1
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Pu C, Liao X, Shi X, Cui Y, Bai Y, Chen L. An efficient extraction method for short single-stranded DNA from agarose gels in aptamer screening. Int J Biol Macromol 2023; 252:126500. [PMID: 37633543 DOI: 10.1016/j.ijbiomac.2023.126500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 08/28/2023]
Abstract
With the rapid advancements in aptamer screening, the efficient extraction of short single-stranded DNA (ssDNA) from agarose gel has become a new requirement. However, the currently available products are primarily designed for double-stranded DNA (dsDNA) and exhibit limited efficacy when applied to the extraction of short ssDNA. In this study, we successfully developed a novel method based on amino-modified silica-coated magnetic particles (ASMPs) for the extraction of short ssDNA from agarose gel. The gel slices containing short ssDNA were subjected to centrifugation in a spin column/centrifugation tube assembly with silica wool, followed by the adsorption using ASMPs. Subsequently, reagents containing phosphate groups were employed to desorb ssDNA from the surface of ASMPs. Through optimization of each step, we realized remarkable efficiency in the extraction of short ssDNA. To assess the efficacy of our method, we utilized it in aptamer screening. The results demonstrated that our method outperformed three commercially available DNA gel extraction products (Q-kit, S-kit, and V-kit). The relative recovery rates of all methods were as follows: M-dNTP (100.00 %) > M-BB (63.38 %) > Q-kit (46.64 %) > S-kit (15.98 %) > V-kit (0.38 %). The results strongly suggest that the developed method holds promise for short ssDNA extraction from agarose gel.
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Affiliation(s)
- Chunmin Pu
- Department of Public Health Laboratory Sciences, College of Public Health, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China; Institute for Agri-food Standards and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Xiaoyan Liao
- Department of Public Health Laboratory Sciences, College of Public Health, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China; Institute for Agri-food Standards and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Xianming Shi
- State Key Lab of Microbial Metabolism, MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Cui
- State Key Lab of Microbial Metabolism, MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yalong Bai
- Institute for Agri-food Standards and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
| | - LiLi Chen
- Department of Public Health Laboratory Sciences, College of Public Health, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
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2
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Sułowicz S, Borymski S, Dulski M, Nowak A, Bondarczuk K, Markowicz A. Nanopesticide risk assessment based on microbiome profiling - Community structure and functional potential as biomarkers in captan@ZnO 35-45 nm and captan@SiO 220-30 nm treated orchard soil. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131948. [PMID: 37392645 DOI: 10.1016/j.jhazmat.2023.131948] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/23/2023] [Accepted: 06/25/2023] [Indexed: 07/03/2023]
Abstract
Nanoformulation should minimise the usage of pesticides and limit their environmental footprint. The risk assessment of two nanopesticides with fungicide captan as an active organic substance and ZnO35-45 nm or SiO220-30 nm as nanocarriers was evaluated using the non-target soil microorganisms as biomarkers. The first time for that kind of nanopesticides next-generation sequencing (NGS) of bacterial 16 S rRNA and fungal ITS region and metagenomics functional predictions (PICRUST2) was made to study structural and functional biodiversity. During a 100-day microcosm study in soil with pesticide application history, the effect of nanopesticides was compared to pure captan and both nanocarriers. Nanoagrochemicals affected microbial composition, especially Acidobacteria-6 class, and alpha diversity, but the observed effect was generally more substantial for pure captan. As for beta diversity, the negative impact was detected only in response to captan and still observed on day 100. Fungal community in the orchard soil showed only a decrease in phylogenetic diversity in captan set-up since day 30. PICRUST2 analysis confirmed several times lower impact of nanopesticides considering the abundance of functional pathways and genes encoding enzymes. Furthermore, the overall data indicated that using SiO220-30 nm as a nanocarrier speeds up a recovery process compared to ZnO35-45 nm.
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Affiliation(s)
- Sławomir Sułowicz
- University of Silesia, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, Jagiellonska 28, 40-032 Katowice, Poland.
| | - Sławomir Borymski
- University of Silesia, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, Jagiellonska 28, 40-032 Katowice, Poland
| | - Mateusz Dulski
- University of Silesia, Institute of Materials Engineering, Silesian Center for Education and Interdisciplinary Research, 75 Pulku Piechoty 1A, 41-500 Chorzow, Poland
| | - Anna Nowak
- University of Silesia, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, Jagiellonska 28, 40-032 Katowice, Poland
| | - Kinga Bondarczuk
- Centre for Bioinformatics and Data Analysis, Medical University of Białystok, Jerzego Waszyngtona 13A, 15-269 Białystok, Poland
| | - Anna Markowicz
- University of Silesia, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, Jagiellonska 28, 40-032 Katowice, Poland
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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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Kim BK, Lee SA, Park M, Jeon EJ, Kim MJ, Kim JM, Kim H, Jung S, Kim SK. Ultrafast Real-Time PCR in Photothermal Microparticles. ACS NANO 2022; 16:20533-20544. [PMID: 36475304 PMCID: PMC9799066 DOI: 10.1021/acsnano.2c07017] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 11/07/2022] [Indexed: 05/20/2023]
Abstract
As the turnaround time of diagnosis becomes important, there is an increasing demand for rapid, point-of-care testing (POCT) based on polymerase chain reaction (PCR), the most reliable diagnostic tool. Although optical components in real-time PCR (qPCR) have quickly become compact and economical, conventional PCR instruments still require bulky thermal systems, making it difficult to meet emerging needs. Photonic PCR, which utilizes photothermal nanomaterials as heating elements, is a promising platform for POCT as it reduces power consumption and process time. Here, we develop a photonic qPCR platform using hydrogel microparticles. Microparticles consisting of hydrogel matrixes containing photothermal nanomaterials and primers are dubbed photothermal primer-immobilized networks (pPINs). Reduced graphene oxide is selected as the most suitable photothermal nanomaterial to generate heat in pPIN due to its superior light-to-heat conversion efficiency. The photothermal reaction volume of 100 nL (predefined by the pPIN dimensions) provides fast heating and cooling rates of 22.0 ± 3.0 and 23.5 ± 2.6 °C s-1, respectively, enabling ultrafast qPCR within 5 min only with optical components. The microparticle-based photonic qPCR facilitates multiplex assays by loading multiple encoded pPIN microparticles in a single reaction. As a proof of concept, four-plex pPIN qPCR for bacterial discrimination are successfully demonstrated.
