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Zhao X, Peng H, Hu J, Wang L, Zhang F. Nanotechnology-Enabled PCR with Tunable Energy Dynamics. JACS AU 2024; 4:3370-3382. [PMID: 39328766 PMCID: PMC11423310 DOI: 10.1021/jacsau.4c00570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 08/08/2024] [Accepted: 08/08/2024] [Indexed: 09/28/2024]
Abstract
This Perspective elucidates the transformative impacts of advanced nanotechnology and dynamic energy systems on the polymer chain reaction (PCR), a cornerstone technique in biomedical research and diagnostic applications. Since its invention, the optimization of PCR-specifically its efficiency, specificity, cycling rate, and detection sensitivity-has been a focal point of scientific exploration. Our analysis spans the modulation of PCR from both material and energetic perspectives, emphasizing the intricate interplay between PCR components and externally added entities such as molecules, nanoparticles (NPs), and optical microcavities. We begin with a foundational overview of PCR, detailing the basic principles of PCR modulation through molecular additives to highlight material-level interactions. Then, we delve into how NPs, with their diverse material and surface properties, influence PCR through interface interactions and hydrothermal conduction, drawing parallels to molecular behaviors. Additionally, this Perspective ventures into the energetic regulation of PCR, examining the roles of electromagnetic radiation and optical resonators. We underscore the advanced capabilities of optical technologies in PCR regulation, characterized by their ultrafast, residue-free, and noninvasive nature, alongside label-free detection methods. Notably, optical resonators present a pioneering approach to control PCR processes even in the absence of light, targeting the often-overlooked water component in PCR. By integrating discussions on photocaging and vibrational strong coupling, this review presents innovative methods for the precise regulation of PCR processes, envisioning a new era of PCR technology that enhances both research and clinical diagnostics. The synergy between nanotechnological enhancements and energy dynamics not only enriches our understanding of PCR but also opens new avenues for developing rapid, accurate, and efficient PCR systems. We hope that this Perspective will inspire further innovations in PCR technology and guide the development of next-generation clinical detection instruments.
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Affiliation(s)
- Xinmin Zhao
- Terahertz Technology Innovation Research Institute, Terahertz Spectrum and Imaging Technology Cooperative Innovation Center, Shanghai Key Lab of Modern Optical System, University of Shanghai for Science and Technology, Shanghai 200093, People's Republic of China
| | - Hongzhen Peng
- Institute of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, People's Republic of China
| | - Jun Hu
- Institute of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, People's Republic of China
| | - Lihua Wang
- Institute of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, People's Republic of China
| | - Feng Zhang
- Terahertz Technology Innovation Research Institute, Terahertz Spectrum and Imaging Technology Cooperative Innovation Center, Shanghai Key Lab of Modern Optical System, University of Shanghai for Science and Technology, Shanghai 200093, People's Republic of China
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2
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Li Y, Lin S, Xue Y, Jia Q, Wang Y, Xie Y, Shi C, Ma C. Boron nitride nanoplate-based improvement of the specificity and sensitivity in loop-mediated isothermal amplification for Vibrio parahaemolyticus detection. Anal Chim Acta 2023; 1280:341851. [PMID: 37858548 DOI: 10.1016/j.aca.2023.341851] [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: 07/26/2023] [Revised: 09/24/2023] [Accepted: 09/26/2023] [Indexed: 10/21/2023]
Abstract
BACKGROUND Nucleic acid testing based on DNA amplification is gradually entering people's modern life for clinical diagnosis, food safety monitoring and infectious disease prevention. Polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP) are the most powerful techniques that have been the gold standard for quantitative nucleic acid analysis. However, the high nonspecific amplification rate caused by the formation of primer dimers, hairpin structures and mismatched hybridization severely restricts their real-world applications. It is highly desirable to explore a way for improving the specificity and sensitivity of PCR and LAMP assays. RESULTS In this work, we demonstrated that a nanomaterial boron nitride nanoplate (BNNP), due to its unique surface properties, can interact with the main components of the amplification reaction, such as single stranded primers and Bst DNA polymerase, and increase the thermal conductivity of the solution. As a result, the presence of BNNPs dramatically improved the specificity of PCR and LAMP. And BNNPs maintained the specificity even after five rounds of PCR. Moreover, the sensitivity of LAMP was also enhanced by BNNPs, and the detection limit of BNNP-based LAMP was two orders of magnitude lower than that of classical LAMP. Then the BNNP-based LAMP was applied to detect Vibrio parahaemolyticus in contaminated seafood samples with high specificity and a 10-fold increase in sensitivity. SIGNIFICANCE This is the first systematic demonstration of BNNPs as a promising additive to enhance the efficiency and fidelity of PCR and LAMP amplification reactions, thereby greatly expanding the application of nucleic acid detection in a wide range of laboratory and clinical settings.
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Affiliation(s)
- Yong Li
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao Key Laboratory of Nucleic Acid Rapid Detection, Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, 266042, Qingdao, China
| | - Shuo Lin
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao Key Laboratory of Nucleic Acid Rapid Detection, Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, 266042, Qingdao, China
| | - Yuxin Xue
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao Key Laboratory of Nucleic Acid Rapid Detection, Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, 266042, Qingdao, China
| | - Qianyue Jia
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao Key Laboratory of Nucleic Acid Rapid Detection, Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, 266042, Qingdao, China
| | - Ye Wang
- Clinical Laboratory, Qingdao Central Hospital, The Second Affiliated Hospital of Medical College of Qingdao University, 266042, Qingdao, China
| | - Yingqiu Xie
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
| | - Chao Shi
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Department of Pathogenic Biology, School of Basic Medicine, Department of the Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao University, 266071, Qingdao, China
| | - Cuiping Ma
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao Key Laboratory of Nucleic Acid Rapid Detection, Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, 266042, Qingdao, China.
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3
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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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4
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Pereira H, Silva PC, Johansson B. Bacteria and Yeast Colony PCR. Methods Mol Biol 2023; 2967:209-221. [PMID: 37608114 DOI: 10.1007/978-1-0716-3358-8_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The bacteria Escherichia coli and the yeast Saccharomyces cerevisiae are currently the two most important organisms in synthetic biology. E. coli is almost always used for fundamental DNA manipulation, while yeast is the simplest host system for studying eukaryotic gene expression and performing large-scale DNA assembly. Yeast expression studies may also require altering the chromosomal DNA by homologous recombination. All these studies require the verification of the expected DNA sequence, and the fastest method of screening is colony PCR, which is direct PCR of DNA in cells without prior DNA purification. Colony PCR is hampered by the difficulty of releasing DNA into the PCR mix and by the presence of PCR inhibitors. We hereby present one protocol for E. coli and two protocols for S. cerevisiae differing in efficiency and complexity as well as an overview of past and possible future developments of efficient S. cerevisiae colony PCR protocols.
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Affiliation(s)
- Humberto Pereira
- CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal
| | - Paulo César Silva
- CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal
| | - Björn Johansson
- CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal.
