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Kalendar R, Ivanov KI, Samuilova O, Kairov U, Zamyatnin AA. Isolation of High-Molecular-Weight DNA for Long-Read Sequencing Using a High-Salt Gel Electroelution Trap. Anal Chem 2023; 95:17818-17825. [PMID: 37993972 DOI: 10.1021/acs.analchem.3c03894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Long-read sequencing technologies require high-molecular-weight (HMW) DNA of sufficient purity and integrity, which can be difficult to obtain from complex biological samples. We propose a method for purifying HMW DNA that takes advantage of the fact that DNA's electrophoretic mobility decreases in a high-ionic-strength environment. The method begins with the separation of HMW DNA from various impurities by electrophoresis in an agarose gel-filled channel. After sufficient separation, a high-salt gel block is placed ahead of the DNA band of interest, leaving a gap between the separating gel and the high-salt gel that serves as a reservoir for sample collection. The DNA is then electroeluted from the separating gel into the reservoir, where its migration slows due to electrostatic shielding of the DNA's negative charge by excess counterions from the high-salt gel. As a result, the reservoir accumulates HMW DNA of high purity and integrity, which can be easily collected and used for long-read sequencing and other demanding applications without additional desalting. The method is simple and inexpensive, yields sequencing-grade HMW DNA even from difficult plant and soil samples, and has the potential for automation and scalability.
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Affiliation(s)
- Ruslan Kalendar
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki 00014, Finland
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
| | - Konstantin I Ivanov
- Department of Microbiology, University of Helsinki, Helsinki 00014, Finland
- Research Center for Translational Medicine, Sirius University of Science and Technology, Sochi 354340, Russian Federation
| | - Olga Samuilova
- Department of Biological Chemistry, Institute of Biodesign and Modeling of Complex Systems, Sechenov First Moscow State Medical University, Moscow 119991, Russian Federation
- HSE University, Faculty of Biology and Biotechnology, Moscow 117418, Russian Federation
| | - Ulykbek Kairov
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
| | - Andrey A Zamyatnin
- Research Center for Translational Medicine, Sirius University of Science and Technology, Sochi 354340, Russian Federation
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russian Federation
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russian Federation
- Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow 119991, Russian Federation
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2
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Schneider L, Richter M, Oelschlaeger C, Rabe KS, Domínguez CM, Niemeyer CM. Accurate quantification of DNA content in DNA hydrogels prepared by rolling circle amplification. Chem Commun (Camb) 2023; 59:12184-12187. [PMID: 37750315 DOI: 10.1039/d3cc04374f] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Accurate quantification of polymerized DNA in rolling circle amplification (RCA)-based hydrogels is challenging due to the high viscosity of these materials, however, it can be achieved with a photometric nucleotide depletion assay or qPCR. We show that the DNA content strongly depends on the template sequence and correlates with the mechanical properties of the hydrogels.
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Affiliation(s)
- Leonie Schneider
- Institute of Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Madleen Richter
- Institute of Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Claude Oelschlaeger
- Institute for Mechanical Process Engineering and Mechanics, Karlsruhe Institute of Technology (KIT), Gotthard-Franz-Straße 3, 76131 Karlsruhe, Germany
| | - Kersten S Rabe
- Institute of Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Carmen M Domínguez
- Institute of Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Christof M Niemeyer
- Institute of Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
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3
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Soni A, Dahiya B, Sheoran A, Kumar V, Guliani A, Kumar N, Hooda V, Yadav A, Nehra K, Mehta PK. Diagnosis of pleural tuberculosis by multi-targeted loop-mediated isothermal amplification assay based on SYBR Green I reaction: comparison with GeneXpert® MTB/RIF assay. Expert Rev Respir Med 2023; 17:1079-1089. [PMID: 38058175 DOI: 10.1080/17476348.2023.2292738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/05/2023] [Indexed: 12/08/2023]
Abstract
BACKGROUND Diagnosis of pleural tuberculosis (TB) is tedious owing to its close resemblance with malignant pleural effusion and sparse bacterial load in clinical specimens. There is an immediate need to design a rapid and dependable diagnostic test to prevent unnecessary morbidity/mortality. RESEARCH DESIGN AND METHODS A multi-targeted loop-mediated isothermal amplification (MT-LAMP) was deliberated using mpt64 and IS6110 to diagnose pleural TB within pleural fluids/biopsies. MT-LAMP products were analyzed by gel-based and visual detection methods, viz. SYBR Green I, SYBR Green I+deoxyuridine triphosphate uracil-N-glycosylase (dUTP-UNG), and dry methyl green reactions. RESULTS In a pilot study, while assessing pleural TB/non-TB control subjects (n = 40), both SYBR Green I+dUTP-UNG/gel-based MT-LAMP assays exhibited better sensitivity/specificity than SYBR Green I and dry methyl green MT-LAMP. Since it is facile to work with SYBR Green I+dUTP-UNG than gel-based MT-LAMP, we validated the performance of SYBR Green I+dUTP-UNG in a higher number of specimens (n = 97), which revealed somewhat higher sensitivity (85.2 vs. 81.5%) and specificity (97.7 vs. 90.7%) than SYBR Green I MT-LAMP. Furthermore, the sensitivity attained by SYBR Green I+dUTP-UNG MT-LAMP was significantly higher (p < 0.001) than GeneXpert. CONCLUSIONS Our SYBR Green I+dUTP-UNG MT-LAMP is a simple and reliable method to diagnose pleural TB, which may translate into a point-of-care test.