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Affiliation(s)
- Bong Kyun Kim
- Division
of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology (UST), Daejeon 34113, Korea
- BioActs
Co., Ltd., Incheon 21666, Korea
- Center
for Augmented Safety Systems with Intelligence, Sensing and Tracking
(ASSIST), KIST, Seoul 02792, Korea
| | - Sang-A Lee
- Center
for Augmented Safety Systems with Intelligence, Sensing and Tracking
(ASSIST), KIST, Seoul 02792, Korea
| | - Minju Park
- Soft
Hybrid Materials Research Center, KIST, Seoul 02792, Korea
| | - Eui Ju Jeon
- Center
for Augmented Safety Systems with Intelligence, Sensing and Tracking
(ASSIST), KIST, Seoul 02792, Korea
| | - Mi Jung Kim
- Center
for Augmented Safety Systems with Intelligence, Sensing and Tracking
(ASSIST), KIST, Seoul 02792, Korea
| | - Jung Min Kim
- Center
for Augmented Safety Systems with Intelligence, Sensing and Tracking
(ASSIST), KIST, Seoul 02792, Korea
| | - Heesuk Kim
- Soft
Hybrid Materials Research Center, KIST, Seoul 02792, Korea
- Division
of Energy and Environmental Technology, KIST School, UST, Daejeon 34113, Korea
| | - Seungwon Jung
- Center
for Advanced Biomolecular Recognition, KIST, Seoul 02792, Korea
- Department
of HY-KIST Bio-convergence, Hanyang University, Seoul 04763, Korea
- Center
for Augmented Safety Systems with Intelligence, Sensing and Tracking
(ASSIST), KIST, Seoul 02792, Korea
| | - Sang Kyung Kim
- Center
for Advanced Biomolecular Recognition, KIST, Seoul 02792, Korea
- KHU-KIST
Department of Converging Science and Technology, Kyung Hee University, Seoul 02447, Korea
- Center
for Augmented Safety Systems with Intelligence, Sensing and Tracking
(ASSIST), KIST, Seoul 02792, Korea
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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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Solvent-sensitive nanoparticle-enhanced PCR assay for the detection of enterotoxigenic Escherichia coli. Sci Rep 2022; 12:20677. [PMID: 36450862 PMCID: PMC9712428 DOI: 10.1038/s41598-022-25088-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/24/2022] [Indexed: 12/05/2022] Open
Abstract
Stimulus-responsive nanoparticles are among the most utilized nanoscale materials in biomedical applications. As these nanoparticles exhibit a manipulable response to a particular stimulus, such as pH, heat, and organic solvent, they are potential signalling units in diagnostic assays. This study aims to enhance the limit of detection and reduce the turnaround time of magnetic nanoparticle polymerase chain reaction (PCR) enzyme-linked gene assay (MELGA), an advanced PCR-based technique termed the solvent-sensitive nanoparticle (SSNP)-enhanced PCR assay. This technique was proposed to detect pathogenic enterotoxigenic Escherichia coli (ETEC) through applying stimulus-responsive nanoparticles. The SSNPs were elaborated with three main components, including mesoporous silica nanoparticles as a structural unit, organic dye (Nile red) as a payload, and the corresponding organic solvent-sensitive polymer shell as "gatekeeper" (poly(maleic anhydride-alt-methyl vinyl ether, PMAMVE). A suitable organic solvent capable of inducing polymer swelling and dye dissolution was investigated by considering a solubility parameter. Using ethanol, the encapsulated Nile red can diffuse out of the SSNPs faster than other solvents and reach a constant concentration within 15 min. For the PCR inhibition study, various SSNPs concentrations (10-30 μg/reaction) were mixed with the ETEC gene and PCR reagent. The results showed that the particles in this concentration range did not inhibit PCR. By comparing the efficacy of conventional PCR, MELGA, and SSNP-enhanced PCR assay, the proposed technique showed a better detection limit than that of PCR, whereas that of MELGA was the lowest. Moreover, compared to MELGA or conventional PCR, this technique provided remarkably faster results in the postamplification process.
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7
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Zhang X, Zhu Z, Liu W, Gao F, Guo J, Song B, Lee LP, Zhang F. The Selective Function of Quantum Biological Electron Transfer between DNA Bases and Metal Ions in DNA Replication. J Phys Chem Lett 2022; 13:7779-7787. [PMID: 35969805 DOI: 10.1021/acs.jpclett.2c01877] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Metal ions play vital roles in the electron transfer between biological molecules in humans, animals, and plants. However, the electron transfer between metal ions and nucleic acids and its impact on DNA-ion binding during DNA replication has been ignored. Here, we present a long-range quantum biological electron transfer (QBET) between DNA bases and metal ions and its selective function of DNA-ion binding in DNA replication. We discover biophysical DNA-ion binding and create biological filters that allow selective DNA replication by dual modulators of the valence and concentration of metal ions. QBET-based DNA replication filters provide powerful tools for ultrasensitive polymerase chain reaction (PCR) to selectively amplify target sequences with a discrete concentration window of metal ions; for example, Au3+ exhibits a concentration window that is approximately 3 orders of magnitude lower than that of Na+. DNA-ion filters provide new perspectives into metal ion-mediated QBET in DNA replication and hold great potential in life sciences and medical 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
| | - Zhi Zhu
- 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
| | - Wenpeng Liu
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Feng Gao
- 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
| | - Luke P Lee
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Bioengineering, Department of Electrical Engineering and Computer Science, University of California, Berkeley, California 94720, United States
- Institute of Quantum Biophysics, Department of Biophysics, Sungkyunkwan University, Suwon 16419, Korea
| | - 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
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, China
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Oral Disease, Stomatology Hospital, School of Biomedical Engineering, Guangzhou Medical University, Guangzhou 511436, China
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8
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Khnouf R, Al Shami F, Albiss BA, Salem N, Ababneh H, Mahasneh A. Enhancement of Salmonella Enteritidis Detection Using Nanoparticle-Assisted Real-Time Polymerase Chain Reaction. J Biomed Nanotechnol 2022. [DOI: 10.1166/jbn.2022.3401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Improved; fast; and specific detection of pathogens has always been of great importance; more so with the increase of human population and human interaction. In this work we investigate the application of metal oxide nanoparticles (ZnO; Fe2O3; and TiO2)
in the detection of the pathogen Salmonella enteritidis using real-time quantitative PCR (qPCR). The nanoparticles were synthesized and characterized; and then they were added at different concentrations to qPCR for Salmonella enteritidis detection. qPCR provides numerical data such
as threshold cycle (Ct); efficiency; and DNA yield which make comparing the different tested conditions easier and more accurate. It has been observed that adding all three types of NPs at an optimum concentration 4×10−11 M for ZnO NPs, and 4×10−9
for Fe2O3 and TiO2 nanoparticles has led to increasing the efficiency of the reaction to 100% and to lowering the threshold cycle value by up to 6.6 for ZnO nanoparticles; hence increasing the DNA yield of the reaction; and lowering the detection time of the
pathogen by up to 50%.