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5
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Yang Z, Shen B, Yue L, Miao Y, Hu Y, Ouyang R. Application of Nanomaterials to Enhance Polymerase Chain Reaction. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248854. [PMID: 36557991 PMCID: PMC9781713 DOI: 10.3390/molecules27248854] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/27/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022]
Abstract
Polymerase Chain Reaction (PCR) is one of the most common technologies used to produce millions of copies of targeted nucleic acid in vitro and has become an indispensable technique in molecular biology. However, it suffers from low efficiency and specificity problems, false positive results, and so on. Although many conditions can be optimized to increase PCR yield, such as the magnesium ion concentration, the DNA polymerases, the number of cycles, and so on, they are not all-purpose and the optimization can be case dependent. Nano-sized materials offer a possible solution to improve both the quality and productivity of PCR. In the last two decades, nanoparticles (NPs) have attracted significant attention and gradually penetrated the field of life sciences because of their unique chemical and physical properties, such as their large surface area and small size effect, which have greatly promoted developments in life science and technology. Additionally, PCR technology assisted by NPs (NanoPCR) such as gold NPs (Au NPs), quantum dots (QDs), and carbon nanotubes (CNTs), etc., have been developed to significantly improve the specificity, efficiency, and sensitivity of PCR and to accelerate the PCR reaction process. This review discusses the roles of different types of NPs used to enhance PCR and summarizes their possible mechanisms.
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Affiliation(s)
- Zhu Yang
- Institute of Bismuth and Rhenium Science, School Materials and Chemistry, University of Shanghai for Science and Technology, Shanghai 200093, China
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Bei Shen
- CAS Key Laboratory of Molecular Virology & Immunology, Institutional Center for Shared Technologies and Facilities, Pathogen Discovery and Big Data Platform, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lihuan Yue
- CAS Key Laboratory of Molecular Virology & Immunology, Institutional Center for Shared Technologies and Facilities, Pathogen Discovery and Big Data Platform, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuqing Miao
- Institute of Bismuth and Rhenium Science, School Materials and Chemistry, University of Shanghai for Science and Technology, Shanghai 200093, China
- Correspondence: (Y.M.); (Y.H.); (R.O.)
| | - Yihong Hu
- CAS Key Laboratory of Molecular Virology & Immunology, Institutional Center for Shared Technologies and Facilities, Pathogen Discovery and Big Data Platform, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
- Correspondence: (Y.M.); (Y.H.); (R.O.)
| | - Ruizhuo Ouyang
- Institute of Bismuth and Rhenium Science, School Materials and Chemistry, University of Shanghai for Science and Technology, Shanghai 200093, China
- Correspondence: (Y.M.); (Y.H.); (R.O.)
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6
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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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7
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Ku J, Chauhan K, Hwang SH, Jeong YJ, Kim DE. Enhanced Specificity in Loop-Mediated Isothermal Amplification with Poly(ethylene glycol)-Engrafted Graphene Oxide for Detection of Viral Genes. BIOSENSORS 2022; 12:bios12080661. [PMID: 36005057 PMCID: PMC9405610 DOI: 10.3390/bios12080661] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/17/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is a nucleic acid amplification method that allows the simple, quick, and low-cost detection of various viral genes. LAMP assays are susceptible to generating non-specific amplicons, as high concentrations of DNA primers can give rise to primer dimerization and mismatched hybridizations, resulting in false-positive signals. Herein, we reported that poly(ethylene glycol)-engrafted nanosized graphene oxide (PEG-nGO) can significantly enhance the specificity of LAMP, owing to its ability to adsorb single-stranded DNA (ssDNA). By adsorbing surplus ssDNA primers, PEG-nGO minimizes the non-specific annealing of ssDNAs, including erroneous priming and primer dimerization, leading to the enhanced specificity of LAMP. The detection of complementary DNAs transcribed from the hepatitis C virus (HCV) RNA was performed by the PEG-nGO-based LAMP. We observed that the inclusion of PEG-nGO significantly enhances the specificity and sensitivity of the LAMP assay through the augmented difference in fluorescence signals between the target and non-target samples. The PEG-nGO-based LAMP assay greatly facilitates the detection of HCV-positive clinical samples, with superior precision to the conventional quantitative real-time PCR (RT-qPCR). Among the 20 clinical samples tested, all 10 HCV-positive samples are detected as positive in the PEG-nGO-based LAMP, while only 7 samples are detected as HCV-positive in the RT-qPCR. In addition, the PEG-nGO-based LAMP method significantly improves the detection precision for the false-positive decision by 1.75-fold as compared to the LAMP without PEG-nGO. Thus, PEG-nGO can significantly improve the performance of LAMP assays by facilitating the specific amplification of target DNA with a decrease in background signal.
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Affiliation(s)
- Jamin Ku
- Department of Bioscience and Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05902, Korea
| | - Khushbu Chauhan
- Department of Bioscience and Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05902, Korea
| | - Sang-Hyun Hwang
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Yong-Joo Jeong
- School of Applied Chemistry, Kookmin University, Seoul 02707, Korea
- Correspondence: (Y.-J.J.); (D.-E.K.)
| | - Dong-Eun Kim
- Department of Bioscience and Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05902, Korea
- Correspondence: (Y.-J.J.); (D.-E.K.)
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8
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Lim RRX, Ang WL, Ambrosi A, Sofer Z, Bonanni A. Electroactive nanocarbon materials as signaling tags for electrochemical PCR. Talanta 2022; 245:123479. [DOI: 10.1016/j.talanta.2022.123479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/08/2022] [Accepted: 04/10/2022] [Indexed: 11/15/2022]
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9
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Su Y, Li X, Zhu L, Chu H, Zhang Y, Tian J, Lyu S, Xu W. MSN/NA-doped nanoflower enhancing isothermal fluorescent sensor with a portable PCR tube fluorescence reader for the on-site detection of Vibrio parahaemolyticus. Anal Chim Acta 2022; 1200:339448. [DOI: 10.1016/j.aca.2022.339448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/15/2021] [Accepted: 01/04/2022] [Indexed: 11/01/2022]
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10
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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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11
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Kim JW, Park KW, Kim M, Lee KK, Lee CS. Highly Specific Loop-Mediated Isothermal Amplification Using Graphene Oxide-Gold Nanoparticles Nanocomposite for Foot-and-Mouth Disease Virus Detection. NANOMATERIALS 2022; 12:nano12020264. [PMID: 35055281 PMCID: PMC8778833 DOI: 10.3390/nano12020264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/04/2022] [Accepted: 01/11/2022] [Indexed: 12/10/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is a molecular diagnosis technology with the advantages of rapid results, isothermal reaction conditions, and high sensitivity. However, this diagnostic system often produces false positive results due to a high rate of non-specific reactions caused by formation of hairpin structures, self-dimers, and mismatched hybridization. The non-specific signals can be due to primers used in the methods because the utilization of multiple LAMP primers increases the possibility of self-annealing of primers or mismatches between primers and templates. In this study, we report a nanomaterial-assisted LAMP method that uses a graphene oxide-gold nanoparticles (AuNPs@GO) nanocomposite to enable the detection of foot-and-mouth disease virus (FMDV) with high sensitivity and specificity. Foot-and-mouth disease (FMD) is a highly contagious and deadly disease in cloven-hoofed animals; hence, a rapid, sensitive, and specific detection method is necessary. The proposed approach exhibited high sensitivity and successful reduction of non-specific signals compared to the traditionally established LAMP assays. Additionally, a mechanism study revealed that these results arose from the adsorption of single-stranded DNA on AuNPs@GO nanocomposite. Thus, AuNPs@GO nanocomposite is demonstrated to be a promising additive in the LAMP system to achieve highly sensitive and specific detection of diverse diseases, including FMD.
