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Zeng R, Du Z, Ma H, Meng X, Li E, Li J. The 60 nm gold nanoparticles improve qPCR amplification efficiency through specific palindromic sequences (GGATCC or ACCGGT) in primers. Biochim Biophys Acta Gen Subj 2024; 1868:130560. [PMID: 38211821 DOI: 10.1016/j.bbagen.2024.130560] [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: 09/18/2023] [Revised: 12/20/2023] [Accepted: 01/08/2024] [Indexed: 01/13/2024]
Abstract
BACKGROUND Polymerase chain reaction (PCR) technology and quantitative real-time PCR (qPCR) technology are widely used in clinical diagnosis and research, but amplification efficiency and sensitivity are still key problems for researchers. An increasing number of reports show that gold nanoparticles (AuNPs) can be used to improve the sensitivity and amplification efficiency of PCR. Here, we found that 60 nm gold nanoparticles with a positive charge (60 nm- Au+) can enhance the amplification efficiency of qPCR. METHODS Mouse DNA was extracted by the alkaline lysis method. Primer 5.0 software was used to design primers and mutation primers, and the DNA fragments were obtained by the method of synthesizing plasmids. The qPCR was applied to amplify target gene fragments. RESULTS The amplification efficiency of qPCR was improved by about 1.828 times in the experimental group with 60 nm- Au+ compared with the control group without 60 nm- Au+. The primer pair contains a specific palindromic sequence (GGATCC or ACCGGT). And 60 nm Au+ did not enhance the amplification efficiency of qPCR when the above primer was mutated. CONCLUSIONS The primers contain special palindrome sequences (GGATCC or ACCGGT) with 60 nm- Au+ can enhance the amplification efficiency of qPCR. Therefore, it suggests a more in-depth understanding of the mechanism and function of gold nanoparticles and primer sequences. This study has presented some implications for gold nanoparticles application in the development of qPCR technology.
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Affiliation(s)
- Ruyu Zeng
- The Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Zhiqun Du
- The Department of Pathology, Dongyang People's Hospital, Zhejiang, China
| | - Hongliang Ma
- The Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Xiuqiong Meng
- The Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Erhua Li
- Guangzhou BDS Biological Technology Co., Ltd. Guangzhou, China
| | - Jiangchao Li
- The Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, 510006, China.
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2
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Vajpayee K, Dash HR, Parekh PB, Shukla RK. PCR inhibitors and facilitators - Their role in forensic DNA analysis. Forensic Sci Int 2023; 349:111773. [PMID: 37399774 DOI: 10.1016/j.forsciint.2023.111773] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 05/01/2023] [Accepted: 06/25/2023] [Indexed: 07/05/2023]
Abstract
Since its inception, DNA typing technology has been practiced as a robust tool in criminal investigations. Experts usually utilize STR profiles to identify and individualize the suspect. However, mtDNA and Y STR analyses are also considered in some sample-limiting conditions. Based on DNA profiles thus generated, forensic scientists often opine the results as Inclusion, exclusion, and inconclusive. Inclusion and exclusion were defined as concordant results; the inconclusive opinions create problems in conferring justice in a trial- since nothing concrete can be interpreted from the profile generated. The presence of inhibitor molecules in the sample is the primary factor behind these indefinite results. Recently, researchers have been emphasizing studying the sources of PCR inhibitors and their mechanism of inhibition. Furthermore, several mitigation strategies- to facilitate the DNA amplification reaction -have now found their place in the routine DNA typing assays with compromised biological samples. The present review paper attempts to provide a comprehensive review of PCR inhibitors, their source, mechanism of inhibition, and ways to mitigate their effect using PCR facilitators.
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Affiliation(s)
- Kamayani Vajpayee
- Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Central Campus, Navrangpura, Ahmedabad, Gujarat, India
| | - Hirak Ranjan Dash
- National Forensic Science University, New Delhi Campus, New Delhi, India
| | - Prakshal B Parekh
- Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Central Campus, Navrangpura, Ahmedabad, Gujarat, India
| | - Ritesh K Shukla
- Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Central Campus, Navrangpura, Ahmedabad, Gujarat, India.
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3
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Zhang X, Guo J, Song B, Zhang F. Spatiotemporal Regulation of Metal Ions in the Polymerase Chain Reaction. ACS OMEGA 2022; 7:33530-33536. [PMID: 36157739 PMCID: PMC9494670 DOI: 10.1021/acsomega.2c04507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/30/2022] [Indexed: 06/16/2023]
Abstract
The polymerase chain reaction (PCR) has been widely used in medical diagnosis and forensic identification due to its ultrahigh sensitivity and signal amplification. Metal ions (i.e., Cu2+, Zn2+) have been considered PCR inhibitors and rarely shown their positive roles in PCR amplification until our report, in which we discovered that metal ions can significantly improve the PCR specificity and the yield of target DNA sequences. For an in-depth investigation with taking copper ions as a typical model, here we found an interesting spatiotemporal regulation mechanism of metal ions in PCR. The ionic concentration window for improving PCR specificity not only was independent of annealing temperature but also can be well regulated by both the annealing time and extension time. Using the ionic concentration window as a measure, the time affects either the amount or the sequence length of nonspecific amplicons in the space. The mechanism proposed in this work will deepen our understanding of the unneglectable roles of metal ions in DNA replication and meanwhile provide a new strategy for designing regulation kits for PCR-based biomedical applications.