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Affiliation(s)
- Ruba Khnouf
- Department of Biomedical Engineering, Jordan University of Science and Technology, Irbid, 22110, Jordan
| | - Farah Al Shami
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid, 22110, Jordan
| | - Borhan A. Albiss
- Department of Applied Physics, Jordan University of Science and Technology, Irbid, 22110, Jordan
| | - Nida’ Salem
- Department of Plant Protection, The University of Jordan, Amman, 11942, Jordan
| | - Haneen Ababneh
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid, 22110, Jordan
| | - Amjad Mahasneh
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid, 22110, Jordan
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9
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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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10
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Sanabria NM, Gulumian M. The use of HRM shifts in qPCR to investigate a much neglected aspect of interference by intracellular nanoparticles. PLoS One 2021; 16:e0260207. [PMID: 34874941 PMCID: PMC8651142 DOI: 10.1371/journal.pone.0260207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 11/04/2021] [Indexed: 11/19/2022] Open
Abstract
Genetic molecular studies used to understand potential risks of engineered nanomaterials (ENMs) are incomplete. Intracellular residual ENMs present in biological samples may cause assay interference. This report applies the high-resolution melt (HRM) feature of RT-qPCR to detect shifts caused by the presence of gold nanoparticles (AuNPs). A universal RNA standard (untreated control) sample was spiked with known amounts of AuNPs and reverse transcribed, where 10 reference genes were amplified. The amplification plots, dissociation assay (melt) profiles, electrophoretic profiles and HRM difference curves were analysed and detected interference caused by AuNPs, which differed according to the amount of AuNP present (i.e. semi-quantitative). Whether or not the assay interference was specific to the reverse transcription or the PCR amplification step was tested. The study was extended to a target gene-of-interest (GOI), Caspase 7. Also, the effect on in vitro cellular samples was assessed (for reference genes and Caspase 7). This method can screen for the presence of AuNPs in RNA samples, which were isolated from biological material in contact with the nanomaterials, i.e., during exposure and risk assessment studies. This is an important quality control procedure to be implemented when quantifying the expression of a GOI from samples that have been in contact with various ENMs. It is recommended to further examine 18S, PPIA and TBP since these were the most reliable for detecting shifts in the difference curves, irrespective of the source of the RNA, or, the point at which the different AuNPs interacted with the assay.
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Affiliation(s)
- Natasha M. Sanabria
- A Division of National Health Laboratory Services, National Institute for Occupational Health, Johannesburg, South Africa
| | - Mary Gulumian
- A Division of National Health Laboratory Services, National Institute for Occupational Health, Johannesburg, South Africa
- Haematology and Molecular Medicine Department, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- Water Research Group, Unit for Environmental Sciences and Management, North West University, Potchefstroom, South Africa
- * E-mail:
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11
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Lin X, Fang M, Yi C, Jiang Y, Zhang C, Pan X, Luo Z. Functional hydrogel for fast, precise and inhibition-free point-of-care bacteria analysis in crude food samples. Biomaterials 2021; 280:121278. [PMID: 34871876 DOI: 10.1016/j.biomaterials.2021.121278] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 10/30/2021] [Accepted: 11/23/2021] [Indexed: 11/02/2022]
Abstract
In this work, instead of performing nucleic acid amplification in the bulk solution, we report a nanoporous hydrogel with controlled release function for rapid, precise, and inhibition-free nucleic acid analysis in crude food samples. The cross-linked PEG hydrogel with nanoporous structures possesses adsorption, release, separation, restriction and self-cleaning abilities. When digital loop-mediated isothermal amplification (LAMP) was performed inside this hydrogel, the surrounding nanostructure act as a temporary reservoir for reagents storage and release them on demand during or after amplification. Meanwhile, the restricted nanoconfined environment of hydrogel also favor the enzymatic amplification process. Thus, an enhanced signal readout, robust anti-inhibition, faster amplification rate, more products yields and specific amplification without primer-dimers were obtained. Moreover, direct amplification in untreated complex food sample was successfully performed inside hydrogel without any sample pretreatment, while conventional droplets digital LAMP failed for detection. Absolute quantification of Escherichia coli and Salmonella typhi directly in fresh fruit and vegetables was achieved within 20 min, with high precision and sensitivity down to single cell. This novel lab-on-hydrogel concept has an enormous potential for future molecular diagnostic assays, and can be also applied for other point-of-care assays.
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Affiliation(s)
- Xingyu Lin
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Zhejiang University, Hangzhou, 310058, PR China.
| | - Mei Fang
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Zhejiang University, Hangzhou, 310058, PR China; College of Environment, Zhejiang University of Technology, Hangzhou, 310014, PR China
| | - Changyu Yi
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Zhejiang University, Hangzhou, 310058, PR China; College of Environment, Zhejiang University of Technology, Hangzhou, 310014, PR China
| | - Yan Jiang
- Chemistry Instrumentation Center, Department of Chemistry, Zhejiang University, Hangzhou, 310027, China
| | - Chao Zhang
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Zhejiang University, Hangzhou, 310058, PR China
| | - Xiangliang Pan
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, PR China
| | - Zisheng Luo
- College of Biosystems Engineering and Food Science, Fuli Institute of Food Science, Zhejiang University, Hangzhou, 310058, PR China
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12
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Xue Z, You M, Peng P, Tong H, He W, Li A, Mao P, Xu T, Xu F, Yao C. Taqman-MGB nanoPCR for Highly Specific Detection of Single-Base Mutations. Int J Nanomedicine 2021; 16:3695-3705. [PMID: 34113098 PMCID: PMC8185130 DOI: 10.2147/ijn.s310254] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/11/2021] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Detection of single-base mutations is important for real-time monitoring of tumor progression, therapeutic effects, and drug resistance. However, the specific detection of single-base mutations from excessive wild-type background sequences with routine PCR technology remains challenging. Our objective is to develop a simple and highly specific qPCR-based single-base mutation detection method. METHODS Using EGRF T790M as a model, gold nanoparticles at different concentrations were separately added into the Taqman-MGB qPCR system to test specificity improvement, leading to the development of the optimal Taqman-MGB nanoPCR system. Then, these optimal conditions were used to test the range of improvement in the specificity of mutant-type and wild-type templates and the detection limit of mutation abundances in a spiked sample. RESULTS The Taqman-MGB nanoPCR was established based on the traditional qPCR, with significantly suppressed background noise and improved specificity for single-base mutation detection. With EGFR T790M as a template, we demonstrated that our Taqman-MGB nanoPCR system could improve specificity across a wide concentration range from 10-9 μM to 10 μM and detect as low as 0.95% mutation abundance in spiked samples, which is lower than what the traditional Taqman-MGB qPCR and existing PCR methods can detect. Moreover, we also proposed an experimentally validated barrier hypothesis for the mechanism of improved specificity. CONCLUSION The developed Taqman-MGB nanoPCR system could be a powerful tool for clinical single-base mutation detection.
