - G. Li
- Key Laboratory of Food Nutrition and Safety(Tianjin University of Science & Technology), Ministry of Education, Tianjin 300457, China
| | - Z. Hua
- Key Laboratory of Food Nutrition and Safety(Tianjin University of Science & Technology), Ministry of Education, Tianjin 300457, China
- China National Japonica Rice Research Center, Tianjin 300457, China
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12
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Higashi T, Minegishi H, Echigo A, Nagaoka Y, Fukuda T, Usami R, Maekawa T, Hanajiri T. Nanomaterial-assisted PCR based on thermal generation from magnetic nanoparticles under high-frequency AC magnetic fields. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.06.070] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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13
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Bai Y, Cui Y, Paoli GC, Shi C, Wang D, Shi X. Nanoparticles Affect PCR Primarily via Surface Interactions with PCR Components: Using Amino-Modified Silica-Coated Magnetic Nanoparticles as a Main Model. ACS APPLIED MATERIALS & INTERFACES 2015; 7:13142-53. [PMID: 26030087 DOI: 10.1021/am508842v] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Nanomaterials have been widely reported to affect the polymerase chain reaction (PCR). However, many studies in which these effects were observed were not comprehensive, and many of the proposed mechanisms have been primarily speculative. In this work, we used amino-modified silica-coated magnetic nanoparticles (ASMNPs, which can be collected very easily using an external magnetic field) as a model and compared them with gold nanoparticles (AuNPs, which have been studied extensively) to reveal the mechanisms by which nanoparticles affect PCR. We found that nanoparticles affect PCR primarily by binding to PCR components: (1) inhibition, (2) specifity, and (3) efficiency and yield of PCR are impacted. (1) Excess nanomaterials inhibit PCR by adsorbing to DNA polymerase, Mg(2+), oligonucleotide primers, or DNA templates. Nanoparticle surface-active groups are particularly important to this effect. (2, a) Nanomaterials do not inhibit nonspecific amplification products caused by false priming as previously surmised. It was shown that relatively low concentrations of nanoparticles inhibited the amplification of long amplicons, and increasing the amount of nanoparticles inhibited the amplification of short amplicons. This concentration phenomenon appears to be the result of the formation of "joints" upon the adsorption of ASMNPs to DNA templates. (b) Nanomaterials are able to inhibit nonspecific amplification products due to incomplete amplification by preferably adsorbing single-stranded incomplete amplification products. (3) Some types of nanomaterials, such as AuNPs, enhance the efficiency and yield of PCR because these types of nanoparticles can adsorb to single-stranded DNA more strongly than to double-stranded DNA. This behavior assists in the rapid and thorough denaturation of double-stranded DNA templates. Therefore, the interaction between the surface of nanoparticles and PCR components is sufficient to explain most of the effects of nanoparticles on PCR.
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14
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Yuan W, Li Y, Li P, Song Q, Li L, Sun J. Development of a nanoparticle-assisted PCR assay for detection of porcine epidemic diarrhea virus. J Virol Methods 2015; 220:18-20. [PMID: 25887451 PMCID: PMC7113876 DOI: 10.1016/j.jviromet.2015.04.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 04/06/2015] [Accepted: 04/07/2015] [Indexed: 11/25/2022]
Abstract
A nanoPCR method was developed for the detection of PEDV. The nanoPCR assay was 100-fold more sensitive than a conventional RT-PCR assay. The lower detection limit was 2.7 × 10−6
ng/μL of PEDV RNA. This test could be applied for clinical diagnosis and field surveillance of PEDV.
Porcine epidemic diarrhea virus (PEDV) is an important pig pathogen that can cause vomiting, diarrhea, and dehydration, leading to serious damage to the swine industry worldwide. In this study, a nanoparticle-assisted polymerase chain reaction (nanoPCR) assay targeting the N gene of PEDV was developed and the sensitivity and specificity were investigated. Under the optimized conditions for detection of PEDV RNA, the nanoPCR assay was 100-fold more sensitive than a conventional RT-PCR assay. The lower detection limit of the nanoPCR assay was 2.7 × 10−6 ng/μL of PEDV RNA and no cross-reaction was observed with other viruses. This is the first report to demonstrate the application of a nanoPCR assay for the detection of PEDV. The sensitive and specific nanoPCR assay developed in this study can be applied widely in clinical diagnosis and field surveillance of PEDV-infection.