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Affiliation(s)
- Xianjing Zhang
- Key
Laboratory of Optical Technology and Instrument for Medicine, Ministry
of Education, School of Optical-Electrical Computer Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Jun Guo
- Key
Laboratory of Optical Technology and Instrument for Medicine, Ministry
of Education, School of Optical-Electrical Computer Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Bo Song
- Key
Laboratory of Optical Technology and Instrument for Medicine, Ministry
of Education, School of Optical-Electrical Computer Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Feng Zhang
- Key
Laboratory of Optical Technology and Instrument for Medicine, Ministry
of Education, School of Optical-Electrical Computer Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
- Quantum
Biophotonic Lab, Wenzhou Institute, University
of Chinese Academy of Sciences, Wenzhou 325001, China
- School
of Biomedical Engineering, Guangzhou Medical
University, Guangzhou 511436, China
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4
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Xia J, Bu T, Jia P, He K, Wang X, Sun X, Wang L. Polydopamine nanospheres-assisted direct PCR for rapid detection of Escherichia coli O157:H7. Anal Biochem 2022; 654:114797. [DOI: 10.1016/j.ab.2022.114797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 06/22/2022] [Indexed: 11/01/2022]
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5
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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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6
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Wang W, Wang X, Liu J, Lin C, Liu J, Wang J. The Integration of Gold Nanoparticles with Polymerase Chain Reaction for Constructing Colorimetric Sensing Platforms for Detection of Health-Related DNA and Proteins. BIOSENSORS 2022; 12:bios12060421. [PMID: 35735568 PMCID: PMC9220820 DOI: 10.3390/bios12060421] [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: 05/24/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 05/02/2023]
Abstract
Polymerase chain reaction (PCR) is the standard tool in genetic information analysis, and the desirable detection merits of PCR have been extended to disease-related protein analysis. Recently, the combination of PCR and gold nanoparticles (AuNPs) to construct colorimetric sensing platforms has received considerable attention due to its high sensitivity, visual detection, capability for on-site detection, and low cost. However, it lacks a related review to summarize and discuss the advances in this area. This perspective gives an overview of established methods based on the combination of PCR and AuNPs for the visual detection of health-related DNA and proteins. Moreover, this work also addresses the future trends and perspectives for PCR-AuNP hybrid biosensors.
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Affiliation(s)
- Wanhe Wang
- Institute of Medical Research, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an 710072, China; (W.W.); (X.W.); (J.L.); (C.L.); (J.L.)
- Research & Development Institute of Northwestern Polytechnical University in Shenzhen, 45 South Gaoxin Road, Shenzhen 518057, China
- Collaborative Innovation Center of NPU, Shanghai 201100, China
- Innovation Center NPU Chongqing, Northwestern Polytechnical University, Chongqing 400000, China
| | - Xueliang Wang
- Institute of Medical Research, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an 710072, China; (W.W.); (X.W.); (J.L.); (C.L.); (J.L.)
- Research & Development Institute of Northwestern Polytechnical University in Shenzhen, 45 South Gaoxin Road, Shenzhen 518057, China
- Collaborative Innovation Center of NPU, Shanghai 201100, China
- Innovation Center NPU Chongqing, Northwestern Polytechnical University, Chongqing 400000, China
| | - Jingqi Liu
- Institute of Medical Research, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an 710072, China; (W.W.); (X.W.); (J.L.); (C.L.); (J.L.)
- Research & Development Institute of Northwestern Polytechnical University in Shenzhen, 45 South Gaoxin Road, Shenzhen 518057, China
- Collaborative Innovation Center of NPU, Shanghai 201100, China
| | - Chuankai Lin
- Institute of Medical Research, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an 710072, China; (W.W.); (X.W.); (J.L.); (C.L.); (J.L.)
- Research & Development Institute of Northwestern Polytechnical University in Shenzhen, 45 South Gaoxin Road, Shenzhen 518057, China
- Collaborative Innovation Center of NPU, Shanghai 201100, China
| | - Jianhua Liu
- Institute of Medical Research, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an 710072, China; (W.W.); (X.W.); (J.L.); (C.L.); (J.L.)
- Research & Development Institute of Northwestern Polytechnical University in Shenzhen, 45 South Gaoxin Road, Shenzhen 518057, China
- Collaborative Innovation Center of NPU, Shanghai 201100, China
| | - Jing Wang
- Institute of Medical Research, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an 710072, China; (W.W.); (X.W.); (J.L.); (C.L.); (J.L.)
- Research & Development Institute of Northwestern Polytechnical University in Shenzhen, 45 South Gaoxin Road, Shenzhen 518057, China
- Collaborative Innovation Center of NPU, Shanghai 201100, China
- Innovation Center NPU Chongqing, Northwestern Polytechnical University, Chongqing 400000, China
- Correspondence: ; Tel.: +86-13268283561
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7
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PCR enhancers: Types, mechanisms, and applications in long-range PCR. Biochimie 2022; 197:130-143. [DOI: 10.1016/j.biochi.2022.02.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 02/06/2022] [Accepted: 02/24/2022] [Indexed: 12/21/2022]
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8
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Nuriding H, Wang X, Shen Y, Liu Y, Yan M. Fos-Related Antigen 1 May Cause Wnt-Fzd Signaling Pathway-Related Nephroblastoma in Children. J Biomed Nanotechnol 2022; 18:527-534. [PMID: 35484756 DOI: 10.1166/jbn.2022.3220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This study aimed to investigate the role of the primary Fos-related antigen 1 (Fosl-1) oncogene in nephroblastoma by studying 60 childhood nephroblastoma and 58 paraneoplastic carcinoma cases. The Fosl-1 expression was detected using immunohistochemistry. In vitro culture of nephroblastoma cells was performed by viral transfection to establish Fosl-1 overexpression and gene knockout models. Flow cytometry and nano-PCR were used to detect apoptosis and mRNA expression in related pathway genes. Immunohistochemical results showed that the positive expression of Fosl-1 in the nuclei of nephroblastoma tissue was 78%, among which metastasis rate was 61.7%; correspondingly, it was 8%, and 100% in adjacent tissues. The qPCR results indicated that MMP9, Wnt1, and Fzd1 were significantly upregulated after Fosl-1 overexpression compared with the normal embryonic tissue cells, control, and gene knockout groups (P <0.05). Fosl-1 could cause the occurrence, development, and metastasis of childhood nephroblastoma through wingless/int1/Frizzled-related signaling pathways.