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Affiliation(s)
- Zhenrui Xue
- Department of Transfusion Medicine, Southwest Hospital, Third Military Medical University, Army Medical University, Chongqing, 400038, People’s Republic of China
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, 710049, People’s Republic of China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an, 710049, People’s Republic of China
| | - Minli You
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, 710049, People’s Republic of China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an, 710049, People’s Republic of China
| | - Ping Peng
- Department of Transfusion Medicine, Southwest Hospital, Third Military Medical University, Army Medical University, Chongqing, 400038, People’s Republic of China
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, 710049, People’s Republic of China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an, 710049, People’s Republic of China
| | - Haoyang Tong
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, 710049, People’s Republic of China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an, 710049, People’s Republic of China
| | - Wanghong He
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, 710049, People’s Republic of China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an, 710049, People’s Republic of China
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, 710049, People’s Republic of China
| | - Ang Li
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, 710049, People’s Republic of China
| | - Ping Mao
- Department of Transfusion Medicine, Southwest Hospital, Third Military Medical University, Army Medical University, Chongqing, 400038, People’s Republic of China
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, 710049, People’s Republic of China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an, 710049, People’s Republic of China
| | - Ting Xu
- Department of Transfusion Medicine, Southwest Hospital, Third Military Medical University, Army Medical University, Chongqing, 400038, People’s Republic of China
| | - Feng Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, 710049, People’s Republic of China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an, 710049, People’s Republic of China
| | - Chunyan Yao
- Department of Transfusion Medicine, Southwest Hospital, Third Military Medical University, Army Medical University, Chongqing, 400038, People’s Republic of China
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13
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You M, Jia P, He X, Wang Z, Feng S, Ren Y, Li Z, Cao L, Gao B, Yao C, Singamaneni S, Xu F. Quantifying and Adjusting Plasmon-Driven Nano-Localized Temperature Field around Gold Nanorods for Nucleic Acids Amplification. SMALL METHODS 2021; 5:e2001254. [PMID: 34928096 DOI: 10.1002/smtd.202001254] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/19/2021] [Indexed: 06/14/2023]
Abstract
Fast nucleic acid (NA) amplification has found widespread biomedical applications, where high thermocycling rate is the key. The plasmon-driven nano-localized thermocycling around the gold nanorods (AuNRs) is a promising alternative, as the significantly reduced reaction volume enables a rapid temperature response. However, quantifying and adjusting the nano-localized temperature field remains challenging for now. Herein, a simple method is developed to quantify and adjust the nano-localized temperature field around AuNRs by combining experimental measurement and numerical simulation. An indirect method to measure the surface temperature of AuNRs is first developed by utilizing the temperature-dependent stability of Authiol bond. Meanwhile, the relationship of AuNRs' surface temperature with the AuNRs concentration and laser intensity, is also studied. In combination with thermal diffusion simulation, the nano-localized temperature field under the laser irradiation is obtained. The results show that the restricted reaction volume (≈aL level) enables ultrafast thermocycling rate (>104 °C s-1 ). At last, a duplex-specific nuclease (DSN)-mediated isothermal amplification is successfully demonstrated within the nano-localized temperature field. It is envisioned that the developed method for quantifying and adjusting the nano-localized temperature field around AuNRs is adaptive for various noble metal nanostructures and will facilitate the development of the biochemical reaction in the nano-localized environment.
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Affiliation(s)
- Minli You
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. Louis, St Louis, MO, 63130, USA
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Pengpeng Jia
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Xiaocong He
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Zheyu Wang
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. Louis, St Louis, MO, 63130, USA
| | - Shangsheng Feng
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Yulin Ren
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Zedong Li
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Lei Cao
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Bin Gao
- Department of Endocrinology, Tangdu Hospital, Air Force Military Medical University, Xi'an, Shaanxi, 710038, P. R. China
| | - Chunyan Yao
- Department of Transfusion Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, P.R. China
| | - Srikanth Singamaneni
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. Louis, St Louis, MO, 63130, USA
| | - Feng Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, 710049, P.R. China
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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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15
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Hao X, Han S, Qin D, Zhang Y, Jin P, Du Q. Superior anti-infective potential of eugenol-casein nanoparticles combined with polyethylene glycol against Colletotrichum musae infections. RSC Adv 2021; 11:4646-4653. [PMID: 35424385 PMCID: PMC8694564 DOI: 10.1039/d0ra09283e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 01/11/2021] [Indexed: 01/21/2023] Open
Abstract
The aim of this study was to improve the stability of eugenol-casein nanoparticles (EL-CS-NPs) through polyethylene glycol (PEG) modification. The results show that modifying the EL-CS-NPs with PEG after loading with eugenol (EL) gives PEG-EL-CS-NPs, with increased stability. The NPs modified with higher-molecular-weight PEG showed better stability. A CS/PEG ratio of 200 : 1 (w/w) yielded the NPs with the best stability. A PEG20 K-EL-CS-NP dispersion remained stable in cold storage for over one year, and also exhibited stronger inhibitory effects against Colletotrichum musae inoculated on bananas than an EL-CS-NP dispersion, since it showed more prolonged sustained release of EL than the EL-CS-NP dispersion. Lyophilized PEG20 K-EL-CS-NP powder showed better effectiveness against mold on bread than lyophilized EL-CS-NPs powder. Using PEG to modify CS-NPs shows potential for improving the stability of CS-NPs loaded with hydrophobic substances for delivery in the fields of food and agriculture.