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Affiliation(s)
- Jong-Won Kim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Korea; (J.-W.K.); (K.-W.P.); (M.K.); (K.K.L.)
| | - Kyoung-Woo Park
- Bionanotechnology Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Korea; (J.-W.K.); (K.-W.P.); (M.K.); (K.K.L.)
- Department of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Korea
| | - Myeongkun Kim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Korea; (J.-W.K.); (K.-W.P.); (M.K.); (K.K.L.)
| | - Kyung Kwan Lee
- Bionanotechnology Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Korea; (J.-W.K.); (K.-W.P.); (M.K.); (K.K.L.)
- Department of Biomedical and Nanopharmaceutical Science, College of Pharmacy, Kyung Hee University, Seoul 02447, Korea
| | - Chang-Soo Lee
- Bionanotechnology Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Korea; (J.-W.K.); (K.-W.P.); (M.K.); (K.K.L.)
- Department of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Korea
- Correspondence: ; Tel.: +82-4-2879-8446
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12
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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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13
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Graphene oxide and self-avoiding molecular recognition systems-assisted recombinase polymerase amplification coupled with lateral flow bioassay for nucleic acid detection. Mikrochim Acta 2020; 187:667. [PMID: 33211195 DOI: 10.1007/s00604-020-04637-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 11/06/2020] [Indexed: 12/12/2022]
Abstract
A new nucleic acid detection technique, termed Nano-SAMRS-RPA, is reported which employed carbon nanomaterial (graphene oxide, GO) and self-avoiding molecular recognition systems (SAMRS) to improve the specificity of recombinase polymerase amplification (RPA). In the presence of GO and SAMRS primers, the assay artifacts, including primer-dimers, nonspecific products, off-target hybrids, and non-canonical folds, are completely suppressed and eliminated, which makes the creation of RPA-based methods faster by simplifying the primer design and eliminating the need for primer optimization and complex probe. Moreover, a lateral flow bioassay (LFB) was also devised for simply and rapidly indicating the Nano-SAMRS-RPA results. Particularly, the new detection system only requires a single-labeled primer, eliminating the false-positive result from hybridization (the labeled probe and reverse primer) and the use of real-time instrument, more complex enzymatic solutions, and probes. As a result, GO, SAMRS primers, and LFB convert RPA from a technique suited only for the research laboratory into one that has a practical value in clinical settings, field environments, and at points-of-care testing. Human papillomaviruses (HPV) genotypes 16 and 18 were applied as model analytes to test the assay's availability. The initial data indicated that Nano-SAMRS-RPA could detect down to 10 copies per reaction, and the sensitivity (14/14 samples collected from HPV16 and HPV 18 patients) and specificity (75/75 samples collected from non-HPV patients) for clinical sample detection were 100%. The proof-of-concept technique can be reconfigured to detect various nucleic acid sequences by redesigning the specific RPA primers.Graphical abstract.
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Rasheed AK, Siddiqui R, Ahmed SMK, Gabriel S, Jalal MZ, John A, Khan NA. hBN Nanoparticle-Assisted Rapid Thermal Cycling for the Detection of Acanthamoeba. Pathogens 2020; 9:pathogens9100824. [PMID: 33036480 PMCID: PMC7601326 DOI: 10.3390/pathogens9100824] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/02/2020] [Accepted: 10/03/2020] [Indexed: 11/16/2022] Open
Abstract
Acanthamoeba are widely distributed in the environment and are known to cause blinding keratitis and brain infections with greater than 90% mortality rate. Currently, polymerase chain reaction (PCR) is a highly sensitive and promising technique in Acanthamoeba detection. Remarkably, the rate of heating-cooling and convective heat transfer of the PCR tube is limited by low thermal conductivity of the reagents mixture. The addition of nanoparticles to the reaction has been an interesting approach that could augment the thermal conductivity of the mixture and subsequently enhance heat transfer through the PCR tube. Here, we have developed hexagonal boron nitride (hBN) nanoparticle-based PCR assay for the rapid detection of Acanthamoeba to amplify DNA from low amoeba cell density. As low as 1 × 10-4 wt % was determined as the optimum concentration of hBN nanoparticles, which increased Acanthamoeba DNA yield up to ~16%. Further, it was able to reduce PCR temperature that led to a ~2.0-fold increase in Acanthamoeba DNA yield at an improved PCR specificity at 46.2 °C low annealing temperature. hBN nanoparticles further reduced standard PCR step time by 10 min and cycles by eight; thus, enhancing Acanthamoeba detection rapidly. Enhancement of Acanthamoeba PCR DNA yield is possibly due to the high adsorption affinity of hBN nanoparticles to purine (Guanine-G) due to the higher thermal conductivity achieved in the PCR mixture due to the addition of hBN. Although further research is needed to demonstrate these findings in clinical application, we propose that the interfacial layers, Brownian motion, and percolation network contribute to the enhanced thermal conductivity effect.
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Affiliation(s)
- Abdul Khaliq Rasheed
- Department of New Energy Science and Engineering, School of Energy and Chemical Engineering, Xiamen University Malaysia Campus, Bandar Sunsuria, Sepang 43900, Malaysia;
| | - Ruqaiyyah Siddiqui
- Department of Biology, Chemistry and Environmental Sciences, College of Arts and Sciences, American University of Sharjah, Sharjah 26666, UAE;
| | - Salma Mohammed Kabir Ahmed
- Department of Biological Sciences, School of Science and Technology, Sunway University, Bandar Sunway 47500, Malaysia; (S.M.K.A.); (S.G.)
| | - Shobana Gabriel
- Department of Biological Sciences, School of Science and Technology, Sunway University, Bandar Sunway 47500, Malaysia; (S.M.K.A.); (S.G.)
| | - Mohammed Zayan Jalal
- Department of Mechanical Engineering, Faculty of Engineering, International Islamic University Malaysia, Jalan Gombak 53100, Malaysia;
| | - Akbar John
- Institute of Oceanography and Maritime Studies, Kulliyyah of Science, International Islamic University Malaysia, Kuantan 25200, Malaysia;
| | - Naveed Ahmed Khan
- Department of Biology, Chemistry and Environmental Sciences, College of Arts and Sciences, American University of Sharjah, Sharjah 26666, UAE;
- Correspondence: ; Tel.: +971-6515-4752
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15
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Kim JW, Kim M, Lee KK, Chung KH, Lee CS. Effects of Graphene Oxide-Gold Nanoparticles Nanocomposite on Highly Sensitive Foot-and-Mouth Disease Virus Detection. NANOMATERIALS 2020; 10:nano10101921. [PMID: 32993046 PMCID: PMC7601864 DOI: 10.3390/nano10101921] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 11/29/2022]
Abstract
The polymerase chain reaction (PCR) has become a powerful molecular diagnostic technique over the past few decades, but remains somewhat impaired due to low specificity, poor sensitivity, and false positive results. Metal and carbon nanomaterials, quantum dots, and metal oxides, can improve the quality and productivity of PCR assays. Here, we describe the ability of PCR assisted with nanomaterials (nano-PCR) comprising a nanocomposite of graphene oxide (GO) and gold nanoparticles (AuNPs) for sensitive detection of the foot-and-mouth disease virus (FMDV). Graphene oxide and AuNPs have been widely applied as biomedical materials for diagnosis, therapy, and drug delivery due to their unique chemical and physical properties. Foot-and-mouth disease (FMD) is highly contagious and fatal for cloven-hoofed animals including pigs, and it can thus seriously damage the swine industry. Therefore, a highly sensitive, specific, and practical method is needed to detect FMDV. The detection limit of real-time PCR improved by ~1000 fold when assisted by GO-AuNPs. We also designed a system of detecting serotypes in a single assay based on melting temperatures. Our sensitive and specific nano-PCR system can be applied to diagnose early FMDV infection, and thus may prove to be useful for clinical and biomedical applications.