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Affiliation(s)
- Hailiqiguli Nuriding
- Department of the First Internal Medicine, Pediatric Center of the First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, Xinjiang, PR China
| | - Xuemei Wang
- Department of the First Internal Medicine, Pediatric Center of the First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, Xinjiang, PR China
| | - Yiping Shen
- Department of Laboratory Medicine, Children's Hospital Boston, Boston, 02115, Massachusetts, United States
| | - Yu Liu
- Department of the First Internal Medicine, Pediatric Center of the First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, Xinjiang, PR China
| | - Mei Yan
- Department of the First Internal Medicine, Pediatric Center of the First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, Xinjiang, PR China
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9
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Sun Y, Huang Y, Qi T, Jin Q, Jia C, Zhao J, Feng S, Liang L. Wet-Etched Microchamber Array Digital PCR Chip for SARS-CoV-2 Virus and Ultra-Early Stage Lung Cancer Quantitative Detection. ACS OMEGA 2022; 7:1819-1826. [PMID: 35036821 PMCID: PMC8751011 DOI: 10.1021/acsomega.1c05082] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/22/2021] [Indexed: 05/02/2023]
Abstract
We report a novel design of chamber-based digital polymerase chain reaction (cdPCR) chip structure. Using a wet etching process and silicon-glass bonding, the chamber size can be adjusted independently of the process and more feasibly in a normal lab. In addition, the structure of the chip is optimized through hydrodynamic computer simulations to eliminate dead space when the sample is injected into the chip. The samples will be distributed to each separated microchambers for an isolated reaction based on Poisson distribution. Due to the difference in expansion coefficients, isolation of the sample in the microchambers by the oil phase on top ensures homogeneity and independence of the sample in the microchambers. The prepared microarray cdPCR chip enables high-throughput and high-sensitivity quantitative measurement of the SARS-CoV-2 virus gene and the mutant lung cancer gene. We applied the chip for the detection of different concentrations of the mix containing the open reading frame 1ab (ORF1ab) gene, the most specific and conservative gene region of the SARS-CoV-2 virus. In addition to this, we also successfully detected the fluorescence of the epidermal growth factor receptor (EGFR) mutant gene in independent microchambers. At a throughput of 46 200 microchambers, solution mixtures containing both genes were successfully tested quantitatively, with a detection limit of 10 copies/μL. Importantly, the chips are individually inexpensive and easy to industrialize. In addition, the microarray can provide a unified solution for other viral sequences, cancer marker assay development, and point-of-care testing (POCT).
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Affiliation(s)
- Yimeng Sun
- State
Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem
and Information Technology, Chinese Academy
of Sciences, Shanghai 200050, China
- Center
of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaru Huang
- State
Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem
and Information Technology, Chinese Academy
of Sciences, Shanghai 200050, China
- School
of Life Sciences, Shanghai Normal University, Shanghai 200235, China
| | - Tong Qi
- State
Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem
and Information Technology, Chinese Academy
of Sciences, Shanghai 200050, China
| | - Qinghui Jin
- State
Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem
and Information Technology, Chinese Academy
of Sciences, Shanghai 200050, China
- Faculty
of Electrical Engineering and Computer Science, Ningbo University, Ningbo 315211, China
| | - Chunping Jia
- State
Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem
and Information Technology, Chinese Academy
of Sciences, Shanghai 200050, China
| | - Jianlong Zhao
- State
Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem
and Information Technology, Chinese Academy
of Sciences, Shanghai 200050, China
- Center
of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shilun Feng
- State
Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem
and Information Technology, Chinese Academy
of Sciences, Shanghai 200050, China
| | - Lijuan Liang
- State
Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem
and Information Technology, Chinese Academy
of Sciences, Shanghai 200050, China
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10
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Su Y, Chu H, Tian J, Du Z, Xu W. Insight into the nanomaterials enhancement mechanism of nucleic acid amplification reactions. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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11
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Hu B, Wang Y, Sun S, Luo G, Zhang S, Zhang J, Chen L, Huang Z. Specificity Enhancement of Deoxyribonucleic Acid Polymerization for Sensitive Nucleic Acid Detection. Anal Chem 2020; 92:15872-15879. [PMID: 33236629 DOI: 10.1021/acs.analchem.0c03223] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Specificity of DNA polymerization plays a critical role in DNA replication and storage of genetic information. Likewise, biotechnological applications, such as nucleic acid detection, DNA amplification, and gene cloning, require high specificity in DNA synthesis catalyzed by DNA polymerases. However, errors in DNA polymerization (such as mis-incorporation and mis-priming) can significantly jeopardize the specificity. Herein, we report our discovery that the specificity of DNA enzymatic synthesis can be substantially enhanced (up to 100-fold higher) by attenuating DNA polymerase kinetics via the phosphorothioate dNTPs. This specificity enhancement allows convenient and sensitive nucleic acid detection, polymerization, PCR, and gene cloning with complex systems (such as human cDNA and genomic DNA). Further, we found that the specificity enhancement offered higher sensitivity (up to 50-fold better) for detecting nucleic acids, such as COVID-19 viral RNAs. Our findings have revealed a simple and convenient strategy for facilitating specificity and sensitivity of nucleic acid detection, amplification, and gene cloning.
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Affiliation(s)
- Bei Hu
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, P. R. China
| | - Yitao Wang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, P. R. China
| | - Shichao Sun
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, P. R. China
| | - Guangcheng Luo
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, P. R. China
| | - Shun Zhang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, P. R. China
| | - Jun Zhang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, P. R. China
| | - Lu Chen
- Szostak-CDHT Institute for Large Nucleic Acids, Chengdu 610041, Sichuan, P.R. China
| | - Zhen Huang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, P. R. China.,Szostak-CDHT Institute for Large Nucleic Acids, Chengdu 610041, Sichuan, P.R. China
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12
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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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13
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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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14
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Enhancement of PCR Sensitivity and Yield Using Thiol-modified Primers. Sci Rep 2018; 8:14858. [PMID: 30291287 PMCID: PMC6173752 DOI: 10.1038/s41598-018-33223-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 09/25/2018] [Indexed: 02/02/2023] Open
Abstract
Various additives can enhance the quality of PCR amplification, but these generally require considerable optimization to achieve peak performance. Here, we demonstrate that the use of thiol-modified primers can enhance both PCR sensitivity and yield. In experiments with V. parahaemolyticus genomic DNA, this primer modification enhances PCR sensitivity by more than 100-fold, with accompanying improvements in amplicon yield. Then, an artificial plasmid with the same primer binding regions and different internal amplification sequence was designed. The result showed that the amplification also be improved by using the same thiol-modified primers. It indicated the enhancement was not caused by the effect of the thiol-modified primers on the second structure of amplification sequence. Subsequent experiments demonstrate that the effects of this modification are potentially due to altered interaction between the primers and proteins in the reaction mixture. Amplification with thiol-modified primers was strongly inhibited by the presence of extraneous proteins relative to standard DNA primers, which indicates that thiol-modified primers may be inhibited due to interaction with these proteins. In contaminant-free reactions, however, the thiol-modified primers might interact more strongly with DNA polymerase, which could in turn improve PCR amplification.