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Affiliation(s)
- Aishwarya Soni
- Centre for Biotechnology, Maharshi Dayanand University (MDU), Rohtak, India
- Department of Biotechnology, Deenbandhu Chhotu Ram University of Science and Technology (DCRUST), Murthal, Sonipat, India
| | - Bhawna Dahiya
- Centre for Biotechnology, Maharshi Dayanand University (MDU), Rohtak, India
- Microbiology Department, Faculty of Allied Health Sciences, Shree Guru Gobind Singh Tricentenary (SGT) University, Gurugram, India
| | - Abhishek Sheoran
- Department of Statistics, Ramanujan College, University of Delhi, New Delhi, India
| | - Vipul Kumar
- Department of TB & Respiratory Medicine, University of Health Sciences (UHS), Rohtak, India
| | - Astha Guliani
- Department of TB & Respiratory Medicine, University of Health Sciences (UHS), Rohtak, India
| | - Nitin Kumar
- Centre for Medical Biotechnology, MDU, Rohtak, India
| | - Vikas Hooda
- Centre for Biotechnology, Maharshi Dayanand University (MDU), Rohtak, India
| | | | - Kiran Nehra
- Department of Biotechnology, Deenbandhu Chhotu Ram University of Science and Technology (DCRUST), Murthal, Sonipat, India
| | - Promod K Mehta
- Centre for Biotechnology, Maharshi Dayanand University (MDU), Rohtak, India
- Microbiology Department, Faculty of Allied Health Sciences, Shree Guru Gobind Singh Tricentenary (SGT) University, Gurugram, India
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4
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Qi G, Wang D, Li C, Ma K, Zhang Y, Jin Y. Plasmonic SERS Au Nanosunflowers for Sensitive and Label-Free Diagnosis of DNA Base Damage in Stimulus-Induced Cell Apoptosis. Anal Chem 2020; 92:11755-11762. [PMID: 32786448 DOI: 10.1021/acs.analchem.0c01799] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Molecular diagnosis and accurate damage analysis of complex genomic DNAs in tumor cells are crucial to the theranostics of cancers but still a huge challenge. Herein, by designed preparation of a uniform plasmonic sunflower-like assembly gold (Au) nanostructure that is capable of efficient DNA capture and providing high-density gap-plasmon "hot spots" for adequate surface-enhanced Raman spectroscopy (SERS) enhancement, we succeeded in sensitive and reliable label-free SERS detection of DNA damage in electrostimulus-induced apoptotic cancer cells at the DNA base level for the first time. The SERS results showed that the external electrostimulus (at 1.2 V, for 5 min) was almost harmless to normal healthy cells, but it caused pronounced double strand break and adenine base damage in cancer cell DNAs, which effectively destroyed the reproduction and transcription of DNAs and ultimately induced cell apoptosis. The developed sensing platform and method are promising for cell study of genetically related diseases.
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Affiliation(s)
- Guohua Qi
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China
| | - Dandan Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China.,University of Science and Technology of China, Hefei 230026, P. R. China
| | - Chuanping Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China.,College of Biological and Chemical Engineering, Anhui Polytechnic University, Wuhu 241000, P. R. China
| | - Kongshuo Ma
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China.,University of Science and Technology of China, Hefei 230026, P. R. China
| | - Ying Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China.,University of Science and Technology of China, Hefei 230026, P. R. China
| | - Yongdong Jin
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China.,University of Science and Technology of China, Hefei 230026, P. R. China
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5
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Ruksakiet K, Hanák L, Farkas N, Hegyi P, Sadaeng W, Czumbel LM, Sang-ngoen T, Garami A, Mikó A, Varga G, Lohinai Z. Antimicrobial Efficacy of Chlorhexidine and Sodium Hypochlorite in Root Canal Disinfection: A Systematic Review and Meta-analysis of Randomized Controlled Trials. J Endod 2020; 46:1032-1041.e7. [PMID: 32413440 DOI: 10.1016/j.joen.2020.05.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 03/20/2020] [Accepted: 05/05/2020] [Indexed: 02/02/2023]
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6
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Shen R, Jia Y, Mak PI, Martins RP. Clip-to-release on amplification (CRoA): a novel DNA amplification enhancer on and off microfluidics. LAB ON A CHIP 2020; 20:1928-1938. [PMID: 32352133 DOI: 10.1039/d0lc00318b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Despite its high sensitivity, low cost, and high efficiency as a DNA amplification indicator with a yes/no answer, dsDNA-binding dye encounters incompatibility when used in microfluidic systems, resulting in problems such as false negative amplification results. Besides, its inhibition of amplification at high concentrations hinders its application both on-chip and off-chip. In this study, we propose a novel DNA amplification enhancer to counteract the drawbacks of dsDNA-binding dyes. It acts as a temporary reservoir for the free-floating dyes in solution and releases them on demand during the amplification process. Through this clip-to-release on amplification mechanism, the enhancer lowered the background fluorescence of sample droplets before amplification, enhanced the signal-to-background ratio of positive samples, and eliminated the false negative signal of on-chip PCR. Moreover, the enhancer increased the off-chip polymerase chain reaction (PCR) efficiency, boosted the fluorescence signal up to 10-fold, and made less nonspecific amplification product. All the factors affecting the enhancer's performance are investigated in detail, including its structure and concentration, and the types of dsDNA-binding dye used in the reaction. Finally, we demonstrated the broad application of the proposed amplification enhancer in various DNA amplification systems, for various genes, and on various amplification platforms. It would reignite the utilization of dsDNA dyes for wider applications in DNA analysis both on-chip and off-chip.
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Affiliation(s)
- Ren Shen
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau, China. and Faculty of Science and Technology - ECE, University of Macau, Macau, China
| | - Yanwei Jia
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau, China. and Faculty of Science and Technology - ECE, University of Macau, Macau, China and Faculty of Health Sciences, University of Macau, Macau, China
| | - Pui-In Mak
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau, China. and Faculty of Science and Technology - ECE, University of Macau, Macau, China
| | - Rui P Martins
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau, China. and Faculty of Science and Technology - ECE, University of Macau, Macau, China and On Leave from Instituto Superior Técnico, Universidade de Lisboa, Portugal
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7
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Muñoz HE, Riche CT, Kong JE, van Zee M, Garner OB, Ozcan A, Di Carlo D. Fractal LAMP: Label-Free Analysis of Fractal Precipitate for Digital Loop-Mediated Isothermal Nucleic Acid Amplification. ACS Sens 2020; 5:385-394. [PMID: 31902202 DOI: 10.1021/acssensors.9b01974] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Nucleic acid amplification assays including loop-mediated isothermal amplification (LAMP) are routinely used in diagnosing diseases and monitoring water and food quality. The results of amplification in these assays are commonly measured with an analog fluorescence readout, which requires specialized optical equipment and can lack quantitative precision. Digital analysis of amplification in small fluid compartments based on exceeding a threshold fluorescence level can enhance the quantitative precision of nucleic acid assays (i.e., digital nucleic acid amplification assays), but still requires specialized optical systems for fluorescence readout and the inclusion of a fluorescent dye. Here, we report Fractal LAMP, an automated method to detect amplified DNA in subnanoliter scale droplets following LAMP in a label-free manner. Our computer vision algorithm achieves high accuracy detecting DNA amplification in droplets by identifying LAMP byproducts that form fractal structures observable in brightfield microscopy. The capabilities of Fractal LAMP are further realized by developing a Bayesian model to estimate DNA concentrations for unknown samples and a bootstrapping method to estimate the number of droplets required to achieve target limits of detection. This digital, label-free assay has the potential to lower reagent and reader cost for nucleic acid measurement while maintaining high quantitative accuracy over 3 orders of magnitude of concentration.