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Affiliation(s)
- Jong-Won Kim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB) 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea; (J.-W.K.); (M.K.); (K.K.L.)
- Dignostics Platform Research Section, Electronics and Telecommunications Research Institute (ETRI) 218 Gajeong-ro, Yuseong-gu, Daejeon 34129, Korea;
| | - Myeongkun Kim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB) 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea; (J.-W.K.); (M.K.); (K.K.L.)
- Dignostics Platform Research Section, Electronics and Telecommunications Research Institute (ETRI) 218 Gajeong-ro, Yuseong-gu, Daejeon 34129, Korea;
| | - Kyung Kwan Lee
- Bionanotechnology Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB) 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea; (J.-W.K.); (M.K.); (K.K.L.)
- Dignostics Platform Research Section, Electronics and Telecommunications Research Institute (ETRI) 218 Gajeong-ro, Yuseong-gu, Daejeon 34129, Korea;
- Department of Life and Nanopharmaceutical Science, College of Pharmacy, Kyung Hee University, Seoul 02447, Korea
| | - Kwang Hyo Chung
- Dignostics Platform Research Section, Electronics and Telecommunications Research Institute (ETRI) 218 Gajeong-ro, Yuseong-gu, Daejeon 34129, Korea;
| | - Chang-Soo Lee
- Bionanotechnology Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB) 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea; (J.-W.K.); (M.K.); (K.K.L.)
- Dignostics Platform Research Section, Electronics and Telecommunications Research Institute (ETRI) 218 Gajeong-ro, Yuseong-gu, Daejeon 34129, Korea;
- Department of Biotechnology, University of Science & Technology (UST), Daejeon 34113, Korea
- Correspondence:
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16
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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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17
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Upadhyay A, Yang H, Zaman B, Zhang L, Wu Y, Wang J, Zhao J, Liao C, Han Q. ZnO Nanolower-Based NanoPCR as an Efficient Diagnostic Tool for Quick Diagnosis of Canine Vector-Borne Pathogens. Pathogens 2020; 9:pathogens9020122. [PMID: 32075178 PMCID: PMC7169380 DOI: 10.3390/pathogens9020122] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 01/27/2020] [Accepted: 02/12/2020] [Indexed: 02/07/2023] Open
Abstract
Polymerase chain reaction (PCR) is a unique technique in molecular biology and biotechnology for amplifying target DNA strands, and is also considered as a gold standard for the diagnosis of many canine diseases as well as many other infectious diseases. However, PCR still faces many challenges and issues related to its sensitivity, specificity, efficiency, and turnaround time. To address these issues, we described the use of unique ZnO nanoflowers in PCR reaction and an efficient ZnO nanoflower-based PCR (nanoPCR) for the molecular diagnosis of canine vector-borne diseases (CVBDs). A total of 1 mM of an aqueous solution of ZnO nanoflowers incorporated in PCR showed a significant enhancement of the PCR assay with respect to its sensitivity and specificity for the diagnosis of two important CVBDs, Babesia canis vogeli and Hepatozoon canis. Interestingly, it drastically reduced the turnaround time of the PCR assay without compromising the yield of the amplified DNA, which can be of benefit for veterinary practitioners for the improved management of diseases. This can be attributed to the favorable adsorption of ZnO nanoflowers to the DNA and thermal conductivity of ZnO nanoflowers. The unique ZnO nanoflower-assisted nanoPCR greatly improved the yield, purity, and quality of the amplified products, but the mechanism behind these properties and the effects and changes due to the different concentrations of ZnO nanoflowers in the PCR system needs to be further studied.
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Affiliation(s)
- Archana Upadhyay
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China; (A.U.); (L.Z.); (J.W.); (J.Z.)
| | - Huan Yang
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Material Science and Engineering, Haikou 570228, China;
| | - Bilal Zaman
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Provincial Key Laboratory of Research on Utilization of Si-Zr-Ti Resources, College of Material Science and Engineering, Hainan University, Haikou 570228, China
| | - Lei Zhang
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China; (A.U.); (L.Z.); (J.W.); (J.Z.)
| | - Yundi Wu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China;
| | - Jinhua Wang
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China; (A.U.); (L.Z.); (J.W.); (J.Z.)
| | - Jianguo Zhao
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China; (A.U.); (L.Z.); (J.W.); (J.Z.)
| | - Chenghong Liao
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China; (A.U.); (L.Z.); (J.W.); (J.Z.)
- Correspondence: (C.L.); (Q.H.)
| | - Qian Han
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China; (A.U.); (L.Z.); (J.W.); (J.Z.)
- Correspondence: (C.L.); (Q.H.)
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18
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Chen ZC, Chang TL, Li CH, Su KW, Liu CC. Thermally stable and uniform DNA amplification with picosecond laser ablated graphene rapid thermal cycling device. Biosens Bioelectron 2019; 146:111581. [PMID: 31629228 PMCID: PMC7126615 DOI: 10.1016/j.bios.2019.111581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 06/02/2019] [Accepted: 08/08/2019] [Indexed: 01/02/2023]
Abstract
Rapid thermal cycling (RTC) in an on-chip device can perform DNA amplification in vitro through precise thermal control at each step of the polymerase chain reaction (PCR). This study reports a straightforward fabrication technique for patterning an on-chip graphene-based device with hole arrays, in which the mechanism of surface structures can achieve stable and uniform thermal control for the amplification of DNA fragments. A thin-film based PCR device was fabricated using picosecond laser (PS-laser) ablation of the multilayer graphene (MLG). Under the optimal fluence of 4.72 J/cm2 with a pulse overlap of 66%, the MLG can be patterned with arrays of 250 μm2 hole surface structures. A 354-bp DNA fragment of VP1, an effective marker for diagnosing the BK virus, was amplified on an on-chip device in less than 60 min. A thin-film electrode with the aforementioned MLG as the heater was demonstrated to significantly enhance temperature stability for each stage of the thermal cycle. The temperature control of the heater was performed by means of a developed programmable PCR apparatus. Our results demonstrated that the proposed integration of a graphene-based device and a laser-pulse ablation process to form a thin-film PCR device has cost benefits in a small-volume reagent and holds great promise for practical medical use of DNA amplification.