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15
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Ye X, Fang X, Li X, Kong J. Gold nanoparticle-mediated nucleic acid isothermal amplification with enhanced specificity. Anal Chim Acta 2018; 1043:150-157. [PMID: 30392663 DOI: 10.1016/j.aca.2018.09.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 09/07/2018] [Accepted: 09/08/2018] [Indexed: 10/28/2022]
Abstract
Loop-mediated isothermal amplification is a promising method in the area of nucleic acid detection. However, it suffers from a high rate of false-positive amplifications that largely restrict its application. In this study, we observed gold nanoparticles (AuNP) absorbing single-stranded DNA primers and interacting with Bst DNA polymerase via electrostatic adsorption. As a result of these interactions, the presence of the gold nanoparticles exerted a hot-start effect on the loop-mediated isothermal amplification system. Based on these results, we developed a novel AuNP-mediated nucleic acid isothermal amplification assay. This assay displays significantly enhanced specificity-the proportion of false positive decreased from 76% to 0% and from 100% to 0% for the detection of rotavirus and the β-actin gene, respectively, with the hot-start temperature of 48 °C. Moreover, our AuNP-based assay maintained good sensitivity and a satisfactory detection limit (1 × 103copies/μL) compared with the conventional assay. This approach has the potential to solve the nonspecificity problem of loop-mediated isothermal amplification, thereby promoting its real-world application, particularly, in clinical settings.
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Affiliation(s)
- Xin Ye
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China
| | - Xueen Fang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China.
| | - Xinxin Li
- Shanghai Suxin Biotechnology Co. Ltd, Shanghai, 201321, PR China
| | - Jilie Kong
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China.
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16
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Liu Q, Li L, Zhao Y, Chen Z. Colorimetric detection of DNA at the nanomolar level based on enzyme-induced gold nanoparticle de-aggregation. Mikrochim Acta 2018; 185:301. [DOI: 10.1007/s00604-018-2833-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 04/30/2018] [Indexed: 10/16/2022]
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17
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Hamdy ME, Del Carlo M, Hussein HA, Salah TA, El-Deeb AH, Emara MM, Pezzoni G, Compagnone D. Development of gold nanoparticles biosensor for ultrasensitive diagnosis of foot and mouth disease virus. J Nanobiotechnology 2018; 16:48. [PMID: 29751767 PMCID: PMC5946443 DOI: 10.1186/s12951-018-0374-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 04/28/2018] [Indexed: 12/22/2022] Open
Abstract
Background Nano-PCR is a recent tool that is used in viral diseases diagnosis. The technique depends on the fundamental effects of gold nanoparticles (AuNPs) and is considered a very effective and sensitive tool in the diagnosis of different diseases including viral diseases. Although several techniques are currently available to diagnose foot and mouth disease virus (FMDV), a highly sensitive, highly specific technique is needed for specific diagnosis of the disease. In the present work, a novel AuNPs biosensor has been designed using thiol-linked oligonucleotides that recognize the conserved 3D gene of FMDV. Results The AuNPs-FMDV biosensor specifically recognizes RNA standards of FMDV, but not that of swine vesicular disease virus (SVDV) isolates. The analytical sensitivity of the AuNPs-FMDV biosensor was 10 copy number RNA standards in RT-PCR and 1 copy number RNA standard in real-time rRT-PCR with a 94.5% efficiency, 0.989 R2, a − 3.544 slope and 100% specificity (no cross-reactivity with SVDV). These findings were confirmed by the specific and sensitive recognition of 31 Egyptian FMDV clinical isolates that represents the three FMDV serotypes (O, A, and SAT2). Conclusions The AuNPs-FMDV biosensor presents in this study demonstrates a superior analytical and clinical performance for FMDV diagnosis. In addition, this biosensor has a simple workflow and accelerates epidemiological surveillance, hence, it is qualified as an efficient FMDV diagnosis tool for quarantine stations and farms particularly in FMDV endemic areas. Electronic supplementary material The online version of this article (10.1186/s12951-018-0374-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mervat E Hamdy
- Department of Biotechnology Animal Health Research Institute, Agriculture Research Centre, Giza, 12618, Egypt
| | - Michele Del Carlo
- Department of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, 64023, Teramo, Italy
| | - Hussein A Hussein
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt.
| | - Taher A Salah
- Nanotechnology Research Centre, British University, Cairo, Egypt.,Nanotechnology and Advanced Materials Central Lab, Agricultural Research Centre, Giza, Egypt
| | - Ayman H El-Deeb
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Mohamed M Emara
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Guilia Pezzoni
- Department of Biotechnology, Zooprofilattico Institute of Lombardy and Emilia Romagna (IZSLER), 25124, Brescia, Italy
| | - Dario Compagnone
- Department of Biosciences and Technology for Food, Agriculture and Environment, University of Teramo, 64023, Teramo, Italy
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18
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Wang L, Huang Z, Wang R, Liu Y, Qian C, Wu J, Liu J. Transition Metal Dichalcogenide Nanosheets for Visual Monitoring PCR Rivaling a Real-Time PCR Instrument. ACS APPLIED MATERIALS & INTERFACES 2018; 10:4409-4418. [PMID: 29327589 DOI: 10.1021/acsami.7b15746] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Monitoring the progress of polymerase chain reactions (PCRs) is of critical importance in bioanalytical chemistry and molecular biology. Although real-time PCR thermocyclers are ideal for this purpose, their high cost has limited their applications in resource-poor areas. Direct visual detection would be a more attractive alternative. To monitor the PCR amplification, DNA-staining dyes, such as SYBR Green I (SG), are often used. Although these dyes give higher fluorescence when binding to double-stranded DNA products, they also yield strong background fluorescence in the presence of a high concentration of single-stranded (ss) DNA primers. In this work, we screened various nanomaterials and found that graphene oxide (GO), reduced GO, molybdenum disulfide (MoS2), and tungsten disulfide (WS2) can quench the fluorescence of nonamplified negative samples while still retaining strong fluorescence of positive ones. The signal ratio of positive-over-negative samples was enhanced by around 50-fold in the presence of these materials. In particular, MoS2 and WS2 nearly fully retained the fluorescence of the positive samples. The mechanism for MoS2 and WS2 to enhance PCR signaling is attributed to the adsorption of both the ssDNA PCR primers and SG with an appropriate strength. MoS2 can also suppress nonspecific amplification caused by excess polymerase. Finally, this method was used to detect extracted transgenic soya GTS 40-3-2 DNA after PCR amplification. Compared with the samples without nanomaterials, the addition of MoS2 could better distinguish the concentration difference of the template DNA, and the sensitivity of visual detection rivaled that from a real-time PCR instrument.