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Affiliation(s)
- Hector E. Muñoz
- Department of Bioengineering, University of California, Los Angeles, California 90095, United States
| | - Carson T. Riche
- Department of Bioengineering, University of California, Los Angeles, California 90095, United States
| | - Janay E. Kong
- Department of Bioengineering, University of California, Los Angeles, California 90095, United States
| | - Mark van Zee
- Department of Bioengineering, University of California, Los Angeles, California 90095, United States
| | - Omai B. Garner
- Department of Pathology & Laboratory Medicine, University of California, Los Angeles, California 90095, United States
| | - Aydogan Ozcan
- Department of Bioengineering, University of California, Los Angeles, California 90095, United States
- Department of Electrical and Computer Engineering, University of California, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Dino Di Carlo
- Department of Bioengineering, University of California, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, California 90095, United States
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8
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Kuzminov A. Half-Intercalation Stabilizes Slipped Mispairing and Explains Genome Vulnerability to Frameshift Mutagenesis by Endogenous "Molecular Bookmarks". Bioessays 2019; 41:e1900062. [PMID: 31379009 DOI: 10.1002/bies.201900062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/06/2019] [Indexed: 01/11/2023]
Abstract
Some 60 years ago chemicals that intercalate between base pairs of duplex DNA were found to amplify frameshift mutagenesis. Surprisingly, the robust induction of frameshifts by intercalators still lacks a mechanistic model, leaving this classic phenomenon annoyingly intractable. A promising idea of asymmetric half-intercalation-stabilizing frameshift intermediates during DNA synthesis has never been developed into a model. Instead, researchers of frameshift mutagenesis embraced the powerful slipped-mispairing concept that unexpectedly struggled with the role of intercalators in frameshifting. It is proposed that the slipped mispairing and the half-intercalation ideas are two sides of the same coin. Further, existing findings are reviewed to test predictions of the combined "half-intercalation into the slipped-mispairing intermediate" model against accumulated knowledge. The existence of potential endogenous intercalators and the phenomenon of "DNA bookmarks" reveal ample possibilities for natural frameshift mutagenisis in the cell. From this alarming perspective, it is discussed how the cell could prevent genome deterioration from frameshift mutagenesis.
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Affiliation(s)
- Andrei Kuzminov
- Department of Microbiology, University of Illinois at Urbana-Champaign, B103 CLSL, 601 South Goodwin Ave, Urbana, IL, 61801-3709, USA
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9
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Vasconcelos LRS, Moura P, Dutra RF. Ultrasensitive Genosensor Based on Minor Grove Binding (MGB) Probe for IL28BSingle Nucleotide Polymorphism (SNP) Detection Using SYBR Green as Electrochemical Indicator. ELECTROANAL 2018. [DOI: 10.1002/elan.201800377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Luydson R. S. Vasconcelos
- Laboratory of Biomedical Engineering, Department of Biomedical EngineeringFederal University of Pernambuco Recife Brazil
- Aggeu Magalhães Research Center, FIOCRUZ-PE Recife Brazil
| | - Patricia Moura
- Insitute of Biological ScienceState University of Pernambuco Recife Brazil
| | - Rosa F. Dutra
- Laboratory of Biomedical Engineering, Department of Biomedical EngineeringFederal University of Pernambuco Recife Brazil
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10
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Weng JH, Chen LC. Confocal epifluorescence sensor with an arc-shaped aperture for slide-based PCR quantification. Biosens Bioelectron 2017; 100:71-78. [PMID: 28863326 DOI: 10.1016/j.bios.2017.08.052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/09/2017] [Accepted: 08/23/2017] [Indexed: 11/30/2022]
Abstract
The increasing needs of point-of-care diagnostics, quarantine of epidemic pathogens, and prevention of terrorism's bio-attacks have promised the future of portable real-time quantitative polymerase chain reaction (qPCR) sensors. This work aims at developing a highly sensitive and low-cost light emitting diode (LED)-based epifluorescence sensor module for qPCR sensor development and relevant bioassay applications. Inspired by the light stop design and dark-field detection of microscopes, this paper first reports a compact confocal LED epifluorescence sensor using a light stop with an arc-shaped aperture for enhancing the flexibility of quick DNA and PCR detection. The sensor features the advantages of the dichroic mirror-free and confocal (shared-focus) characteristics, which benefits size reduction and minimal optics used. It also allows extension to integrate with in situ real-time PCR thermal cycling since the sample slide is placed apart from the epi-sensing module. The epifluorescence sensor can detect as low as sub-ng/μL standard DNA and 101 copies of Salmonella typhimurium InvA gene sequences (cloned in E. coli and after 30-cycle PCR) with SYBR® Green I from non-purified culture samples, having highly sensitive and specific signal responses comparable with that of a commercial qPCR instrument.
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Affiliation(s)
- Jui-Hong Weng
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Lin-Chi Chen
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan.
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11
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Current Nucleic Acid Extraction Methods and Their Implications to Point-of-Care Diagnostics. BIOMED RESEARCH INTERNATIONAL 2017; 2017:9306564. [PMID: 28785592 PMCID: PMC5529626 DOI: 10.1155/2017/9306564] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/05/2017] [Indexed: 12/12/2022]
Abstract
Nucleic acid extraction (NAE) plays a vital role in molecular biology as the primary step for many downstream applications. Many modifications have been introduced to the original 1869 method. Modern processes are categorized into chemical or mechanical, each with peculiarities that influence their use, especially in point-of-care diagnostics (POC-Dx). POC-Dx is a new approach aiming to replace sophisticated analytical machinery with microanalytical systems, able to be used near the patient, at the point of care or point of need. Although notable efforts have been made, a simple and effective extraction method is still a major challenge for widespread use of POC-Dx. In this review, we dissected the working principle of each of the most common NAE methods, overviewing their advantages and disadvantages, as well their potential for integration in POC-Dx systems. At present, it seems difficult, if not impossible, to establish a procedure which can be universally applied to POC-Dx. We also discuss the effects of the NAE chemicals upon the main plastic polymers used to mass produce POC-Dx systems. We end our review discussing the limitations and challenges that should guide the quest for an efficient extraction method that can be integrated in a POC-Dx system.