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Affiliation(s)
- Zhao-Chi Chen
- Department of Mechatronic Engineering, National Taiwan Normal University, Taipei, Taiwan, ROC
| | - Tien-Li Chang
- Department of Mechatronic Engineering, National Taiwan Normal University, Taipei, Taiwan, ROC.
| | - Ching-Hao Li
- Department of Physiology, School of Medicine, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan, ROC
| | - Kai-Wen Su
- Integrated Science, University of British Columbia, Columbia, Canada
| | - Cheng-Che Liu
- Graduate Institute of Physiology, National Defense Medical Center, Taipei, Taiwan, ROC.
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19
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Maleki MJ, Ghasemi Y, Pourhassan-Moghaddam M, Asadi N, Dadashpour M, Abolghasem Mohammadi S, Akbarzadeh A, Zarghami N. Effect of green GO/Au nanocomposite on in-vitro amplification of human DNA. IET Nanobiotechnol 2019; 13:887-890. [PMID: 31811755 DOI: 10.1049/iet-nbt.2018.5082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Recently nanomaterials have attracted interest for increasing efficiency of polymerase chain reaction (PCR) systems. Here, the authors report on the usefulness of green graphene oxide/gold (GO/Au) nanocomposites for enhancement of PCR reactions. In this study, green GO/Au nanocomposite was prepared with Matricaria chamomilla extract as reducing/capping agent for site-directed nucleation of Auo atoms on surface of GO sheets. The as-prepared green GO/Au nanocomposites were then characterised with UV-VIS spectrophotometer and scanning electron microscopy. Later, the effect of these nanocomposites was studied on end-point and real-time PCR employed for amplification of human glyceraldehyde-3-phosphate dehydrogenase gene. The results indicated that GO/Au nanocomposite can improve both end-point and real-time PCR methods at the optimum concentrations, possibly through interaction between GO/Au nanocomposite and the materials in PCR reaction, and through providing increased thermal convection by the GO surface as well as the Au nanostructures. In conclusion, it can be suggested that green GO/Au nanocomposite is a biocompatible and eco-friendly candidate as enhancer of in-vitro molecular amplification strategies.
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Affiliation(s)
- Mohammad Jafar Maleki
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yaghoob Ghasemi
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Pourhassan-Moghaddam
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Nahideh Asadi
- Department of Medical Nanotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Dadashpour
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Abolfazl Akbarzadeh
- Department of Chemical Engineering, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115-5000, USA
| | - Nosratollah Zarghami
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
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20
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Sun C, Cheng Y, Pan Y, Yang J, Wang X, Xia F. Efficient polymerase chain reaction assisted by metal-organic frameworks. Chem Sci 2019; 11:797-802. [PMID: 34123055 PMCID: PMC8145698 DOI: 10.1039/c9sc03202a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
As a powerful tool for obtaining sufficient DNA from rare DNA resources, polymerase chain reaction (PCR) has been widely used in various fields, and the optimization of PCR is still in progress due to the dissatisfactory specificity, sensitivity and efficiency. Although many nanomaterials have been proven to be capable of optimizing PCR, their underlying mechanisms are still unclear. So far, the scientifically compelling and functionally evolving metal–organic framework (MOF) materials with high specific surface area, tunable pore sizes, alterable surface charges and favourable thermal conductivity have not been used for PCR optimization. In this study, UiO-66 and ZIF-8 were used to optimize error-prone two round PCR. The results demonstrated that UiO-66 and ZIF-8 not only enhanced the sensitivity and efficiency of the first round PCR, but also increased the specificity and efficiency of the second round PCR. Moreover, they could widen the annealing temperature range of the second round PCR. The interaction of DNA and Taq polymerase with MOFs may be the main reason. This work provided a candidate enhancer for PCR, deepened our understanding on the enhancement mechanisms of nano-PCR, and explored a new application field for MOFs. Many new materials have the ability to optimize polymerase chain reaction (PCR). Metal-organic frame materials UiO-66 and ZIF-8 can enhance sensitivity, specificity and efficiency of PCR, indicating their potential as PCR enhancers.![]()
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Affiliation(s)
- Chunli Sun
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology Wuhan 430074 China
| | - Yong Cheng
- School of Materials Science and Engineering, Huazhong University of Science and Technology Wuhan 430074 China
| | - Yong Pan
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology Wuhan 430074 China
| | - Juliang Yang
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences Wuhan 430074 China
| | - Xudong Wang
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology Wuhan 430074 China
| | - Fan Xia
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology Wuhan 430074 China .,Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences Wuhan 430074 China
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21
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Lin Q, Ye X, Huang Z, Yang B, Fang X, Chen H, Kong J. Graphene Oxide-Based Suppression of Nonspecificity in Loop-Mediated Isothermal Amplification Enabling the Sensitive Detection of Cyclooxygenase-2 mRNA in Colorectal Cancer. Anal Chem 2019; 91:15694-15702. [PMID: 31725282 DOI: 10.1021/acs.analchem.9b03861] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cyclooxygenase-2 (COX2) mRNA represents a key biomarker for identifying subjects with colorectal cancer (CRC), while there is still no rapid and sensitive detection method for COX2 mRNA. Loop-mediated isothermal amplification (LAMP) is extensively developed for the amplification of nucleic acids; however, its application is frequently hindered by serious nonspecific amplification. Herein, this work reported a graphene oxide (GO)-based LAMP method to enable the one-step detection of COX2 mRNA in cancer cells and serum samples. We found that GO greatly enhanced the specificity of LAMP through decreasing nonspecific hybridization and the fluorescence background signal because of the simultaneous adsorption of single-stranded primers and DNA staining dyes on GO. The detection limit of developed GO-based LAMP was 2 orders of magnitude more sensitive compared to that of classical LAMP. Then a GO-based reverse transcription (RT)-LAMP strategy was further developed and applied to detect COX2 mRNA in CRC cancer cells and serum samples with high specificity. The GO-based LAMP platform with advantages of low cost, simplicity, high specificity, and sensitivity holds considerable potential for real-time fluorescence monitoring of nucleic acid amplification in a wide range of fields.