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Affiliation(s)
- Liu Wang
- College of Biosystems Engineering and Food Science, Zhejiang University , Hangzhou 310058, China
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo N2L 3G1, Ontario, Canada
| | - Zhicheng Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo N2L 3G1, Ontario, Canada
| | - Rui Wang
- College of Biosystems Engineering and Food Science, Zhejiang University , Hangzhou 310058, China
| | - Yibo Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo N2L 3G1, Ontario, Canada
| | - Cheng Qian
- College of Biosystems Engineering and Food Science, Zhejiang University , Hangzhou 310058, China
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University , Hangzhou 310058, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo N2L 3G1, Ontario, Canada
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19
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Development of Nano-Polymerase Chain Reaction and Its Application. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2017. [DOI: 10.1016/s1872-2040(17)61051-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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20
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Yang W, Cao X, Li X. Enhanced simultaneous overlap extension-PCR by gold nanoparticles. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2017; 13:2263-2266. [DOI: 10.1016/j.nano.2017.06.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 06/10/2017] [Accepted: 06/19/2017] [Indexed: 12/27/2022]
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21
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Zhang H, Peng C, Li A, Shi X, Cao X. Effect of antifouling dendrimers and Au DENPs on the enhancement of PCR amplification. CAN J CHEM 2017. [DOI: 10.1139/cjc-2017-0055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The polymerase chain reaction (PCR) has been considered as one of the most fundamental techniques to amplify and analyze specific DNA fragments in the field of molecular biology and clinical medicine. Recently, a variety of nanoparticles (NPs) have been regarded as a novel method to enhance both the quality and yield of PCR technique. Herein, we report the use of generation 5 (G5) poly(amidoamine) (PAMAM) dendrimers and dendrimer-entrapped gold nanoparticles (Au DENPs) modified with polyethylene glycol (PEG) moieties and (or) acetyl groups as a novel class of enhancers to improve the PCR amplification. We set up the nonspecific PCR and two-round PCR as model systems to investigate mechanisms of enhanced PCR. Our results show that dendrimer-based derivatives seem to enhance the PCR specificity. It is worth noting that the modification of antifouling PEG significantly lowered the optimization capability of the corresponding dendrimers, although this inhibition effect can be remarkably compromised by the entrapment of Au NPs. Furthermore, we found that in the presence of Au NPs, the thermal conductivity induced by Au NPs could play the dominant role in the PCR optimization, whereas in the absence of Au NPs, the electrostatic interaction of the dendrimers with PCR components may be the major factor affecting the PCR system. Our results also showed that the optimal concentrations of the materials in the two test systems were very close, which indicates that the developed dendrimer derivatives with good thermal stability may be the efficient PCR additives for enhancing different PCR systems.
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Affiliation(s)
- Haixia Zhang
- Department of Radiology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai 200072, People’s Republic of China
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, People’s Republic of China
| | - Chen Peng
- Department of Radiology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai 200072, People’s Republic of China
| | - Aijun Li
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, People’s Republic of China
| | - Xiangyang Shi
- Department of Radiology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai 200072, People’s Republic of China
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, People’s Republic of China
| | - Xueyan Cao
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, People’s Republic of China
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22
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Li A, Zhou B, Alves CS, Xu B, Guo R, Shi X, Cao X. Mechanistic Studies of Enhanced PCR Using PEGylated PEI-Entrapped Gold Nanoparticles. ACS APPLIED MATERIALS & INTERFACES 2016; 8:25808-25817. [PMID: 27599792 DOI: 10.1021/acsami.6b09310] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The polymerase chain reaction (PCR) is considered an excellent technique and is widely used in both molecular biology research and various clinical applications. However, the presence of byproducts and low output are limitations generally associated with this technique. Recently, the use of nanoparticles (NPs) has been shown to be very effective at enhancing PCR. Although mechanisms underlying this process have been suggested, most of them are mainly based on PCR results under certain situations without abundant systematic experimental strategy. In order to overcome these challenges, we synthesized a series of polyethylene glycol (PEG)-modified polyethylenimine (PEI)-entrapped gold nanoparticles (PEG-Au PENPs), each having different gold contents. The role of the synthesized NPs in improving the PCR technique was then systematically evaluated using the error-prone two-round PCR and GC-rich PCR (74% GC content). Our results suggest a possible mechanism of PCR enhancement. In the error-prone two-round PCR system, the improvement of the specificity and efficiency of the technique using the PEG-Au PENPs mainly depends on surface-charge-mediated electrostatic interactions. In the GC-rich PCR system, thermal conduction may be the dominant factor. These important findings offer a breakthrough in understanding the mechanisms involved in improving PCR amplification, as well as in the application of nanomaterials in different fields, particularly in biology and medicine.
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Affiliation(s)
- Aijun Li
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University , Shanghai 201620, People's Republic of China
| | - Benqing Zhou
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University , Shanghai 201620, People's Republic of China
| | - Carla S Alves
- CQM-Centro de Quimica da Madeira, Universidade da Madeira , Campus da Penteada, 9020-105 Funchal, Portugal
| | - Bei Xu
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University , Shanghai 201620, People's Republic of China
| | - Rui Guo
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University , Shanghai 201620, People's Republic of China
| | - Xiangyang Shi
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University , Shanghai 201620, People's Republic of China
- CQM-Centro de Quimica da Madeira, Universidade da Madeira , Campus da Penteada, 9020-105 Funchal, Portugal
| | - Xueyan Cao
- College of Chemistry, Chemical Engineering and Biotechnology, Donghua University , Shanghai 201620, People's Republic of China
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23
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Chao J, Zhang P, Wang Q, Wu N, Zhang F, Hu J, Fan CH, Li B. Single-molecule imaging of DNA polymerase I (Klenow fragment) activity by atomic force microscopy. NANOSCALE 2016; 8:5842-5846. [PMID: 26932823 DOI: 10.1039/c5nr06544e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We report a DNA origami-facilitated single-molecule platform that exploits atomic force microscopy to study DNA replication. We imaged several functional activities of the Klenow fragment of E. coli DNA polymerase I (KF) including binding, moving, and dissociation from the template DNA. Upon completion of these actions, a double-stranded DNA molecule was formed. Furthermore, the direction of KF activities was captured and then confirmed by shifting the KF binding sites on the template DNA.
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Affiliation(s)
- J Chao
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.