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12
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Jansson L, Koliana M, Sidstedt M, Hedman J. Blending DNA binding dyes to improve detection in real-time PCR. ACTA ACUST UNITED AC 2017; 14:34-37. [PMID: 28459006 PMCID: PMC5397098 DOI: 10.1016/j.btre.2017.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 02/10/2017] [Accepted: 02/12/2017] [Indexed: 11/19/2022]
Abstract
The success of real-time PCR (qPCR) analysis is partly limited by the presence of inhibitory compounds in the nucleic acid samples. For example, humic acid (HA) from soil and aqueous sediment interferes with amplification and also quenches the fluorescence of double-stranded (ds) DNA binding dyes, thus hindering amplicon detection. We aimed to counteract the HA fluorescence quenching effect by blending complementary dsDNA binding dyes, thereby elevating the dye saturation levels and increasing the fluorescence signals. A blend of the four dyes EvaGreen, ResoLight, SYBR Green and SYTO9 gave significantly higher fluorescence intensities in the presence and absence of HA, compared with the dyes applied separately and two-dye blends. We propose blending of dyes as a generally applicable means for elevating qPCR fluorescence signals and thus enabling detection in the presence of quenching substances.
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Affiliation(s)
- Linda Jansson
- Applied Microbiology, Department of Chemistry, Lund University, Lund, SE-221 00, Sweden
| | - Marianne Koliana
- Applied Microbiology, Department of Chemistry, Lund University, Lund, SE-221 00, Sweden
| | - Maja Sidstedt
- Applied Microbiology, Department of Chemistry, Lund University, Lund, SE-221 00, Sweden
- Swedish National Forensic Centre, Linköping, SE-591 94, Sweden
| | - Johannes Hedman
- Applied Microbiology, Department of Chemistry, Lund University, Lund, SE-221 00, Sweden
- Swedish National Forensic Centre, Linköping, SE-591 94, Sweden
- Corresponding author at: Applied Microbiology, Department of Chemistry, Lund University, Lund, SE-221 00, Sweden.Applied MicrobiologyDepartment of ChemistryLund UniversityLundSE-221 00Sweden
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13
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Kong JE, Wei Q, Tseng D, Zhang J, Pan E, Lewinski M, Garner OB, Ozcan A, Di Carlo D. Highly Stable and Sensitive Nucleic Acid Amplification and Cell-Phone-Based Readout. ACS NANO 2017; 11:2934-2943. [PMID: 28234452 DOI: 10.1021/acsnano.6b08274] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Key challenges with point-of-care (POC) nucleic acid tests include achieving a low-cost, portable form factor, and stable readout, while also retaining the same robust standards of benchtop lab-based tests. We addressed two crucial aspects of this problem, identifying a chemical additive, hydroxynaphthol blue, that both stabilizes and significantly enhances intercalator-based fluorescence readout of nucleic acid concentration, and developing a cost-effective fiber-optic bundle-based fluorescence microplate reader integrated onto a mobile phone. Using loop-mediated isothermal amplification on lambda DNA we achieve a 69-fold increase in signal above background, 20-fold higher than the gold standard, yielding an overall limit of detection of 25 copies/μL within an hour using our mobile-phone-based platform. Critical for a point-of-care system, we achieve a >60% increase in fluorescence stability as a function of temperature and time, obviating the need for manual baseline correction or secondary calibration dyes. This field-portable and cost-effective mobile-phone-based nucleic acid amplification and readout platform is broadly applicable to other real-time nucleic acid amplification tests by similarly modulating intercalating dye performance and is compatible with any fluorescence-based assay that can be run in a 96-well microplate format, making it especially valuable for POC and resource-limited settings.
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Affiliation(s)
- Janay E Kong
- Department of Bioengineering, ‡Department of Electrical Engineering, ∥Department of Pathology & Laboratory Medicine, ^Department of Mechanical and Aerospace Engineering, ⊥California NanoSystems Institute, and ¶Jonsson Comprehensive Cancer Center, University of California Los Angeles , Los Angeles, California 90095, United States
| | - Qingshan Wei
- Department of Bioengineering, ‡Department of Electrical Engineering, ∥Department of Pathology & Laboratory Medicine, ^Department of Mechanical and Aerospace Engineering, ⊥California NanoSystems Institute, and ¶Jonsson Comprehensive Cancer Center, University of California Los Angeles , Los Angeles, California 90095, United States
| | - Derek Tseng
- Department of Bioengineering, ‡Department of Electrical Engineering, ∥Department of Pathology & Laboratory Medicine, ^Department of Mechanical and Aerospace Engineering, ⊥California NanoSystems Institute, and ¶Jonsson Comprehensive Cancer Center, University of California Los Angeles , Los Angeles, California 90095, United States
| | - Jingzi Zhang
- Department of Bioengineering, ‡Department of Electrical Engineering, ∥Department of Pathology & Laboratory Medicine, ^Department of Mechanical and Aerospace Engineering, ⊥California NanoSystems Institute, and ¶Jonsson Comprehensive Cancer Center, University of California Los Angeles , Los Angeles, California 90095, United States
| | - Eric Pan
- Department of Bioengineering, ‡Department of Electrical Engineering, ∥Department of Pathology & Laboratory Medicine, ^Department of Mechanical and Aerospace Engineering, ⊥California NanoSystems Institute, and ¶Jonsson Comprehensive Cancer Center, University of California Los Angeles , Los Angeles, California 90095, United States
| | - Michael Lewinski
- Department of Bioengineering, ‡Department of Electrical Engineering, ∥Department of Pathology & Laboratory Medicine, ^Department of Mechanical and Aerospace Engineering, ⊥California NanoSystems Institute, and ¶Jonsson Comprehensive Cancer Center, University of California Los Angeles , Los Angeles, California 90095, United States
| | - Omai B Garner
- Department of Bioengineering, ‡Department of Electrical Engineering, ∥Department of Pathology & Laboratory Medicine, ^Department of Mechanical and Aerospace Engineering, ⊥California NanoSystems Institute, and ¶Jonsson Comprehensive Cancer Center, University of California Los Angeles , Los Angeles, California 90095, United States
| | - Aydogan Ozcan
- Department of Bioengineering, ‡Department of Electrical Engineering, ∥Department of Pathology & Laboratory Medicine, ^Department of Mechanical and Aerospace Engineering, ⊥California NanoSystems Institute, and ¶Jonsson Comprehensive Cancer Center, University of California Los Angeles , Los Angeles, California 90095, United States
| | - Dino Di Carlo
- Department of Bioengineering, ‡Department of Electrical Engineering, ∥Department of Pathology & Laboratory Medicine, ^Department of Mechanical and Aerospace Engineering, ⊥California NanoSystems Institute, and ¶Jonsson Comprehensive Cancer Center, University of California Los Angeles , Los Angeles, California 90095, United States
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Hu Y, Xu P, Luo J, He H, Du W. Absolute Quantification of H5-Subtype Avian Influenza Viruses Using Droplet Digital Loop-Mediated Isothermal Amplification. Anal Chem 2016; 89:745-750. [PMID: 28105842 DOI: 10.1021/acs.analchem.6b03328] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Human infection with avian influenza A H5N1 viruses can cause severe diseases with high mortality rate and continues to pose a significant threat to global public health. Rapid diagnosis is needed for identifying the types of influenza viruses for making timely treatment decisions. Here, we demonstrate absolute quantification of H5-subtype influenza viruses by digital loop-mediated isothermal amplification (dLAMP) on our recently developed cross-interface emulsification (XiE) method. Our results show that XiE-based dLAMP is highly specific and displays comparable sensitivity to real-time PCR (qPCR) and digital PCR (dPCR). Notably, dLAMP is more tolerant to inhibitory substances than PCR methods and demonstrated similar detection efficiency to qPCR for real H5N1 samples. Therefore, it can serve as a robust and precise alternative to qPCR or dPCR and is especially suitable for environmental and clinical samples with hard-to-remove contaminants. We believe that our dLAMP method offers great potential for rapid and accurate diagnosis of influenza and other infectious diseases.