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Affiliation(s)
- Xueyan Hao
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, The College of Agricultural and Food Sciences, Zhejiang A & F University Linan 311300 China
| | - Shuya Han
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, The College of Agricultural and Food Sciences, Zhejiang A & F University Linan 311300 China
| | - Dingkui Qin
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, The College of Agricultural and Food Sciences, Zhejiang A & F University Linan 311300 China
| | - Yahui Zhang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, The College of Agricultural and Food Sciences, Zhejiang A & F University Linan 311300 China
| | - Peng Jin
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, The College of Agricultural and Food Sciences, Zhejiang A & F University Linan 311300 China
| | - Qizhen Du
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, The College of Agricultural and Food Sciences, Zhejiang A & F University Linan 311300 China
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16
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Farouk F, El Shimy R, Abdel-Motaleb A, Essam S, Azzazy HM. Detection of Acinetobacter baumannii in fresh produce using modified magnetic nanoparticles and PCR. Anal Biochem 2020; 609:113890. [DOI: 10.1016/j.ab.2020.113890] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 07/10/2020] [Accepted: 07/23/2020] [Indexed: 12/19/2022]
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17
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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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18
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Yamkamon V, Htoo KPP, Yainoy S, Suksrichavalit T, Tangchaikeeree T, Eiamphungporn W. Urinary PCA3 detection in prostate cancer by magnetic nanoparticles coupled with colorimetric enzyme-linked oligonucleotide assay. EXCLI JOURNAL 2020; 19:501-513. [PMID: 32398974 PMCID: PMC7214775 DOI: 10.17179/excli2020-1036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 04/06/2020] [Indexed: 12/19/2022]
Abstract
PCA3 is one of the most prostate cancer-specific genes described to date. Of note, PCA3 expression is detectable at high level in the urine of prostate cancer (PCa) patients. Accordingly, PCA3 is an ideal biomarker for PCa diagnosis. Several techniques for the measurement of this biomarker in urine have been developed but there are still some drawbacks. In this study, magnetic nanoparticle-based PCR coupled with streptavidin-horseradish peroxidase and a substrate for colorimetric detection was established as a potential assay for urinary PCA3 detection. The method provided a high specificity for PCA3 gene in LNCaP prostate cancer cell line. Additionally, this technique could detect PCA3 at femtogram level which was approximately 1,000-fold more sensitive than the conventional RT-PCR followed by agarose gel electrophoresis. The effectiveness of the method was assessed by PCA3 detection in clinical specimens. The relative PCA3 expression of PCa patients determined by this assay was significantly greater than that of benign prostatic hyperplasia (BPH) patients and healthy controls. The results of our test were comparable with the results of qRT-PCR. The proposed method is promising to distinguish between cancerous and non-cancerous groups. Altogether, this simple assay is practicable and useful for prostate cancer diagnosis.
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Affiliation(s)
- Vichanan Yamkamon
- Department of Clinical Microscopy, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Khin Phyu Pyar Htoo
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand.,Department of Medical Laboratory Technology, University of Medical Technology, Mandalay, Myanmar
| | - Sakda Yainoy
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Thummaruk Suksrichavalit
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Tienrat Tangchaikeeree
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Warawan Eiamphungporn
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
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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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A method based on amino-modified magnetic nanoparticles to extract DNA for PCR-based analysis. Colloids Surf B Biointerfaces 2019; 179:87-93. [DOI: 10.1016/j.colsurfb.2019.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 02/15/2019] [Accepted: 03/03/2019] [Indexed: 01/10/2023]
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21
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Bai Y, Cui Y, Suo Y, Shi C, Wang D, Shi X. A Rapid Method for Detection of Salmonella in Milk Based on Extraction of mRNA Using Magnetic Capture Probes and RT-qPCR. Front Microbiol 2019; 10:770. [PMID: 31024515 PMCID: PMC6459957 DOI: 10.3389/fmicb.2019.00770] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 03/26/2019] [Indexed: 11/17/2022] Open
Abstract
Magnetic separation is an efficient method for target enrichment and elimination of inhibitors in the molecular detection systems for foodborne pathogens. In this study, we prepared magnetic capture probes by modifying oligonucleotides complementary to target sequences on the surface of amino-modified silica-coated magnetic nanoparticles and optimized the conditions and parameters of probe synthesis and hybridization. We innovatively put the complexes of magnetic capture probes and target sequences into qPCR without any need for denaturation and purification steps. This strategy can reduce manual steps and save time. We used the magnetic capture probes to separate invA mRNA from Salmonella in artificially contaminated milk samples. The detection sensitivity was 104 CFU/ml, which could be increased to 10 CFU/ml after a 12 h enrichment step. The developed method is robust enough to detect live bacteria in a complex environmental matrix.
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Affiliation(s)
- Yalong Bai
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China.,Institute for Agri-food Standards and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yan Cui
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Yujuan Suo
- Institute for Agri-food Standards and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Chunlei Shi
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Dapeng Wang
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Xianming Shi
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
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22
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Jin P, Yao R, Qin D, Chen Q, Du Q. Enhancement in Antibacterial Activities of Eugenol-Entrapped Ethosome Nanoparticles via Strengthening Its Permeability and Sustained Release. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:1371-1380. [PMID: 30624923 DOI: 10.1021/acs.jafc.8b06278] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The antibacterial efficiency and synergistic mechanisms of novel formulated eugenol entrapped ethosome nanoparticles (ELG-NPs) against fruit anthracnose were investigated. The results showed that concentrations of eugenol and ethanol significantly influenced the particle size and entrapment efficiency of nanoethosome, and the particle size significantly influenced the antibacterial effect. Superior ELG-NPs with optimized process (0.5% eugenol, 2% lecithin, and 30% ethanol) were obtained with a size of 44.21 nm and entrapment efficiency of 82%. ELG-NPs exhibited an antibacterial activity (>93%) against fruit pathogens that was greater than that of free eugenol and showed 100% inhibition of the anthracnose incidence in postharvest loquat after 6 d. The permeability study, first visualized in banana cortex with fluorescent indicators, demonstrated that eugenol delivered to the interior with ELG-NPs was 6-fold higher than that of free eugenol. ELG-NPs showed a satisfactory slow-release and prolonged antibacterial action. This work provides a promising strategy for disease controls in agricultural, food, cosmetic, and medical areas.