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24
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El-Husseini DM, Helmy NM, Tammam RH. The effect of gold nanoparticles on the diagnostic polymerase chain reaction technique for equine herpes virus 1 (EHV-1). RSC Adv 2016. [DOI: 10.1039/c6ra08513j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We experimented the effect of 15 nm unmodified citrate coated GNPs on the key PCR reactants to see if these would enhance the overall outcomes of the reaction. Thus, the optimized GNPs-assisted PCR could be used for more efficient diagnosis of EHV-1.
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Affiliation(s)
- Dalia M. El-Husseini
- Biotechnology Department
- Animal Health Research Institute
- Agriculture Research Centre
- Giza
- Egypt
| | - Nashwa M. Helmy
- Biotechnology Department
- Animal Health Research Institute
- Agriculture Research Centre
- Giza
- Egypt
| | - Reham H. Tammam
- Department of Chemistry
- Faculty of Science
- Cairo University
- Giza
- Egypt
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25
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Park JY, Back SH, Chang SJ, Lee SJ, Lee KG, Park TJ. Dopamine-assisted synthesis of carbon-coated silica for PCR enhancement. ACS APPLIED MATERIALS & INTERFACES 2015; 7:15633-40. [PMID: 26112101 DOI: 10.1021/acsami.5b04404] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Polymerase chain reaction (PCR) has become one of the most popular methods to identify genomic information on cells and tissues as well as to solve crimes and check genetic diseases. Recently, the nanomaterials including nanocomposite and nanoparticles have been considered as a next generation of solution to improve both quality and productivity of PCR. Herein, taking into these demands, carbon-coated silica was synthesized using silica particles via polymerization of biocompatible dopamine (PD) to form polydopamine (PDA) film and carbonization of PDA into graphitic structures. For further investigation of the effects of as-prepared silica, PDA-coated silica (PDA silica), and carbonized PDA silica (C-PDA silica), two different types of genes were adopted to investigate the influences of them in the PCR. Furthermore, the strong interaction between the nanocomposites and PCR reagents including polymerase and primers enables regulation of the PCR performance. The effectiveness of the nanocomposites was also confirmed through adopting the conventional PCR and real-time PCR with two different types of DNA as realistic models and different kinds of analytical methods. These findings could provide helpful insight for the potential application in biosensors and biomedical diagnosis.
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Affiliation(s)
- Ji Young Park
- †Department of Chemistry, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 156-756, Republic of Korea
| | - Seung Hun Back
- †Department of Chemistry, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 156-756, Republic of Korea
| | - Sung-Jin Chang
- †Department of Chemistry, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 156-756, Republic of Korea
| | - Seok Jae Lee
- ‡National Nanofab Center, 291 Daehak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Kyoung G Lee
- ‡National Nanofab Center, 291 Daehak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Tae Jung Park
- †Department of Chemistry, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 156-756, Republic of Korea
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26
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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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27
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Sensitive and specific colorimetric DNA detection by invasive reaction coupled with nicking endonuclease-assisted nanoparticles amplification. Biosens Bioelectron 2015; 66:50-4. [DOI: 10.1016/j.bios.2014.10.077] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 10/19/2014] [Accepted: 10/31/2014] [Indexed: 11/18/2022]
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28
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Walsh T, Lee J, Park K. Laser-assisted photothermal heating of a plasmonic nanoparticle-suspended droplet in a microchannel. Analyst 2015; 140:1535-42. [DOI: 10.1039/c4an01750a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The present article reports the numerical and experimental investigations on the laser-assisted photothermal heating of a nanoliter-sized droplet in a microchannel when plasmonic particles are suspended in the droplet.
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Affiliation(s)
- Timothy Walsh
- Department of Mechanical
- Industrial and Systems Engineering
- University of Rhode Island
- Kingston
- USA
| | - Jungchul Lee
- Department of Mechanical Engineering
- Sogang University
- Seoul
- South Korea
| | - Keunhan Park
- Department of Mechanical Engineering
- University of Utah
- Salt Lake City
- USA
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29
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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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30
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Yuan L, He Y. Effect of surface charge of PDDA-protected gold nanoparticles on the specificity and efficiency of DNA polymerase chain reaction. Analyst 2014; 138:539-45. [PMID: 23170311 DOI: 10.1039/c2an36145k] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The polymerase chain reaction (PCR) has become an indispensable technique in molecular biology, however, it suffers from low efficiency and specificity problems. Developing suitable additives to effectively avoid nonspecific PCR reactions and explore the mechanism for PCR enhancing is a significant challenge. In this paper, we report three different modified gold nanoparticles (AuNPs) with different surface charge polarities and poly (diallyl dimethylammonium) chloride (PDDA) for use as novel PCR enhancers to improve the efficiency and specificity. These AuNPs included the positively charged PDDA protected AuNPs (PDDA-AuNPs), the neutral PDDA-AuNPs modified with excess chloride ion (PDDA.C-AuNPs), and the negatively charged sodium citrate (Na(3)Ct) protected AuNPs (Na(3)Ct-AuNPs). Our data clearly suggests that the positively charged PDDA-AuNPs with an optimum concentration as low as 1.54 pM could significantly enhance the specificity and efficiency of PCR, however, the optimum concentration of the negatively charged Na(3)Ct-AuNPs (2.02 nM) was more than 3 orders of magnitude higher than that of positively charged PDDA-AuNPs. The PCR specificity and efficiency are also improved by the neutral PDDA.C-AuNPs with an optimum concentration, much more than that of the PDDA-AuNPs. This suggests that there should be an electrostatic interaction between the positively charged PDDA-AuNPs and the negatively charged PCR components, and the surface charge polarities of PDDA-AuNPs may play an important role in improving the PCR specificity and efficiency.
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Affiliation(s)
- Longfei Yuan
- College of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
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31
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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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32
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Li K, Du S, Van Ginkel S, Chen Y. Atomic Force Microscopy Study of the Interaction of DNA and Nanoparticles. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 811:93-109. [DOI: 10.1007/978-94-017-8739-0_6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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33
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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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34
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Yang W, Li X, Sun J, Shao Z. Enhanced PCR amplification of GC-rich DNA templates by gold nanoparticles. ACS APPLIED MATERIALS & INTERFACES 2013; 5:11520-11524. [PMID: 24206448 DOI: 10.1021/am4040448] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Gold nanoparticles (AuNPs) have been reported to facilitate double-stranded DNA dissociation and improve performance of several PCR systems. Here we investigated AuNPs' effect on GC-rich DNA amplification. We found that AuNPs could enhance PCR amplification of the GNAS1 promoter region (∼84% GC) mediated by Pfu or Taq DNA polymerase. However, under optimal concentrations of AuNPs, higher amounts of Taq were required. Furthermore, the GC-rich FMR1 (80.4% GC) gene of Homo sapiens as well as exoT (67.3% GC), exsE (71% GC) and pqqF genes (74% GC) of Pseudomonas aeruginosa were also efficiently amplified. AuNPs can become an effective additive in GC-rich PCR and facilitate analysis of challenging genomic sequence in basic and clinical research.