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Affiliation(s)
- Yi Hu
- National Research Center for Wildlife Born Diseases, Institute of Zoology, Chinese Academy of Sciences , Beijing 100101, China
| | - Peng Xu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China
| | - Jing Luo
- National Research Center for Wildlife Born Diseases, Institute of Zoology, Chinese Academy of Sciences , Beijing 100101, China
| | - Hongxuan He
- National Research Center for Wildlife Born Diseases, Institute of Zoology, Chinese Academy of Sciences , Beijing 100101, China
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China
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Park J, Song M, Jang W, Chae H, Lee GD, Kim K, Park H, Kim M, Kim Y. Peptide nucleic acid probe-based fluorescence melting curve analysis for rapid screening of common JAK2, MPL, and CALR mutations. Clin Chim Acta 2016; 465:82-90. [PMID: 27939919 DOI: 10.1016/j.cca.2016.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 11/30/2016] [Accepted: 12/02/2016] [Indexed: 01/26/2023]
Abstract
BACKGROUND We developed and evaluated the feasibility of peptide nucleic acid (PNA)-based fluorescence melting curve analysis (FMCA) to detect common mutations in myeloproliferative neoplasms (MPNs). METHODS We have set up two separate reactions of PNA-based FMCA: JAK2 V617F &CALR p.Leu367fs*46 (set A) and MPL W515L/K &CALR p.Lys385fs*47 (set B). Clinical usefulness was validated with allele-specific real-time PCR, fragment analysis, Sanger sequencing in 57 BCR-ABL1-negative MPNs. RESULTS The limit of detection (LOD) of PNA-based FMCA was approximately 10% for each mutation and interference reactions using mixtures of different mutations were not observed. Non-specific amplification was not observed in normal control. PNA-based FMCA was able to detect all JAK2 V617F (n=20), CALR p.Leu367fs*46 (n=10) and p.Lys385fs*47 (n=8). Three of six MPL mutations were detected except three samples with low mutant concentration in out of LOD. JAK2 exon 12 mutations (n=7) were negative without influencing V617F results. Among six variant CALR exon 9 mutations, two were detected by this method owing to invading of probe binding site. CONCLUSIONS PNA-based FMCA for detecting common JAK2, MPL, and CALR mutations is a rapid, simple, and sensitive technique in BCR-ABL1-negative MPNs with >10% mutant allele at the time of initial diagnosis.
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Affiliation(s)
- Joonhong Park
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Minsik Song
- SeaSun Biomaterials, Daejeon, Republic of Korea
| | - Woori Jang
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hyojin Chae
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Gun Dong Lee
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | | | | | - Myungshin Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
| | - Yonggoo Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
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16
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Forghani F, Wei S, Oh DH. A Rapid Multiplex Real-Time PCR High-Resolution Melt Curve Assay for the Simultaneous Detection of Bacillus cereus, Listeria monocytogenes, and Staphylococcus aureus in Food. J Food Prot 2016; 79:810-5. [PMID: 27296430 DOI: 10.4315/0362-028x.jfp-15-428] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Three important foodborne pathogens, Bacillus cereus, Listeria monocytogenes, and Staphylococcus aureus, are of great concern for food safety. They may also coexist in food matrices and, in the case of B. cereus and S. aureus, the resulting illnesses can resemble each other owing to similar symptoms. Therefore, their simultaneous detection may have advantages in terms of cost savings and rapidity. Given this context, a rapid multiplex real-time PCR high-resolution melt curve assay for the simultaneous detection of these three pathogens in food was developed. The assay successfully detected B. cereus (gyrB), L. monocytogenes (hly), and S. aureus (nuc) in a single reaction, and the average melting temperatures were 76.23, 80.19, and 74.01°C, respectively. The application of SYTO9 dye and a slow melt curve analysis ramp rate (0.1°C/s) enabled the production of sharp, high-resolution melt curve peaks that were easily distinguishable from each other. The detection limit in food (milk, rice, and lettuce) was 3.7 × 10(3) CFU/g without an enrichment step and 3.7 × 10(1) CFU/g following the 10-h enrichment. Hence, the assay developed here is specific and sensitive, providing an efficient tool for implementation in food for the simultaneous detection of B. cereus, L. monocytogenes, and S. aureus .
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Affiliation(s)
- Fereidoun Forghani
- Department of Bioconvergence Science and Technology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon 200-701, Republic of Korea; Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Shuai Wei
- Department of Bioconvergence Science and Technology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon 200-701, Republic of Korea
| | - Deog-Hwan Oh
- Department of Bioconvergence Science and Technology, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, Gangwon 200-701, Republic of Korea.