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Affiliation(s)
- Peng Jin
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, The College of Agricultural and Food Sciences , Zhejiang A & F University , Linan 311300 , China
| | - Rui Yao
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, The College of Agricultural and Food Sciences , Zhejiang A & F University , Linan 311300 , China
| | - Dingkui Qin
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, The College of Agricultural and Food Sciences , Zhejiang A & F University , Linan 311300 , China
| | - Qing Chen
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, The College of Agricultural and Food Sciences , Zhejiang A & F University , Linan 311300 , China
| | - Qizhen Du
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, The College of Agricultural and Food Sciences , Zhejiang A & F University , Linan 311300 , China
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23
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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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24
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Enhancement of PCR Sensitivity and Yield Using Thiol-modified Primers. Sci Rep 2018; 8:14858. [PMID: 30291287 PMCID: PMC6173752 DOI: 10.1038/s41598-018-33223-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 09/25/2018] [Indexed: 02/02/2023] Open
Abstract
Various additives can enhance the quality of PCR amplification, but these generally require considerable optimization to achieve peak performance. Here, we demonstrate that the use of thiol-modified primers can enhance both PCR sensitivity and yield. In experiments with V. parahaemolyticus genomic DNA, this primer modification enhances PCR sensitivity by more than 100-fold, with accompanying improvements in amplicon yield. Then, an artificial plasmid with the same primer binding regions and different internal amplification sequence was designed. The result showed that the amplification also be improved by using the same thiol-modified primers. It indicated the enhancement was not caused by the effect of the thiol-modified primers on the second structure of amplification sequence. Subsequent experiments demonstrate that the effects of this modification are potentially due to altered interaction between the primers and proteins in the reaction mixture. Amplification with thiol-modified primers was strongly inhibited by the presence of extraneous proteins relative to standard DNA primers, which indicates that thiol-modified primers may be inhibited due to interaction with these proteins. In contaminant-free reactions, however, the thiol-modified primers might interact more strongly with DNA polymerase, which could in turn improve PCR amplification.
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25
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Sailapu S, Dutta D, Sahoo AK, Ghosh SS, Chattopadhyay A. Single Platform for Gene and Protein Expression Analyses Using Luminescent Gold Nanoclusters. ACS OMEGA 2018; 3:2119-2129. [PMID: 30023824 PMCID: PMC6045389 DOI: 10.1021/acsomega.7b01739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 02/07/2018] [Indexed: 05/05/2023]
Abstract
A single platform for gene and protein expression studies is proposed to pursue rapid diagnostics. A common method to synthesize gold (Au) nanoclusters on both DNA and protein template was developed using a benchtop device. The method of synthesis is rapid and versatile and can be applied to different classes of DNA/protein. Employing luminescent Au nanoclusters as the signal-generating agents, the device enables carrying out reverse transcriptase polymerase chain reaction and array-based analyses of multiple genes/proteins simultaneously using switchable holders and custom-designed software. The device and methods were applied to evaluate gene profiling related to apoptosis in HeLa cancer cells and further to analyze the protein expressions of glutathione-S-transferase (GST) and GST-tagged human granulocyte macrophage colony-stimulating factor (GST-hGMCSF) recombinant proteins purified from bacterial strains of BL21(DE3) Escherichia coli (E. coli). The device with user-friendly methods for diagnosis using the luminescence of Au nanoclusters offers potential use in disease diagnostics with a vision to extend health care facilities especially to remote geographical locations.
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Affiliation(s)
- Sunil
Kumar Sailapu
- Centre
for Nanotechnology, Department of Biosciences and Bioengineering, and Department of
Chemistry, Indian Institute of Technology
Guwahati, Guwahati 781 039, Assam, India
| | - Deepanjalee Dutta
- Centre
for Nanotechnology, Department of Biosciences and Bioengineering, and Department of
Chemistry, Indian Institute of Technology
Guwahati, Guwahati 781 039, Assam, India
| | - Amaresh Kumar Sahoo
- Centre
for Nanotechnology, Department of Biosciences and Bioengineering, and Department of
Chemistry, Indian Institute of Technology
Guwahati, Guwahati 781 039, Assam, India
| | - Siddhartha Sankar Ghosh
- Centre
for Nanotechnology, Department of Biosciences and Bioengineering, and Department of
Chemistry, Indian Institute of Technology
Guwahati, Guwahati 781 039, Assam, India
| | - Arun Chattopadhyay
- Centre
for Nanotechnology, Department of Biosciences and Bioengineering, and Department of
Chemistry, Indian Institute of Technology
Guwahati, Guwahati 781 039, Assam, India
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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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Zhao J, Gao J, Zheng T, Yang Z, Chai Y, Chen S, Yuan R, Xu W. Highly sensitive electrochemical assay for Nosema bombycis gene DNA PTP1 via conformational switch of DNA nanostructures regulated by H + from LAMP. Biosens Bioelectron 2018; 106:186-192. [PMID: 29427924 DOI: 10.1016/j.bios.2018.02.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 01/16/2018] [Accepted: 02/01/2018] [Indexed: 10/18/2022]
Abstract
The portable and rapid detection of biomolecules via pH meters to monitor the concentration of hydrogen ions (H+) from biological reactions (e.g. loop-mediated isothermal amplification, LAMP) has attracted research interest. However, this assay strategy suffered from inherent drawback of low sensitivity, resulting in great limitations in practical applications. Herein, a novel electrochemical biosensor was constructed for highly sensitive detection of Nosema bombycis gene DNA (PTP1) through transducing chemical stimuli H+ from PTP1-based LAMP into electrochemical output signal of electroactive ferrocene (Fc). With use of target PTP1 as the template, the H+ from LAMP induced the conformational switch of pH-responsive DNA nanostructures (DNA NSs, Fc-Sp@Ts) that was assembled by the hybridization of Fc-labeled signal probe (Fc-Sp) with DNA-based receptor (Ts). Due to the folding of Ts into stable triplex structure at decreased pH, the configuration change of Fc-Sp@Ts led to the releasing of Fc-Sp, which was subsequently immobilized in the electrode interface through the hybridization with the capture probe modified with -SH (SH-Cp), generating amplified electrochemical signal from Fc. The developed biosensor for PTP1 exhibited a reliable linear range of 1 fg µL-1 to 50 ng µL-1 with the limit of detection of 0.31 fg µL-1. Thus, by the regulation of H+ from LAMP reaction on DNA NSs allostery, this novel and simple transduction scheme would be interesting and promising to open up a novel analytical route for sensitive monitoring of different target DNAs in related disease diagnosis.