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Affiliation(s)
- Wenchao Yang
- School of Biomedical Engineering and ‡Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University , Shanghai 200240, China
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35
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Lou X, Zhang Y. Mechanism studies on nanoPCR and applications of gold nanoparticles in genetic analysis. ACS APPLIED MATERIALS & INTERFACES 2013; 5:6276-84. [PMID: 23734951 DOI: 10.1021/am4013209] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Recently, the applications of nanomaterial-assisted polymerase chain reaction (nanoPCR) have received considerable attention. Several potential mechanisms have been proposed, but mainly according to the results of PCR assays under specific conditions and lacking direct and general evidence. The mechanism of nanoPCR has not been elucidated yet. Here, taking gold nanoparticles (AuNPs) as an example, we report the three general effects of AuNPs: (1) AuNPs adsorb polymerase and modulate the amount of active polymerase in PCR, which was directly demonstrated by a simple and straightforward colorimetric assay and the dynamic light scattering measurements. (2) AuNPs adsorb primers and decrease the melting temperatures (Tm) of the duplexes formed with perfectly matched and mismatched primers and increase the Tm difference between them. (3) AuNPs adsorb PCR products and facilitate the dissociation of them in the denaturing step. All these effects were confirmed by addition of a rationally selected surface adsorbent, bovine thrombin, to highly efficiently modulate the surface adsorption of PCR components. These findings suggested that AuNPs should have multiple effects on PCR: (1) to regulate PCR in a case-by-case way via modulating the amount of active polymerase in PCR; (2) to improve PCR specificity in the annealing step via increasing the Tm difference between the perfectly matched and mismatched primers; (3) to improve PCR efficiency via speeding up the dissociation of the PCR products in the denaturing step. Taken together, we proposed the mechanism of nanoPCR is that the surface interaction of PCR components (polymerase, primers, and products) with AuNPs regulates nanoPCR. We further demonstrated that the applications of these findings improve the PCR of the amelogenin genes and Hepatitis B virus gene for genetic analysis. These findings could also provide helpful insight for the applications of other nanomaterials in nanoPCR.
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Affiliation(s)
- Xinhui Lou
- Department of Chemistry, Capital Normal University, Beijing, China.
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36
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Su S, Zuo X, Pan D, Pei H, Wang L, Fan C, Huang W. Design and applications of gold nanoparticle conjugates by exploiting biomolecule-gold nanoparticle interactions. NANOSCALE 2013; 5:2589-2599. [PMID: 23423633 DOI: 10.1039/c3nr33870c] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Gold nanoparticles (AuNPs) are a type of widely used nanomaterials with unique chemical and physical properties. AuNPs can be readily synthesized, and modified with various chemical or biological molecules, making them promising candidates for catalysis, drug delivery and biological imaging applications. In this review, we mainly focus on recent advances in the design and synthesis of conjugates of AuNPs by exploiting biomolecule-AuNP interactions. We will also discuss a variety of bioapplications of AuNP-based conjugates.
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Affiliation(s)
- Shao Su
- Key Laboratory for Organic Electronics & Information Displays, Institute of Advanced Materials, School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210046, China
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37
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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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38
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Prospects of nanoparticle–DNA binding and its implications in medical biotechnology. Biotechnol Adv 2012; 30:1721-32. [DOI: 10.1016/j.biotechadv.2012.03.007] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 02/28/2012] [Accepted: 03/20/2012] [Indexed: 01/10/2023]
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39
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Li L, Wang C, Song B, Mi L, Hu J. Kinetic Parameters Estimation in the Polymerase Chain Reaction Process Using the Genetic Algorithm. Ind Eng Chem Res 2012. [DOI: 10.1021/ie3003717] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lanting Li
- Laboratory of Physical Biology,
Shanghai Institute of Applied Physics, Chinese Academy of Science, Shanghai 201800, China
| | - Chao Wang
- Department of Biomedical Engineering, Oregon Health & Science University, Beaverton, Oregon 97006, United States
| | - Bo Song
- Laboratory of Physical Biology,
Shanghai Institute of Applied Physics, Chinese Academy of Science, Shanghai 201800, China
| | - Lijuan Mi
- Laboratory of Physical Biology,
Shanghai Institute of Applied Physics, Chinese Academy of Science, Shanghai 201800, China
| | - Jun Hu
- Laboratory of Physical Biology,
Shanghai Institute of Applied Physics, Chinese Academy of Science, Shanghai 201800, China
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40
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Cao X, Shen M, Zhang X, Hu J, Wang J, Shi X. Effect of the surface functional groups of dendrimer-entrapped gold nanoparticles on the improvement of PCR. Electrophoresis 2012; 33:2598-603. [DOI: 10.1002/elps.201200061] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Xueyan Cao
- College of Chemistry; Chemical Engineering and Biotechnology; Donghua University; Shanghai; People's Republic of China
| | - Mingwu Shen
- College of Chemistry; Chemical Engineering and Biotechnology; Donghua University; Shanghai; People's Republic of China
| | - Xiaodong Zhang
- Nanobiology Laboratory,; Bio-X Life Science Research Center; College of Life Science and Biotechnology; Shanghai JiaoTong University; Shanghai; People's Republic of China
| | | | - Jianhua Wang
- Department of Biochemistry and Molecular & Cell Biology; School of Medicine; Shanghai Jiao Tong University; Shanghai; People's Republic of China
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41
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Jia J, Sun L, Hu N, Huang G, Weng J. Graphene enhances the specificity of the polymerase chain reaction. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2012; 8:2011-2015. [PMID: 22488835 DOI: 10.1002/smll.201200139] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Indexed: 05/31/2023]
Abstract
Graphene can inhibit non-specific DNA fragments, and the specificity of the polymerase chain reaction (PCR) can be retained even after eight rounds of repeated amplification in the presence of graphene in the form of reduced graphene oxide (RGO). In the figure, the numbers at the top give the number of rounds of PCR; lanes marked with C correspond to controls (no RGO), and the concentration of RGO in the other samples is 12 μg mL(-1) .