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A novel pentaplex real time (RT)- PCR high resolution melt curve assay for simultaneous detection of emetic and enterotoxin producing Bacillus cereus in food. Food Control 2016. [DOI: 10.1016/j.foodcont.2015.08.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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18
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Haines AM, Tobe SS, Kobus HJ, Linacre A. Effect of nucleic acid binding dyes on DNA extraction, amplification, and STR typing. Electrophoresis 2015. [DOI: 10.1002/elps.201500170] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Alicia M. Haines
- School of Biological Sciences; Flinders University; Adelaide South Australia
| | - Shanan S. Tobe
- School of Biological Sciences; Flinders University; Adelaide South Australia
| | - Hilton J. Kobus
- School of Chemical and Physical Sciences; Flinders University; Adelaide South Australia
| | - Adrian Linacre
- School of Biological Sciences; Flinders University; Adelaide South Australia
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19
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Zhang C, Fu J, Wang Y, Bao Z, Zhao H. Identification of Suitable Reference Genes for Gene Expression Normalization in the Quantitative Real-Time PCR Analysis of Sweet Osmanthus (Osmanthus fragrans Lour.). PLoS One 2015; 10:e0136355. [PMID: 26302211 PMCID: PMC4547725 DOI: 10.1371/journal.pone.0136355] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 08/01/2015] [Indexed: 01/25/2023] Open
Abstract
Quantitative real-time PCR (RT-qPCR), a sensitive technique for quantifying gene expression, depends on the stability of the reference gene(s) used for data normalization. Several studies examining the selection of reference genes have been performed in ornamental plants but none in sweet osmanthus (Osmanthus fragrans Lour.). Based on transcriptomic sequencing data from O. fragrans buds at four developmental stages, six reference genes (OfACT, OfEF1α, OfIDH, OfRAN1, OfTUB, and OfUBC2) with stable expression (0.5 to 2 fold change in expression levels between any two developmental stages), as well as the commonly used reference gene Of18S, were selected as candidates for gene expression normalization in the RT-qPCR analysis of O. fragrans. For the normalization of RT-qPCR with two dyes, SYBR Green and EvaGreen, the expressional stability of seven candidate reference genes in 43 O. fragrans samples was analyzed using geNorm, NormFinder and BestKeeper. For RT-qPCR using SYBR Green, OfRAN1 and OfUBC2 were the optimal reference genes for all samples and different cultivars, OfACT and OfEF1α were suitable for different floral developmental stages, and OfACT was the optimal reference gene for different temperature treatments. The geometric mean values of the optimal reference gene pairs for the normalization of RT-qPCR are recommended to be used for all samples, different cultivars and different floral developmental stages in O. fragrans. For RT-qPCR using EvaGreen, OfUBC2 was the optimal reference gene for all samples and different cultivars, and OfACT was the optimal reference gene for different floral developmental stages and different temperature treatments. As the worst reference gene, Of18S should not be used as a reference gene in O. fragrans in the future. Our results provide a reference gene application guideline for O. fragrans gene expression characterization using RT-qPCR.
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Affiliation(s)
- Chao Zhang
- Department of Ornamental Horticulture, School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Lin’an, Zhejiang, China
| | - Jianxin Fu
- Department of Ornamental Horticulture, School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Lin’an, Zhejiang, China
| | - Yiguang Wang
- Department of Ornamental Horticulture, School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Lin’an, Zhejiang, China
| | - Zhiyi Bao
- Department of Ornamental Horticulture, School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Lin’an, Zhejiang, China
| | - Hongbo Zhao
- Department of Ornamental Horticulture, School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Lin’an, Zhejiang, China
- Nurturing Station for State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Lin’an, Zhejiang, China
- * E-mail:
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20
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Masetti M, Xie HN, Krpetić Ž, Recanatini M, Alvarez-Puebla RA, Guerrini L. Revealing DNA Interactions with Exogenous Agents by Surface-Enhanced Raman Scattering. J Am Chem Soc 2014; 137:469-76. [DOI: 10.1021/ja511398w] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Matteo Masetti
- Department
of Pharmacy and Biotechnology, Alma Mater Studiorum—Università di Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Hai-nan Xie
- Medcom Advance SA, Viladecans
Bussines Park, Edificio Brasil, C/Bertran i Musitu, 83-85, 08840 Viladecans (Barcelona), Spain
| | - Željka Krpetić
- Centre
for BioNano Interactions, School of Chemistry and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Maurizio Recanatini
- Department
of Pharmacy and Biotechnology, Alma Mater Studiorum—Università di Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Ramon A. Alvarez-Puebla
- Medcom Advance SA, Viladecans
Bussines Park, Edificio Brasil, C/Bertran i Musitu, 83-85, 08840 Viladecans (Barcelona), Spain
- ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
- Universitat Rovira i Virgili, Carrer
de Marcellí Domingo s/n, 43007 Tarragona, Spain
| | - Luca Guerrini
- Medcom Advance SA, Viladecans
Bussines Park, Edificio Brasil, C/Bertran i Musitu, 83-85, 08840 Viladecans (Barcelona), Spain
- Universitat Rovira i Virgili, Carrer
de Marcellí Domingo s/n, 43007 Tarragona, Spain
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21
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Singh P, Mustapha A. Development of a real-time PCR melt curve assay for simultaneous detection of virulent and antibiotic resistant Salmonella. Food Microbiol 2014; 44:6-14. [DOI: 10.1016/j.fm.2014.04.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 04/04/2014] [Accepted: 04/25/2014] [Indexed: 12/11/2022]
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22
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Wang LJ, Zhang Y, Zhang CY. A target-triggered exponential amplification-based DNAzyme biosensor for ultrasensitive detection of folate receptors. Chem Commun (Camb) 2014; 50:15393-6. [DOI: 10.1039/c4cc07230h] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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23
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Hedman J, Knutsson R, Ansell R, Rådström P, Rasmusson B. Pre-PCR processing in bioterrorism preparedness: improved diagnostic capabilities for laboratory response networks. Biosecur Bioterror 2014; 11 Suppl 1:S87-101. [PMID: 23971826 DOI: 10.1089/bsp.2012.0090] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Diagnostic DNA analysis using polymerase chain reaction (PCR) has become a valuable tool for rapid detection of biothreat agents. However, analysis is often challenging because of the limited size, quality, and purity of the biological target. Pre-PCR processing is an integrated concept in which the issues of analytical limit of detection and simplicity for automation are addressed in all steps leading up to PCR amplification--that is, sampling, sample treatment, and the chemical composition of PCR. The sampling method should maximize target uptake and minimize uptake of extraneous substances that could impair the analysis--so-called PCR inhibitors. In sample treatment, there is a trade-off between yield and purity, as extensive purification leads to DNA loss. A cornerstone of pre-PCR processing is to apply DNA polymerase-buffer systems that are tolerant to specific sample impurities, thereby lowering the need for expensive purification steps and maximizing DNA recovery. Improved awareness among Laboratory Response Networks (LRNs) regarding pre-PCR processing is important, as ineffective sample processing leads to increased cost and possibly false-negative or ambiguous results, hindering the decision-making process in a bioterrorism crisis. This article covers the nature and mechanisms of PCR-inhibitory substances relevant for agroterrorism and bioterrorism preparedness, methods for quality control of PCR reactions, and applications of pre-PCR processing to optimize and simplify the analysis of various biothreat agents. Knowledge about pre-PCR processing will improve diagnostic capabilities of LRNs involved in the response to bioterrorism incidents.