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Affiliation(s)
- Qiuyuan Lin
- Department of Chemistry , Fudan University , Shanghai 200438 , P. R. China
| | - Xin Ye
- Department of Chemistry , Fudan University , Shanghai 200438 , P. R. China
| | - Zhipeng Huang
- Department of Chemistry , Fudan University , Shanghai 200438 , P. R. China
| | - Bin Yang
- Department of Chemistry , Fudan University , Shanghai 200438 , P. R. China
| | - Xueen Fang
- Department of Chemistry , Fudan University , Shanghai 200438 , P. R. China
| | - Hui Chen
- Department of Chemistry , Fudan University , Shanghai 200438 , P. R. China
| | - Jilie Kong
- Department of Chemistry , Fudan University , Shanghai 200438 , P. R. China
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22
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Zhang D, Li Y, Zhang X, Cheng Y, Li Z. Enhancement of the polymerase chain reaction by tungsten disulfide. RSC Adv 2019; 9:9373-9378. [PMID: 35520733 PMCID: PMC9062020 DOI: 10.1039/c8ra09689a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 03/14/2019] [Indexed: 12/15/2022] Open
Abstract
In this paper, we demonstrated that the polymerase chain reaction (PCR) could be dramatically enhanced by tungsten disulfide (WS2). The results showed that the PCR efficiency could be increased with the addition of WS2 and at a lower annealing temperature, which simplified the design and operation of PCR. Moreover, PCR with WS2 showed better specificity and efficiency as compared with graphene oxide (GO) for a human genome DNA sample. The mechanism of enhancement of PCR by WS2 was discussed according to the typical structure and the characteristics of selective adsorption of single-stranded DNA by WS2. The results suggested that WS2 as a PCR enhancer can promote the PCR performance and extend the PCR application in biomedical research, clinical diagnostic, and bioanalysis. WS2 as a PCR enhancer can promote the PCR performance and extend PCR bioapplication.![]()
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Affiliation(s)
- Dong Zhang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education
- Key Laboratory of Analytical Science and Technology of Hebei Province
- College of Chemistry and Environmental Science
- Hebei University
| | - Yingcun Li
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education
- Key Laboratory of Analytical Science and Technology of Hebei Province
- College of Chemistry and Environmental Science
- Hebei University
| | - Xuange Zhang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education
- Key Laboratory of Analytical Science and Technology of Hebei Province
- College of Chemistry and Environmental Science
- Hebei University
| | - Yongqiang Cheng
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education
- Key Laboratory of Analytical Science and Technology of Hebei Province
- College of Chemistry and Environmental Science
- Hebei University
| | - Zhengping Li
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education
- Key Laboratory of Analytical Science and Technology of Hebei Province
- College of Chemistry and Environmental Science
- Hebei University
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23
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Mao D, Chen T, Chen H, Zhou M, Zhai X, Chen G, Zhu X. pH-Based immunoassay: explosive generation of hydrogen ions through an immuno-triggered nucleic acid exponential amplification reaction. Analyst 2019; 144:4060-4065. [DOI: 10.1039/c9an00506d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A pH-based immunoassay is developed based on an immuno-triggered explosive generation of hydrogen ions strategy.
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Affiliation(s)
- Dongsheng Mao
- Center for Molecular Recognition and Biosensing
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- China
| | - Tianshu Chen
- Center for Molecular Recognition and Biosensing
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- China
| | - Huinan Chen
- Center for Molecular Recognition and Biosensing
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- China
| | - Mengru Zhou
- Center for Molecular Recognition and Biosensing
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- China
| | - Xingwei Zhai
- Center for Molecular Recognition and Biosensing
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- China
| | - Guifang Chen
- Center for Molecular Recognition and Biosensing
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- China
| | - Xiaoli Zhu
- Center for Molecular Recognition and Biosensing
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- China
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24
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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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25
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Sang F, Zhang Z, Yuan L, Liu D. Quantum dots for a high-throughput Pfu polymerase based multi-round polymerase chain reaction (PCR). Analyst 2018; 143:1259-1267. [DOI: 10.1039/c7an01764b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We developed a Pfu polymerase based multi-round PCR technique assisted by quantum dots (QDs).
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Affiliation(s)
- Fuming Sang
- School of Marine Science and Technology
- Harbin Institute of Technology
- Weihai
- People's Republic of China
| | - Zhizhou Zhang
- School of Marine Science and Technology
- Harbin Institute of Technology
- Weihai
- People's Republic of China
| | - Lin Yuan
- School of Marine Science and Technology
- Harbin Institute of Technology
- Weihai
- People's Republic of China
| | - Deli Liu
- School of Marine Science and Technology
- Harbin Institute of Technology
- Weihai
- People's Republic of China
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26
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Graphene oxide enhances the specificity of the polymerase chain reaction by modifying primer-template matching. Sci Rep 2017; 7:16510. [PMID: 29184216 PMCID: PMC5705716 DOI: 10.1038/s41598-017-16836-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 11/17/2017] [Indexed: 11/17/2022] Open
Abstract
Aiming at improved specificity, nanoparticle assisted polymerase chain reaction (PCR) has been widely studied and shown to improve PCR. However, the reliability and mechanism of this method are still controversial. Here, we demonstrated that 1 μg/mL of graphene oxide (GO) effectively enhances the specificity of the error-prone multi-round PCR. Mismatched primers were designed as interference to produce nonspecific products when the same amounts of matched and mismatched primers were added into semi-multiplex PCR. It was found that GO can enhance specificity by suppressing the amplification of mismatched primers. We monitored the primer-template-polymerase-GO interactions involved in the PCR using a capillary electrophoresis/laser-induced fluorescence polarization (CE-LIFP) assay. The results showed that the addition of GO promoted the formation of a matched primer-template complex, but suppressed the formation of a mismatched primer-template complex during PCR, suggesting that interactions between the primers and GO play an essential role. Furthermore, we successfully amplified the FOXL2 gene from PEGFP-N1 vectors using GO to eliminate the nonspecific products in PCR. Taken together, these results suggest that the GO can be used as an efficient additive for improving the conventional PCR system.
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27
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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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28
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Abstract
Escherichia coli and Saccharomyces cerevisiae are currently the two most important organisms in synthetic biology. E.coli is almost always used for fundamental DNA manipulation while yeast is the simplest host system for studying eukaryotic gene expression and performing large scale DNA assembly. Yeast expression studies may also require altering of the chromosomal DNA by homologous recombination. All these studies require the verification of the expected DNA sequence and the fastest method of screening is colony PCR, which is direct PCR of DNA in cells without prior DNA purification. Colony PCR is hampered by the difficulty of releasing DNA into the PCR mix and the presence of PCR inhibitors. We hereby present one protocol for E. coli and two protocols for S. cerevisiae differing in efficiency and complexity as well as an overview of past and possible future developments of efficient S. cerevisiae colony PCR protocols.
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Affiliation(s)
- Flávio Azevedo
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Humberto Pereira
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Björn Johansson
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
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29
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Zhong Y, Huang L, Zhang Z, Xiong Y, Sun L, Weng J. Enhancing the specificity of polymerase chain reaction by graphene oxide through surface modification: zwitterionic polymer is superior to other polymers with different charges. Int J Nanomedicine 2016; 11:5989-6002. [PMID: 27956830 PMCID: PMC5113928 DOI: 10.2147/ijn.s120659] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Graphene oxides (GOs) with different surface characteristics, such as size, reduction degree and charge, are prepared, and their effects on the specificity of polymerase chain reaction (PCR) are investigated. In this study, we demonstrate that GO with a large size and high reduction degree is superior to small and nonreduced GO in enhancing the specificity of PCR. Negatively charged polyacrylic acid (PAA), positively charged polyacrylamide (PAM), neutral polyethylene glycol (PEG) and zwitterionic polymer poly(sulfobetaine) (pSB) are used to modify GO. The PCR specificity-enhancing ability increases in the following order: GO-PAA < GO-PAM < GO-PEG < GO-pSB. Thus, zwitterionic polymer-modified GO is superior to other GO derivatives with different charges in enhancing the specificity of PCR. GO derivatives are also successfully used to enhance the specificity of PCR for the amplification of human mitochondrial DNA using blood genomic DNA as template. Molecular dynamics simulations and molecular docking are performed to elucidate the interaction between the polymers and Pfu DNA polymerase. Our data demonstrate that the size, reduction degree and surface charge of GO affect the specificity of PCR. Based on our results, zwitterionic polymer-modified GO may be used as an efficient additive for enhancing the specificity of PCR.