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Affiliation(s)
- Jing Jia
- Department of Biomaterials, College of Materials, Xiamen University, Xiamen, P. R. of China
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42
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Tong W, Cao X, Wen S, Guo R, Shen M, Wang J, Shi X. Enhancing the specificity and efficiency of polymerase chain reaction using polyethyleneimine-based derivatives and hybrid nanocomposites. Int J Nanomedicine 2012; 7:1069-78. [PMID: 22393296 PMCID: PMC3289439 DOI: 10.2147/ijn.s28947] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
There is a general necessity to improve the specificity and efficiency of the polymerase chain reaction (PCR), and exploring the PCR-enhancing mechanism still remains a great challenge. In this paper we report the use of branched polyethyleneimine (PEI)-based derivatives and hybrid nanocomposites as a novel class of enhancers to improve the specificity and efficiency of a nonspecific PCR system. We show that the surface-charge polarity of PEI and PEI derivatives plays a major role in their effectiveness to enhance the PCR. Positively charged amine-terminated pristine PEI, partially (50%) acetylated PEI (PEI-Ac(50)), and completely acetylated PEI (PEI-Ac) are able to improve PCR efficiency and specificity with an optimum concentration order of PEI < PEI-Ac(50) < PEI-Ac, whereas negatively charged carboxyl-terminated PEI (PEI-SAH; SAH denotes succinamic acid groups) and neutralized PEI modified with both polyethylene glycol (PEG) and acetyl (Ac) groups (PEI-PEG-Ac) are unable to improve PCR specificity and efficiency even at concentrations three orders of magnitude higher than that of PEI. Our data clearly suggests that the PCR-enhancing effect is primarily based on the interaction between the PCR components and the PEI derivatives, where electrostatic interaction plays a major role in concentrating the PCR components locally on the backbones of the branched PEI. In addition, multiwalled carbon nanotubes modified with PEI and PEI-stabilized gold nanoparticles are also able to improve the PCR specificity and efficiency with an optimum PEI concentration less than that of the PEI alone, indicating that the inorganic component of the nanocomposites may help improve the interaction between PEI and the PCR components. The developed PEI-based derivatives or nanocomposites may be used as efficient additives to enhance other PCR systems for different biomedical applications.
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Affiliation(s)
- Weiwei Tong
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Donghua University, Shanghai, People’s Republic of China
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43
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Zhao Y, Xu L, Kuang H, Wang L, Xu C. Asymmetric and symmetric PCR of gold nanoparticles: A pathway to scaled-up self-assembly with tunable chirality. ACTA ACUST UNITED AC 2012. [DOI: 10.1039/c2jm15800k] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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44
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Sang F, Yang Y, Wang H, Ju X, Zhang Z. Quantum dots induce hot-start effects for Taq-based polymerase chain reaction. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/jbise.2012.56038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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45
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Chen J, Cao X, Guo R, Shen M, Peng C, Xiao T, Shi X. A highly effective polymerase chain reactionenhancer based on dendrimer-entrapped gold nanoparticles. Analyst 2012; 137:223-8. [DOI: 10.1039/c1an15816c] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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46
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Chen P, Pan D, Fan C, Chen J, Huang K, Wang D, Zhang H, Li Y, Feng G, Liang P, He L, Shi Y. Gold nanoparticles for high-throughput genotyping of long-range haplotypes. NATURE NANOTECHNOLOGY 2011; 6:639-44. [PMID: 21892166 DOI: 10.1038/nnano.2011.141] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Accepted: 07/26/2011] [Indexed: 05/26/2023]
Abstract
Completion of the Human Genome Project and the HapMap Project has led to increasing demands for mapping complex traits in humans to understand the aetiology of diseases. Identifying variations in the DNA sequence, which affect how we develop disease and respond to pathogens and drugs, is important for this purpose, but it is difficult to identify these variations in large sample sets. Here we show that through a combination of capillary sequencing and polymerase chain reaction assisted by gold nanoparticles, it is possible to identify several DNA variations that are associated with age-related macular degeneration and psoriasis on significant regions of human genomic DNA. Our method is accurate and promising for large-scale and high-throughput genetic analysis of susceptibility towards disease and drug resistance.
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Affiliation(s)
- Peng Chen
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, China
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47
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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: 16] [Impact Index Per Article: 1.2] [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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48
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Cao X, Chen J, Wen S, Peng C, Shen M, Shi X. Effect of surface charge of polyethyleneimine-modified multiwalled carbon nanotubes on the improvement of polymerase chain reaction. NANOSCALE 2011; 3:1741-1747. [PMID: 21340081 DOI: 10.1039/c0nr00833h] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In molecular biology, polymerase chain reaction (PCR) has played an important role but suffers a general problem with low efficiency and specificity. Development of suitable additives to improve the PCR specificity and efficiency and the understanding of the PCR enhancing mechanism still remain a great challenge. Here we report the use of polyethyleneimine (PEI)-modified multiwalled carbon nanotubes (MWCNTs) with different surface charge polarities as a novel class of enhancers to improve the specificity and efficiency of PCR. The materials used included the positively charged PEI-modified MWCNTs (CNT/PEI), the neutral CNT/PEI modified with acetic anhydride (CNT/PEI.Ac), and the negatively charged CNT/PEI modified with succinic anhydride (CNT/PEI.SAH). We show that the specificity and efficiency of an error-prone two-round PCR are greatly impacted by the surface charge polarity of the PEI-modified MWCNTs. Positively charged CNT/PEI could significantly enhance the specificity and efficiency of PCR with an optimum concentration as low as 0.39 mg L(-1), whereas neutral CNT/PEI.Ac had no such effect. Although negatively charged CNT/PEI.SAH could enhance the PCR, the optimum concentration required (630 mg L(-1)) was more than 3 orders of magnitude higher than that of positively charged CNT/PEI. The present study suggests that the PCR enhancing effect may be primarily based on the electrostatic interaction between the positively charged CNT/PEI and the negatively charged PCR components, rather than only on the thermal conductivity of MWCNTs.
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Affiliation(s)
- Xueyan Cao
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Donghua University, Shanghai, 201620, PR China
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