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Affiliation(s)
- Jianmin Zhao
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Jiaxi Gao
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ting Zheng
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Zhehan Yang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yaqin Chai
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Shihong Chen
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
| | - Wenju Xu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
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28
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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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29
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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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30
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Tangchaikeeree T, Polpanich D, Bentaher A, Baraket A, Errachid A, Agusti G, Elaissari A, Jangpatarapongsa K. Combination of PCR and dual nanoparticles for detection of Plasmodium falciparum. Colloids Surf B Biointerfaces 2017; 159:888-897. [DOI: 10.1016/j.colsurfb.2017.08.063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 08/17/2017] [Accepted: 08/31/2017] [Indexed: 01/10/2023]
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31
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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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32
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Sanabria NM, Gulumian M. The presence of residual gold nanoparticles in samples interferes with the RT-qPCR assay used for gene expression profiling. J Nanobiotechnology 2017. [PMID: 29017502 DOI: 10.1186/s12951-017-0299-9.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND RT-qPCR is routinely used in expression profiling of toxicity pathway genes. However, genetic and molecular level studies used to determine, understand and clarify potential risks of engineered nanomaterials (ENMs) are still incomplete. Concerns regarding possible interference caused by intracellular ENMs during analyses have been raised. The aim of this study was to verify a qPCR procedure for gene expression assays, which can be used in toxicity and exposure assessments. RESULTS Amplification of ten reference genes was performed to test the expression stability. A preliminary study was performed on RNA from BEAS-2B cells that had been treated with AuNPs. Also, a reference total RNA standard from ten cell lines was spiked with various amounts of the same AuNP. This treatment mimics exposure assessment studies, where assay-interference may be caused by intracellular residual ENMs still being present in the biological samples (during and after isolation/purification procedures). Both types of RNA samples were reverse transcribed and then amplified by qPCR. The qPCR-related software and statistical programs used included BestKeeper, NormFinder, REST and qBase+. These results proved that using standard qPCR analysis and statistical programs should not be the only procedure applied to verify the assay for gene expression assessment related to ENMs. A comparison of SYBR Green to EVA Green was discussed, in addition to a comparison to the latest reports regarding the influence of ENM thermal conductivity, surface interactions with ENMs, effects of ENM size and charge, as well as, the limit of detection in a qPCR assay. CONCLUSIONS AuNPs have the potential to interfere with the assay mechanism of RT-qPCR, thus, assay verification is required for AuNP-related gene expression studies used to evaluate toxicity. It is recommended to use HSP90 and YWHAZ as reference genes, i.e. these were the most stable in our study, irrespective of the source of the RNA, or, the point at which the AuNPs interacted with the assay. This report describes steps that can be utilised to generate a suitable method for gene expression studies associated with toxicity testing of various ENMs. For example, RNA standards that have been spiked with known amounts of ENMs should be run in conjunction with the unknown samples, in order to verify any RT-qPCR assay and determine the degree of error.
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Affiliation(s)
| | - Mary Gulumian
- National Institute for Occupational Health, Johannesburg, South Africa. .,Haematology and Molecular Medicine Department, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa.
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33
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Sanabria NM, Gulumian M. The presence of residual gold nanoparticles in samples interferes with the RT-qPCR assay used for gene expression profiling. J Nanobiotechnology 2017; 15:72. [PMID: 29017502 PMCID: PMC5633869 DOI: 10.1186/s12951-017-0299-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 09/23/2017] [Indexed: 12/29/2022] Open
Abstract
Background RT-qPCR is routinely used in expression profiling of toxicity pathway genes. However, genetic and molecular level studies used to determine, understand and clarify potential risks of engineered nanomaterials (ENMs) are still incomplete. Concerns regarding possible interference caused by intracellular ENMs during analyses have been raised. The aim of this study was to verify a qPCR procedure for gene expression assays, which can be used in toxicity and exposure assessments. Results Amplification of ten reference genes was performed to test the expression stability. A preliminary study was performed on RNA from BEAS-2B cells that had been treated with AuNPs. Also, a reference total RNA standard from ten cell lines was spiked with various amounts of the same AuNP. This treatment mimics exposure assessment studies, where assay-interference may be caused by intracellular residual ENMs still being present in the biological samples (during and after isolation/purification procedures). Both types of RNA samples were reverse transcribed and then amplified by qPCR. The qPCR-related software and statistical programs used included BestKeeper, NormFinder, REST and qBase+. These results proved that using standard qPCR analysis and statistical programs should not be the only procedure applied to verify the assay for gene expression assessment related to ENMs. A comparison of SYBR Green to EVA Green was discussed, in addition to a comparison to the latest reports regarding the influence of ENM thermal conductivity, surface interactions with ENMs, effects of ENM size and charge, as well as, the limit of detection in a qPCR assay. Conclusions AuNPs have the potential to interfere with the assay mechanism of RT-qPCR, thus, assay verification is required for AuNP-related gene expression studies used to evaluate toxicity. It is recommended to use HSP90 and YWHAZ as reference genes, i.e. these were the most stable in our study, irrespective of the source of the RNA, or, the point at which the AuNPs interacted with the assay. This report describes steps that can be utilised to generate a suitable method for gene expression studies associated with toxicity testing of various ENMs. For example, RNA standards that have been spiked with known amounts of ENMs should be run in conjunction with the unknown samples, in order to verify any RT-qPCR assay and determine the degree of error. Electronic supplementary material The online version of this article (doi:10.1186/s12951-017-0299-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Mary Gulumian
- National Institute for Occupational Health, Johannesburg, South Africa. .,Haematology and Molecular Medicine Department, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa.
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Yang W, Cao X, Li X. Enhanced simultaneous overlap extension-PCR by gold nanoparticles. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2017; 13:2263-2266. [DOI: 10.1016/j.nano.2017.06.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 06/10/2017] [Accepted: 06/19/2017] [Indexed: 12/27/2022]
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35
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Overcoming qRT-PCR interference by select carbon nanotubes in assessments of gene expression. Biotechniques 2017; 63:81-84. [PMID: 28803544 DOI: 10.2144/000114578] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 06/30/2017] [Indexed: 11/23/2022] Open
Abstract
Nanomaterials (NMs) of various types, including carbon nanotubes (CNTs), can interfere with standard quantitative real-time PCR (qRT-PCR) assays, resulting in inaccurate gene expression measurements; however, the precise step in the qRT-PCR pipeline where this interference occurs has not been well described. Here, we investigated where in the process surface-oxidized multi-walled CNTs (oxMWNTs) inhibited qRT-PCR measurement of the expression of the housekeeping gene GAPDH and explored several strategies to minimize such inhibition. We determined that the interference occurred during the reverse transcription (RT) step and found that doubling reaction reagents or adding BSA successfully mitigated the inhibition. We observed assay interference in the presence of CNTs that were surface-oxidized, but pristine CNTs did not cause the same level of interference. These results highlight the importance of monitoring qRT-PCR assays for interference by CNTs that differ by surface chemistry, as these NMs are commonly used in gene expression assays at concentrations that we have shown to be inhibitory.