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Affiliation(s)
- Yong Zhong
- Department of Biomaterials, College of Materials
| | - Lihong Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences
| | - Zhisen Zhang
- Department of Physics, Research Institute for Biomimetics and Soft Matter, Xiamen University, Xiamen, People’s Republic of China
| | | | - Liping Sun
- Department of Biomaterials, College of Materials
| | - Jian Weng
- Department of Biomaterials, College of Materials
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30
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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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31
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Xu M, Zhu J, Wang F, Xiong Y, Wu Y, Wang Q, Weng J, Zhang Z, Chen W, Liu S. Improved In Vitro and In Vivo Biocompatibility of Graphene Oxide through Surface Modification: Poly(Acrylic Acid)-Functionalization is Superior to PEGylation. ACS NANO 2016; 10:3267-3281. [PMID: 26855010 DOI: 10.1021/acsnano.6b00539] [Citation(s) in RCA: 242] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The unique physicochemical properties of two-dimensional (2D) graphene oxide (GO) could greatly benefit the biomedical field; however, recent research demonstrated that GO could induce in vitro and in vivo toxicity. We determined the mechanism of GO induced toxicity, and our in vitro experiments revealed that pristine GO could impair cell membrane integrity and functions including regulation of membrane- and cytoskeleton-associated genes, membrane permeability, fluidity and ion channels. Furthermore, GO induced platelet depletion, pro-inflammatory response and pathological changes of lung and liver in mice. To improve the biocompatibility of pristine GO, we prepared a series of GO derivatives including aminated GO (GO-NH2), poly(acrylamide)-functionalized GO (GO-PAM), poly(acrylic acid)-functionalized GO (GO-PAA) and poly(ethylene glycol)-functionalized GO (GO-PEG), and compared their toxicity with pristine GO in vitro and in vivo. Among these GO derivatives, GO-PEG and GO-PAA induced less toxicity than pristine GO, and GO-PAA was the most biocompatible one in vitro and in vivo. The differences in biocompatibility were due to the differential compositions of protein corona, especially immunoglobulin G (IgG), formed on their surfaces that determine their cell membrane interaction and cellular uptake, the extent of platelet depletion in blood, thrombus formation under short-term exposure and the pro-inflammatory effects under long-term exposure. Overall, our combined data delineated the key molecular mechanisms underlying the in vivo and in vitro biological behaviors and toxicity of pristine GO, and identified a safer GO derivative that could be used for future applications.
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Affiliation(s)
- Ming Xu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China
| | - Jianqiang Zhu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology , Tianjin 300211, China
| | - Fanfan Wang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, Nankai University , Tianjin 300071, China
| | - Yunjing Xiong
- Research Center of Biomedical Engineering, Department of Biomaterials, College of Materials, Xiamen University , Xiamen 361005, China
| | - Yakun Wu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China
| | - Qiuquan Wang
- Research Center of Biomedical Engineering, Department of Biomaterials, College of Materials, Xiamen University , Xiamen 361005, China
| | - Jian Weng
- Research Center of Biomedical Engineering, Department of Biomaterials, College of Materials, Xiamen University , Xiamen 361005, China
| | - Zhihong Zhang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Institute of Urology , Tianjin 300211, China
| | - Wei Chen
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, Nankai University , Tianjin 300071, China
| | - Sijin Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China
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32
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Vanzha E, Pylaev T, Khanadeev V, Konnova S, Fedorova V, Khlebtsov N. Gold nanoparticle-assisted polymerase chain reaction: effects of surface ligands, nanoparticle shape and material. RSC Adv 2016. [DOI: 10.1039/c6ra20472d] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The concentration, shape, material, and surface functionalization effects of gold nanoparticles on PCR outcome have been studied with two PCR gene diagnostic models.
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Affiliation(s)
- Ekaterina Vanzha
- Institute of Biochemistry and Physiology of Plants and Microorganisms
- Russian Academy of Sciences
- Saratov 410049
- Russia
| | - Timofey Pylaev
- Institute of Biochemistry and Physiology of Plants and Microorganisms
- Russian Academy of Sciences
- Saratov 410049
- Russia
| | - Vitaly Khanadeev
- Institute of Biochemistry and Physiology of Plants and Microorganisms
- Russian Academy of Sciences
- Saratov 410049
- Russia
| | - Svetlana Konnova
- Saratov Scientific and Research Veterinary Institute
- Russian Academy of Agricultural Sciences
- Saratov 410028
- Russia
| | - Valentina Fedorova
- Saratov Scientific and Research Veterinary Institute
- Russian Academy of Agricultural Sciences
- Saratov 410028
- Russia
| | - Nikolai Khlebtsov
- Institute of Biochemistry and Physiology of Plants and Microorganisms
- Russian Academy of Sciences
- Saratov 410049
- Russia
- Saratov National Research State University
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33
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Lv X, Hu B, Wang Z, Peng J, Weng J. Two-Electron Oxidation of Dopamine Controlled by Surface Modification of Few-Layer Graphene. Electrochim Acta 2015. [DOI: 10.1016/j.electacta.2015.08.075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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34
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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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35
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Zhu X, Shen Y, Cao J, Yin L, Ban F, Shu Y, Li G. Detection of microRNA SNPs with ultrahigh specificity by using reduced graphene oxide-assisted rolling circle amplification. Chem Commun (Camb) 2015; 51:10002-5. [DOI: 10.1039/c5cc02039e] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
By adopting reduced graphene oxide into a rolling cycle amplification system, we find that the specificity can be greatly improved, which would contribute to the accurate identification of miRNA SNPs.
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Affiliation(s)
- Xiaoli Zhu
- Laboratory of Biosensing Technology
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- P. R. China
| | - Yalan Shen
- Laboratory of Biosensing Technology
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- P. R. China
| | - Jiepei Cao
- Laboratory of Biosensing Technology
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- P. R. China
| | - Li Yin
- Department of Oncology
- the First Affiliated Hospital of Nanjing Medical University
- Nanjing 210029
- P. R. China
| | - Fangfang Ban
- Laboratory of Biosensing Technology
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- P. R. China
| | - Yongqian Shu
- Department of Oncology
- the First Affiliated Hospital of Nanjing Medical University
- Nanjing 210029
- P. R. China
| | - Genxi Li
- Laboratory of Biosensing Technology
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- P. R. China
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36
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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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37
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Zhang Y, Li X, Zou R, Xue Y, Lou X, He M. Bovine thrombin enhances the efficiency and specificity of polymerase chain reaction. Biotechniques 2014; 57:289-94. [PMID: 25495728 DOI: 10.2144/000114237] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 09/25/2014] [Indexed: 11/23/2022] Open
Abstract
The polymerase chain reaction (PCR) has become one of the central techniques in molecular biology since its invention. However, PCR can be fraught with difficulties in various situations, and it is desirable to find novel PCR enhancers suitable for universal applications. Here we show that bovine thrombin (BT), a well-known coagulation protein, is exceptionally effective at preventing the formation of primer dimers and enhancing the formation of the desired PCR products. The PCR enhancement effects of BT were demonstrated by testing various types of samples, including low-copy synthetic single-stranded DNAs (ssDNAs), synthetic ssDNA pools, human genomic DNA, and hepatitis B virus genomic DNA. In addition, BT was also able to effectively relieve PCR inhibition by nanomaterial inhibitors such as gold nanoparticles (AuNPs) and graphene oxide (GO). Compared with BSA, one of the most popular PCR enhancers, BT was more effective and required concentrations 18-178 times less than that of BSA to achieve a similar level of PCR enhancement.