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Affiliation(s)
- Johannes Hedman
- Johannes Hedman, PhD, is employed as a specialist at the Swedish National Laboratory of Forensic Science (SKL) and holds a research position at Applied Microbiology, Lund University. Rickard Knutsson, PhD, is Director of Security Department, National Veterinary Institute (SVA), Uppsala, Sweden . Ricky Ansell, PhD, is employed as forensic advisor and senior reporting officer at the Swedish National Laboratory of Forensic Science (SKL). Birgitta Rasmusson, PhD, is employed as research director at the Swedish National Laboratory of Forensic Science (SKL) and holds a position as adjunct professor at Applied Microbiology, Lund University. Peter Rådström, PhD, is employed as professor Applied Microbiology, Lund University
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Monti M, Martini M, Tedeschi R. EvaGreen real-time PCR protocol for specific 'Candidatus Phytoplasma mali' detection and quantification in insects. Mol Cell Probes 2013; 27:129-36. [PMID: 23474195 DOI: 10.1016/j.mcp.2013.02.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Revised: 02/09/2013] [Accepted: 02/19/2013] [Indexed: 10/27/2022]
Abstract
In this paper the validation and implementation of a Real-time PCR protocol based on ribosomal protein genes has been carried out for sensitive and specific quantification of 'Candidatus (Ca.) Phytoplasma mali' (apple proliferation phytoplasma, APP) in insects. The method combines the use of EvaGreen(®) dye as chemistry detection system and the specific primer pair rpAP15f-mod/rpAP15r3, which amplifies a fragment of 238 bp of the ribosomal protein rplV (rpl22) gene of APP. Primers specificity was demonstrated by running in the same Real-time PCR 'Ca. Phytoplasma mali' samples with phytoplasmas belonging to the same group (16SrX) as 'Ca. Phytoplasma pyri' and 'Ca. Phytoplasma prunorum', and also phytoplasmas from different groups, as 'Ca. Phytoplasma phoenicium' (16SrIX) and Flavescence dorée phytoplasma (16SrV). 'Ca. Phytoplasma mali' titre in insects was quantified using a specific approach, which relates the concentration of the phytoplasma to insect 18S rDNA. Absolute quantification of APP and insect 18S rDNA were calculated using standard curves prepared from serial dilutions of plasmids containing rplV-rpsC and a portion of 18S rDNA genes, respectively. APP titre in insects was expressed as genome units (GU) of phytoplasma per picogram (pg) of individual insect 18S rDNA. 'Ca. Phytoplasma mali' concentration in examined samples (Cacopsylla melanoneura overwintered adults) ranged from 5.94 × 10(2) to 2.51 × 10(4) GU/pg of insect 18S rDNA. Repeatability and reproducibility of the method were also evaluated by calculation of the coefficient of variation (CV%) of GU of phytoplasma and pg of 18S rDNA fragment for both assays. CV less than 14% and 9% (for reproducibility test) and less than 10 and 11% (for repeatability test) were obtained for phytoplasma and insect qPCR assays, respectively. Sensitivity of the method was also evaluated, in comparison with conventional 16S rDNA-based nested-PCR procedure. The method described has been demonstrated reliable, sensitive and specific for the quantification of 'Ca. Phytoplasma mali' in insects. The possibility to study the trend of phytoplasma titre in the vectors will allow a deepen investigation on the epidemiology of the disease.
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Affiliation(s)
- Monia Monti
- Dipartimento di Scienze Agrarie, Forestali e Alimentari DISAFA, University of Torino, Via Leonardo da Vinci 44, 10095 Grugliasco TO, Italy
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25
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Terenzi A, Ducani C, Male L, Barone G, Hannon MJ. DNA interaction of CuII, NiII and ZnII functionalized salphen complexes: studies by linear dichroism, gel electrophoresis and PCR. Dalton Trans 2013; 42:11220-6. [DOI: 10.1039/c3dt51090e] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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26
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Hatt JK, Löffler FE. Quantitative real-time PCR (qPCR) detection chemistries affect enumeration of the Dehalococcoides 16S rRNA gene in groundwater. J Microbiol Methods 2012; 88:263-70. [DOI: 10.1016/j.mimet.2011.12.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 12/08/2011] [Accepted: 12/08/2011] [Indexed: 11/15/2022]
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27
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Zhang Y, Zhang CY. Sensitive Detection of microRNA with Isothermal Amplification and a Single-Quantum-Dot-Based Nanosensor. Anal Chem 2011; 84:224-31. [DOI: 10.1021/ac202405q] [Citation(s) in RCA: 194] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yan Zhang
- Single-Molecule Detection and Imaging Laboratory, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Chun-yang Zhang
- Single-Molecule Detection and Imaging Laboratory, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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Yu Z, Zhu Y, Zhang Y, Li J, Fang Q, Xi J, Yao B. Nanoliter droplet array for microRNA detection based on enzymatic stem-loop probes ligation and SYBR Green real-time PCR. Talanta 2011; 85:1760-5. [DOI: 10.1016/j.talanta.2011.06.075] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2011] [Revised: 06/30/2011] [Accepted: 06/30/2011] [Indexed: 12/19/2022]
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Kouguchi Y, Teramoto M, Kuramoto M. Real-time nucleic acid sequence-based amplification (NASBA) using an adenine-induced quenching probe and an intercalator dye. J Appl Microbiol 2010; 109:1724-32. [PMID: 20629802 DOI: 10.1111/j.1365-2672.2010.04801.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS We found that an adenine base caused fluorescence quenching of a fluorescein (FL)-labelled probe in DNA:RNA hybrid sequences, and applied this finding to a nucleic acid sequence-based amplification (NASBA) method. METHODS AND RESULTS The present NASBA method employed a probe containing an FL-modified thymine at its 3' end and ethidium bromide (EtBr) on the basis of a combination of adenine-induced quenching and fluorescence resonance energy transfer (FRET) between the FL donor and EtBr acceptor. This NASBA was used to detect Shiga toxin (STX) stx-specific mRNA in STX-producing Escherichia coli, demonstrating rapid quantification of the target gene with high sensitivity. CONCLUSION Although the inherent quenching effect of adenine was inferior to that of guanine, FRET between the FL and EtBr moieties enhanced the adenine-induced quenching, allowing rapid and sensitive real-time NASBA detection. SIGNIFICANCE AND IMPACT OF THE STUDY This study gives a novel real-time diagnostic system based on NASBA for a sensitive mRNA (or viral RNA) detection.
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Affiliation(s)
- Y Kouguchi
- Fukuyama City Public Health Center, Fukuyama, Hiroshima, Japan.