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Moore LR, Williams PS, Chalmers JJ, Zborowski M. Tessellated permanent magnet circuits for flow-through, open gradient separations of weakly magnetic materials. JOURNAL OF MAGNETISM AND MAGNETIC MATERIALS 2017; 427:325-330. [PMID: 29104346 PMCID: PMC5667671 DOI: 10.1016/j.jmmm.2016.11.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Emerging microfluidic-based cell assays favor label-free red blood cell (RBC) depletion. Magnetic separation of RBC is possible because of the paramagnetism of deoxygenated hemoglobin but the process is slow for open-gradient field configurations. In order to increase the throughput, periodic arrangements of the unit magnets were considered, consisting of commercially available Nd-Fe-B permanent magnets and soft steel flux return pieces. The magnet design is uniquely suitable for multiplexing by magnet tessellation, here meaning the tiling of the magnet assembly cross-sectional plane by periodic repetition of the magnet and the flow channel shapes. The periodic pattern of magnet magnetizations allows a reduction of the magnetic material per channel with minimal distortion of the field cylindrical symmetry inside the magnet apertures. A number of such magnet patterns are investigated for separator performance, size and economy with the goal of designing an open-gradient magnetic separator capable of reducing the RBC number concentration a hundred-fold in 1 mL whole blood per hour.
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Affiliation(s)
- Lee R. Moore
- Department of Biomedical Engineering, Cleveland Clinic, 9500 Euclid Ave., Cleveland, OH 44195
| | | | - Jeffrey J. Chalmers
- William G. Lowrie Department of Chemical and Biomedical Engineering, 151 W. Woodruff Avenue, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Maciej Zborowski
- Department of Biomedical Engineering, Cleveland Clinic, 9500 Euclid Ave., Cleveland, OH 44195
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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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Tangchaikeeree T, Sawaisorn P, Somsri S, Polpanich D, Putaporntip C, Tangboriboonrat P, Udomsangpetch R, Jangpatarapongsa K. Enhanced Sensitivity for Detection of Plasmodium falciparum gametocytes by magnetic nanoparticles combined with enzyme substrate system. Talanta 2016; 164:645-650. [PMID: 28107985 DOI: 10.1016/j.talanta.2016.10.106] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 10/15/2016] [Accepted: 10/15/2016] [Indexed: 10/20/2022]
Abstract
The highly sensitive and specific detection of Pfg377 gene of Plasmodium falciparum gametocyte using Magnetic Nanoparticles PCR Enzyme-Linked Gene Assay (MELGA) was successfully developed. The MELGA included amplification of the Pfg377 gene by polymerase chain reaction (PCR) using magnetic nanoparticles (MNPs)-conjugated forward primer and biotinylated reverse primer, followed by post-analytical process using horseradish peroxidase (HRP)-conjugated streptavidin (SA). The complexes of MELGA product were incubated with the peroxidase substrate and hydrogen peroxide to produce the signal for colorimetric measurement. Altogether, the MELGA technique provided a highly sensitive and specific detection at 1 P. falciparum gametocyte/µL, which was more efficient than that of microscopic examination and rapid diagnostic tests (RDTs). Additionally, the MELGA could detect target gene at femtogram level, which was greater sensitive than the conventional PCR, nested PCR and loop-mediated isothermal amplification (LAMP). The MELGA technique could become a novel and practical method that overcome limitation of traditional gametocyte detection.
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Affiliation(s)
- Tienrat Tangchaikeeree
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Piamsiri Sawaisorn
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Sangdao Somsri
- Graduate Program in Biomedical Sciences, Faculty of Allied Health Sciences, Thammasat University, Pathum Thani 12120, Thailand
| | - Duangporn Polpanich
- National Nanotechnology Center, National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani 12120, Thailand
| | - Chaturong Putaporntip
- Molecular Biology of Malaria and Opportunistic Parasites Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | | | - Rachanee Udomsangpetch
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Kulachart Jangpatarapongsa
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand.
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Bai Y, Cui Y, Paoli GC, Shi C, Wang D, Zhou M, Zhang L, Shi X. Synthesis of amino-rich silica-coated magnetic nanoparticles for the efficient capture of DNA for PCR. Colloids Surf B Biointerfaces 2016; 145:257-266. [PMID: 27187190 DOI: 10.1016/j.colsurfb.2016.05.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 04/23/2016] [Accepted: 05/02/2016] [Indexed: 11/26/2022]
Abstract
Magnetic separation has great advantages over traditional bio-separation methods and has become popular in the development of methods for the detection of bacterial pathogens, viruses, and transgenic crops. Functionalization of magnetic nanoparticles is a key factor for efficient capture of the target analytes. In this paper, we report the synthesis of amino-rich silica-coated magnetic nanoparticles using a one-pot method. This type of magnetic nanoparticle has a rough surface and a higher density of amino groups than the nanoparticles prepared by a post-modification method. Furthermore, the results of hydrochloric acid treatment indicated that the magnetic nanoparticles were stably coated. The developed amino-rich silica-coated magnetic nanoparticles were used to directly adsorb DNA. After magnetic separation and blocking, the magnetic nanoparticles and DNA complexes were used directly for the polymerase chain reaction (PCR), without onerous and time-consuming purification and elution steps. The results of real-time quantitative PCR showed that the nanoparticles with higher amino group density resulted in improved DNA capture efficiency. The results suggest that amino-rich silica-coated magnetic nanoparticles are of great potential for efficient bio-separation of DNA prior to detection by PCR.
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Affiliation(s)
- Yalong Bai
- MOST-USDA Joint Research Center for Food Safety & Bor Luh Food Safety Center, School of Agriculture and Biology & State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Yan Cui
- MOST-USDA Joint Research Center for Food Safety & Bor Luh Food Safety Center, School of Agriculture and Biology & State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - George C Paoli
- USDA-MOST Joint Research Center for Food Safety & Molecular Characterization of Foodborne Pathogens Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, PA 19038, USA
| | - Chunlei Shi
- MOST-USDA Joint Research Center for Food Safety & Bor Luh Food Safety Center, School of Agriculture and Biology & State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Dapeng Wang
- MOST-USDA Joint Research Center for Food Safety & Bor Luh Food Safety Center, School of Agriculture and Biology & State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Min Zhou
- MOST-USDA Joint Research Center for Food Safety & Bor Luh Food Safety Center, School of Agriculture and Biology & State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, PR China; School of Food Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, PR China
| | - Lida Zhang
- MOST-USDA Joint Research Center for Food Safety & Bor Luh Food Safety Center, School of Agriculture and Biology & State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Xianming Shi
- MOST-USDA Joint Research Center for Food Safety & Bor Luh Food Safety Center, School of Agriculture and Biology & State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, PR China.
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