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Affiliation(s)
- Wanzhe Yuan
- College of Animal Medicine, Agricultural University of Hebei, Baoding, Hebei 071001, China; Hebei Engineering and Technology Research Center of Veterinary Biotechnology, Baoding, Hebei 071001, China; North China Research Center of Animal Epidemic Pathogen Biology, China Agriculture Ministry, Baoding, Hebei 071001, China.
| | - Yanan Li
- College of Animal Medicine, Agricultural University of Hebei, Baoding, Hebei 071001, China
| | - Peng Li
- China Animal Disease Control Center, China Agriculture Ministry, Beijing 100125, China
| | - Qinye Song
- College of Animal Medicine, Agricultural University of Hebei, Baoding, Hebei 071001, China; Hebei Engineering and Technology Research Center of Veterinary Biotechnology, Baoding, Hebei 071001, China; North China Research Center of Animal Epidemic Pathogen Biology, China Agriculture Ministry, Baoding, Hebei 071001, China
| | - Limin Li
- College of Animal Medicine, Agricultural University of Hebei, Baoding, Hebei 071001, China; Hebei Engineering and Technology Research Center of Veterinary Biotechnology, Baoding, Hebei 071001, China; North China Research Center of Animal Epidemic Pathogen Biology, China Agriculture Ministry, Baoding, Hebei 071001, China
| | - Jiguo Sun
- College of Animal Medicine, Agricultural University of Hebei, Baoding, Hebei 071001, China; Hebei Engineering and Technology Research Center of Veterinary Biotechnology, Baoding, Hebei 071001, China; North China Research Center of Animal Epidemic Pathogen Biology, China Agriculture Ministry, Baoding, Hebei 071001, China
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15
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Luo Y, Liang L, Zhou L, Zhao K, Cui S. Concurrent infections of pseudorabies virus and porcine bocavirus in China detected by duplex nanoPCR. J Virol Methods 2015; 219:46-50. [PMID: 25813598 DOI: 10.1016/j.jviromet.2015.03.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 03/16/2015] [Accepted: 03/16/2015] [Indexed: 12/31/2022]
Abstract
Nanoparticle-assisted polymerase chain reaction (nanoPCR) is a novel method for the simple, rapid, and specific amplification of DNA and has been used to detect viruses. A duplex nanoPCR molecular detection system was developed to detect pseudorabies virus (PRV) and porcine bocavirus (PBoV). Primers were selected to target conserved regions within the PRV gE gene and the PBoV NS1 gene. Under optimized nanoPCR reaction conditions, two specific fragments of 316 bp (PRV) and 996 bp (PBoV) were amplified by the duplex nanoPCR with a detection limit of 6 copies for PRV and 95 copies for PBoV; no fragments were amplified when other porcine viruses were used as template. When used to test 550 clinical samples, the duplex nanoPRC assay and a conventional duplex PCR assay provided very similar results (98.1% consistency); single PRV infections, single PBoV infections, and concurrent PRV and PBoV infections were detected in 37%, 15%, and 9% of the samples, respectively. The results indicate that the novel duplex nanoPCR assay is useful for the rapid detection of PRV and PBoV in pigs.
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Affiliation(s)
- Yakun Luo
- Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences, Beijing 100193, China; State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, 427 Maduan Street, Nangang District, Harbin 150001, Heilongjiang, China
| | - Lin Liang
- Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ling Zhou
- Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Kai Zhao
- College of Life Science, Heilongjiang University, Harbin 150080, China.
| | - Shangjin Cui
- Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences, Beijing 100193, China; State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, 427 Maduan Street, Nangang District, Harbin 150001, Heilongjiang, China.
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16
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Zhu M, Luo C, Zhang F, Liu F, Zhang J, Guo S. Interactions of the primers and Mg2+with graphene quantum dots enhance PCR performance. RSC Adv 2015. [DOI: 10.1039/c5ra12729g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
GQDs enhance PCR performance through stacking the primers selectively, tuning the activity of polymeraseviachelating Mg2+, and accelerating the PCR reaction by adsorbing PCR reaction components together to increase their proximity.