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Affiliation(s)
- Ying Zhang
- Department of Chemistry, Capital Normal University, Beijing, China
| | - Xiaoning Li
- Department of Chemistry, Capital Normal University, Beijing, China
| | - Ruxing Zou
- Department of Chemistry, Capital Normal University, Beijing, China
| | - Ying Xue
- Beijing Municipal Center for Disease Prevention and Control, Beijing, China
| | - Xinhui Lou
- Department of Chemistry, Capital Normal University, Beijing, China
| | - Miao He
- School of Environment, Tsinghua University, Beijing, China
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38
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Chen N, Li J, Song H, Chao J, Huang Q, Fan C. Physical and biochemical insights on DNA structures in artificial and living systems. Acc Chem Res 2014; 47:1720-30. [PMID: 24588263 DOI: 10.1021/ar400324n] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
CONSPECTUS: Highly specific DNA base-pairing is the basis for both fulfilling its genetic role and constructing novel nanostructures and hybrid conjugates with inorganic nanomaterials (NMs). There exist many remarkable differences in the physical properties of single-stranded (ss) and double-stranded (ds) DNA, which play important roles in regulation of biological processes in nature. Rapid advances in nanoscience and nanotechnology pose new questions on how DNA and DNA structures interact with inorganic nanomaterials or cells and animals, which should be important for their biological and biomedical applications. In this Account, we intend to provide an overview on many facets of DNA and DNA structures in artificial and living systems, with the focus on their properties and functions at the interfaces of inorganic nanomaterials and biological systems. ssDNA, dsDNA, and DNA nanostructures interact with NMs in different ways. In particular, gold nanoparticles and graphene oxide exhibit strikingly different affinity toward ssDNA and dsDNA. Such binding differences can be coupled with optical properties of NMs. For example, DNA hybridization can effectively modulate the plasmonic and catalytic properties of gold nanoparticles. By exploitation of these interactions, there have been many ways for sensitive transduction of biomolecular recognition for various sensing applications. Alternatively, modulation of the properties of DNA and DNA structures with NMs has led to new tools for genetic analysis including genotyping and haplotyping. Self-assembled DNA nanostructures have emerged as a new type of NMs with pure biomolecules. These nanostructures can be designed in one, two, or three dimensions with various sizes, shapes, and geometries. They also have characteristics of uniform size, precise addressability, excellent water solubility, and biocompatibility. These nanostructures provide a new toolbox for biophysical studies with unparalleled advantages, for example, NMR-based protein structure determination and single-molecule studies. Also importantly, DNA nanostructures have proven highly useful in various applications including biological detection, bioreactors, and nanomedicine. In particular, DNA nanostructures exhibit high cellular permeability, a property that is not available for ssDNA and dsDNA, which is required for their drug delivery applications. DNA and DNA structures can also form hybrids with inorganic NMs. Notably, DNA anchored at the interface of inorganic NMs behaves differently from that at the macroscopic interface. Several types of DNA-NM conjugates have exerted beneficial effects for bioassays and in vitro translation of proteins. Even more interestingly, hybrid nanoconjugates demonstrate distinct properties under the context of biological systems such as cultured cells or animal models. These unprecedented properties not only arouse great interest in studying such interfaces but also open new opportunities for numerous applications in artificial and living systems.
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Affiliation(s)
- Nan Chen
- Division of Physical Biology & Bioimaging Center, Shanghai Sychrotron Radiation Facility (SSRF), CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Jiang Li
- Division of Physical Biology & Bioimaging Center, Shanghai Sychrotron Radiation Facility (SSRF), CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Haiyun Song
- Key
Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jie Chao
- Division of Physical Biology & Bioimaging Center, Shanghai Sychrotron Radiation Facility (SSRF), CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Qing Huang
- Division of Physical Biology & Bioimaging Center, Shanghai Sychrotron Radiation Facility (SSRF), CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Sychrotron Radiation Facility (SSRF), CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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39
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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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40
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Lv X, Weng J. Ternary composite of hemin, gold nanoparticles and graphene for highly efficient decomposition of hydrogen peroxide. Sci Rep 2013; 3:3285. [PMID: 24257652 PMCID: PMC3836040 DOI: 10.1038/srep03285] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 11/04/2013] [Indexed: 11/09/2022] Open
Abstract
A ternary composite of hemin, gold nanoparticles and graphene is prepared by a two-step process. Firstly, graphene-hemin composite is synthesized through π-π interaction and then hydrogen tetracholoroauric acid is reduced in situ by ascorbic acid. This ternary composite shows a higher catalytic activity for decomposition of hydrogen peroxide than that of three components alone or the mixture of three components. The Michaelis constant of this composite is 5.82 times lower and the maximal reaction velocity is 1.81 times higher than those of horseradish peroxidase, respectively. This composite also shows lower apparent activation energy than that of other catalysts. The excellently catalytic performance could be attributed to the fast electron transfer on the surface of graphene and the synergistic interaction of three components, which is further confirmed by electrochemical characterization. The ternary composite has been used to determine hydrogen peroxide in three real water samples with satisfactory results.
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Affiliation(s)
- Xincong Lv
- Department of Biomaterials, College of Materials, Xiamen University, Xiamen 361005, P.R. China
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41
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Song ZL, Zhao XH, Liu WN, Ding D, Bian X, Liang H, Zhang XB, Chen Z, Tan W. Magnetic graphitic nanocapsules for programmed DNA fishing and detection. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:951-957. [PMID: 23208981 DOI: 10.1002/smll.201201975] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 11/05/2012] [Indexed: 05/18/2023]
Abstract
Graphene nanomaterials are typically used in biosensing applications, and they have been demonstrated as good fluorescence quenchers. While many conventional amplification platforms are available, developing new nanomaterials and establishing simple, enzyme-free and low-cost strategies for high sensitivity biosensing is still challenging. Therefore, in this work, a core-shell magnetic graphitic nanocapsule (MGN) material is synthesized and its capabilities for the detection of biomolecules are investigated. MGN combines the unique properties of graphene and magnetic particles into one simple and sensitive biosensing platform, which quenches around 98% of the dye fluorescence within minutes. Based on a programmed multipurpose DNA capturing and releasing strategy, the MGN sensing platform demonstrates an outstanding capacity to fish, enrich, and detect DNA. Target DNA molecules as low as 50 pM could be detected, which is 3-fold lower than the limit of detection commonly achieved by carbon nanotube and graphene-based fluorescent biosensors. Moreover, the MGN platform exhibits good sensing specificity against DNA mismatch tests. Overall, therefore, these magnetic graphitic nanocapsules demonstrate a promising tool for molecular disease diagnosis and biomedicine. This simple fishing and enrichment strategy may also be extended to other biological and environmental applications and systems.
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Affiliation(s)
- Zhi-Ling Song
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, PR China
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Dong J, Ding J, Weng J, Dai L. Graphene Enhances the Shape Memory of Poly (acrylamide-co
-acrylic acid) Grafted on Graphene. Macromol Rapid Commun 2013; 34:659-64. [DOI: 10.1002/marc.201200814] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 01/22/2013] [Indexed: 11/09/2022]
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