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Affiliation(s)
- Meidong Zhu
- State Key Laboratory of Bioreactor Engineering
- Shanghai Key Laboratory of New Drug Design
- School of Pharmacy
- East China University of Science and Technology
- Shanghai
| | - Chao Luo
- State Key Laboratory of Bioreactor Engineering
- Shanghai Key Laboratory of New Drug Design
- School of Pharmacy
- East China University of Science and Technology
- Shanghai
| | - Fangwei Zhang
- School of Electronic Information and Electrical Engineering
- Shanghai Jiao Tong University
- Shanghai
- P. R. China
| | - Fei Liu
- State Key Laboratory of Bioreactor Engineering
- Shanghai Key Laboratory of New Drug Design
- School of Pharmacy
- East China University of Science and Technology
- Shanghai
| | - Jingyan Zhang
- State Key Laboratory of Bioreactor Engineering
- Shanghai Key Laboratory of New Drug Design
- School of Pharmacy
- East China University of Science and Technology
- Shanghai
| | - Shouwu Guo
- School of Electronic Information and Electrical Engineering
- Shanghai Jiao Tong University
- Shanghai
- P. R. China
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17
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Yuce M, Kurt H, Mokkapati VRSS, Budak H. Employment of nanomaterials in polymerase chain reaction: insight into the impacts and putative operating mechanisms of nano-additives in PCR. RSC Adv 2014. [DOI: 10.1039/c4ra06144f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The latest developments in the field of nanomaterial-assisted PCR are evaluated with a focus on putative operating mechanisms.
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Affiliation(s)
- Meral Yuce
- Sabanci University
- Nanotechnology Research and Application Centre
- Istanbul, Turkey
| | - Hasan Kurt
- Sabanci University
- Faculty of Engineering and Natural Sciences
- Istanbul, Turkey
| | | | - Hikmet Budak
- Sabanci University
- Nanotechnology Research and Application Centre
- Istanbul, Turkey
- Sabanci University
- Faculty of Engineering and Natural Sciences
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18
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Tian L, Cronin TM, Weizmann Y. Enhancing-effect of gold nanoparticles on DNA strand displacement amplifications and their application to an isothermal telomerase assay. Chem Sci 2014. [DOI: 10.1039/c4sc01393j] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AuNPs take the reliability of a typical isothermal DNA amplification assay to a new level of accuracy, specificity, and sensitivity.
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Affiliation(s)
- Leilei Tian
- Department of Chemistry and Institute for Biophysical Dynamics
- The University of Chicago
- Chicago, USA
| | - Timothy M. Cronin
- Department of Chemistry and Institute for Biophysical Dynamics
- The University of Chicago
- Chicago, USA
| | - Yossi Weizmann
- Department of Chemistry and Institute for Biophysical Dynamics
- The University of Chicago
- Chicago, USA
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19
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Wu J, Kodzius R, Cao W, Wen W. Extraction, amplification and detection of DNA in microfluidic chip-based assays. Mikrochim Acta 2013. [DOI: 10.1007/s00604-013-1140-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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20
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Ma X, Cui Y, Qiu Z, Zhang B, Cui S. A nanoparticle-assisted PCR assay to improve the sensitivity for rapid detection and differentiation of wild-type pseudorabies virus and gene-deleted vaccine strains. J Virol Methods 2013; 193:374-8. [PMID: 23872268 DOI: 10.1016/j.jviromet.2013.07.018] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 07/03/2013] [Accepted: 07/10/2013] [Indexed: 11/17/2022]
Abstract
Nanoparticle-assisted polymerase chain reaction (nanoPCR) is a novel method for the rapid amplification of DNA and has been adopted for the detection of virus because of its simplicity, rapidity, and specificity. A nanoPCR assay was developed to detect and differentiate wild-type and gene-deleted pseudorabies virus (PRV). Three pairs of primers for nanoPCR developed in this study were selected from conserved regions of PRV, producing specific amplicons of 431 bp (gB), 316 bp (gE), and 202 bp (gG). The sensitivity of this assay using purified plasmid constructs containing the specific gene fragments was 100-1000 fold higher than conventional PCR. The PRV nanoPCR assay did not amplify porcine parvovirus, porcine circovirus type 2, porcine reproductive and respiratory syndrome virus, porcine teschovirus, or African swine fever virus but produced three bands of expected size with PRV and two bands of expected size with the gene-deleted PRV-Bartha-K61. Of 110 clinical samples collected from seven provinces in China, 53% and 48% were positive for wild-type PRV according to the nanoPCR assay and virus isolation, respectively.
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Affiliation(s)
- Xingjie Ma
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, China
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21
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He J, Xu W, Shang Y, Zhu P, Mei X, Tian W, Huang K. Development and optimization of an efficient method to detect the authenticity of edible oils. Food Control 2013. [DOI: 10.1016/j.foodcont.2012.07.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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22
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Abstract
Polymerase chain reaction (PCR) has become a standard and important molecular biological technique with numerous applications in genetic analysis, forensics and in vitro diagnostics. Since its invention in the 1980s, there has been dramatic performance improvement arising from long-lasting efforts to optimize amplification conditions in both academic studies and commercial applications. More recently, a range of nanometer-sized materials including metal nanoparticles, semiconductor quantum dots, carbon nanomaterials and polymer nanoparticles, have shown unique effects in tuning amplification processes of PCR. It is proposed that these artificial nanomaterials mimic protein components in the natural DNA replication machinery in vivo. These so-called nanomaterials-assisted PCR (nanoPCR) strategies shed new light on powerful PCR with unprecedented sensitivity, selectivity and extension rate. In this review, we aim to summarize recent progress in this direction and discuss possible mechanisms for such performance improvement and potential applications in genetic analysis (particularly gene typing and haplotyping) and diagnostics.
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Affiliation(s)
- Dun Pan
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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23
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Sang F, Zhang Z, Xu Z, Ju X, Wang H, Zhang S, Guo C. CdTe Quantum Dots Enhance Feasibility of EvaGreen-Based Real-Time PCR with Decent Amplification Fidelity. Mol Biotechnol 2013; 54:969-76. [DOI: 10.1007/s12033-013-9650-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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24
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Effects of Superparamagnetic Nanoparticle Clusters on the Polymerase Chain Reaction. APPLIED SCIENCES-BASEL 2012. [DOI: 10.3390/app2020303] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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25
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An H, Jin B. DNA exposure to buckminsterfullerene (C60): toward DNA stability, reactivity, and replication. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2011; 45:6608-6616. [PMID: 21718073 DOI: 10.1021/es2012319] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Buckminsterfullerene (C(60)) has received great research interest due to its extraordinary properties and increasing applications in manufacturing industry and biomedical technology. We recently reported C(60) could enter bacterial cells and bind to DNA molecules. This study was to further determine how the DNA-C(60) binding affected the thermal stability and enzymatic digestion of DNA molecules, and DNA mutations. Nano-C(60) aggregates and water-soluble fullerenols were synthesized and their impact on DNA biochemical and microbial activity was investigated. Our results revealed that water-soluble fullerenols could bind to lambda DNA and improve DNA stability remarkably against thermal degradation at 70-85 °C in a dose-dependent manner. DNase I and HindIII restriction endonuclease activities were inhibited after interacting with fullerenols at a high dose. Experimental results also showed the different influence of fullerenol and nano-C(60) on their antibacterial mechanisms, where fullerenols contributed considerable impact on cell damage and mutation rate. This preliminary study indicated that the application of fullerenols results in significant changes in the physical structures and biochemical functions of DNA molecules.
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Affiliation(s)
- Hongjie An
- School of Earth and Environmental Sciences, The University of Adelaide, Adelaide, SA, Australia
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26
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An H, Liu Q, Ji Q, Jin B. DNA binding and aggregation by carbon nanoparticles. Biochem Biophys Res Commun 2010; 393:571-6. [DOI: 10.1016/j.bbrc.2010.02.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2010] [Accepted: 02/02/2010] [Indexed: 10/19/2022]
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