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Zhang Z, Kermekchiev MB, Barnes WM. Direct DNA amplification from crude clinical samples using a PCR enhancer cocktail and novel mutants of Taq. J Mol Diagn 2010; 12:152-61. [PMID: 20075207 DOI: 10.2353/jmoldx.2010.090070] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PCR-based clinical and forensic tests often have low sensitivity or even false-negative results caused by potent PCR inhibitors found in blood and soil. It is widely accepted that purification of target DNA before PCR is necessary for successful amplification. In an attempt to overcome PCR inhibition, enhance PCR amplification, and simplify the PCR protocol, we demonstrate improved PCR-enhancing cocktails containing nonionic detergent, l-carnitine, d-(+)-trehalose, and heparin. These cocktails, in combination with two inhibitor-resistant Taq mutants, OmniTaq and Omni Klentaq, enabled efficient amplification of exogenous, endogenous, and high-GC content DNA targets directly from crude samples containing human plasma, serum, and whole blood without DNA purification. In the presence of these enhancer cocktails, the mutant enzymes were able to tolerate at least 25% plasma, serum, or whole blood and as high as 80% GC content templates in PCR reactions. These enhancer cocktails also improved the performance of the novel Taq mutants in real-time PCR amplification using crude samples, both in SYBR Green fluorescence detection and TaqMan assays. The novel enhancer mixes also facilitated DNA amplification from crude samples with various commercial Taq DNA polymerases.
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Affiliation(s)
- Zhian Zhang
- DNA Polymerase Technology Inc., 1508 South Grand Blvd., St. Louis, MO 63104, USA.
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Niederstätter H, Parson W. Fluorescent duplex allele-specific PCR and amplicon melting for rapid homogeneous mtDNA haplogroup H screening and sensitive mixture detection. PLoS One 2009; 4:e8374. [PMID: 20020064 PMCID: PMC2793010 DOI: 10.1371/journal.pone.0008374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Accepted: 11/23/2009] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND For large scale studies aiming at a better understanding of mitochondrial DNA (mtDNA), sequence variation in particular mt haplogroups (hgs) and population structure, reliable low-cost high-throughput genotyping assays are needed. Furthermore, methods facilitating sensitive mixture detection and relative quantification of allele proportions are indispensable for the study of heteroplasmy, mitochondrial sequence evolution, and mitochondrial disorders. Here the properties of a homogeneous competitive duplex allele specific PCR (ARMS) assay were scrutinized in the light of these requirements. METHODOLOGY/PRINCIPAL FINDINGS A duplex ARMS assay amplifying either the ancestral mtDNA 2706G allele (non-hg H samples) or the derived 7028C allele (hg H samples) in the presence of SYBR Green fluorescent reporter dye was developed and characterized. Product detection, allele calling, and hg inference were based on the amplicon-characteristic melting-point temperatures obtained with on-line post-PCR fluorescent dissociation curve analysis (DCA). The analytical window of the assay covered at least 5 orders of magnitude of template DNA input with a detection limit in the low picogram range of genomic DNA. A set of forensically relevant test specimens was analyzed successfully. The presence of mtDNA mixtures was detected over a broad range of input DNA amounts and mixture ratios, and the estimation of allele proportions in samples with known total mtDNA content was feasible with limitations. A qualified DNA analyst successfully analyzed approximately 2,200 DNA extracts within three regular working days, without using robotic lab-equipment. By performing the amplification on-line, the assay also facilitated absolute mtDNA quantification. CONCLUSIONS Although this assay was developed just for a particular purpose, the approach is general in that it is potentially suitable in a broad variety of assay-layouts for many other applications, including the analysis of mixtures. Homogeneous ARMS-DCA is a valuable tool for large-volume studies targeting small numbers of single nucleotide polymorphisms (SNPs).
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Liang M, Liu X, Nakamura K, Chen X, Cheng D, Liu G, Dou S, Wang Y, Rusckowski M, Hnatowich DJ. A convenient thiazole orange fluorescence assay for the evaluation of DNA duplex hybridization stability. Mol Imaging Biol 2009; 11:439-45. [PMID: 19444399 DOI: 10.1007/s11307-009-0221-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2008] [Revised: 01/06/2009] [Accepted: 01/16/2009] [Indexed: 11/25/2022]
Abstract
OBJECTIVE A simple and rapid method for measuring the hybridization stability of duplexes of DNAs and other oligomers in different environments is described. When added to an oligomer duplex, the thiazole orange (TO) dye intercalates and in this state is fluorescent. Therefore, when duplex dissociation occurs, the release of TO results in a detectable change in fluorescence intensity. This assay was developed primarily to screen antisense oligomer duplexes that are stable in serum and in the cytoplasm but unstable in the presence of their target messenger RNA (mRNA). METHODS The two antisense oligomers of this investigation were both 25 mer phosphorothioate (PS) DNAs, one directed against the RIalpha mRNA and the other directed against the mdr1 mRNA. The former duplex was first used in the solution studies, in most cases duplexed with a 16 mer phosphodiester (PO) complementary DNA (i.e., PS-DNA25/PO-cDNA16). Both duplexes were then tested in a series of cell studies using SK-BR-3 (RIalpha+), KB-G2 (mdr1++), and KB-31 (mdr1+/-) cells. RESULTS Preliminary measurements in solution showed that maximum fluorescence was achieved when more than ten TO molecules were bound to each duplex. When a 25 mer PO-DNA or PO-RNA with the base sequence of the RIalpha mRNA was added, the dramatic change in fluorescence intensity that followed signified dissociation of the antisense DNA from the study duplex and reassociation with the target DNA. Kinetic measurements showed that this process was completed in about 3 min. Fluorescent measurements of SK-BR-3 (RIalpha+) cells incubated at 37 degrees C with the anti-RIalpha study duplex over time showed a maximum at the point where the loss of fluorescence due to dissociation of the study duplex, probably by an antisense mechanism, began to dominate over the increasing fluorescence due to continuing cellular accumulation. A similar result was observed in the KB-G2 (mdr1+) cells incubated with the anti-mdr1 study duplex. CONCLUSIONS When study duplexes shown to be stable in serum were incubated with their target cells, the assay successfully detected evidence of dissociation, most likely by an antisense mechanism. Thus, a TO fluorescence assay has been developed that is capable of detecting the dissociation of DNA duplexes.
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Affiliation(s)
- Minmin Liang
- Department of Radiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
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Kermekchiev MB, Kirilova LI, Vail EE, Barnes WM. Mutants of Taq DNA polymerase resistant to PCR inhibitors allow DNA amplification from whole blood and crude soil samples. Nucleic Acids Res 2009; 37:e40. [PMID: 19208643 PMCID: PMC2655666 DOI: 10.1093/nar/gkn1055] [Citation(s) in RCA: 169] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Potent PCR inhibitors in blood and soil samples can cause false negative results from PCR-based clinical and forensic tests. We show that the effect of these inhibitors is primarily upon Taq DNA polymerase, since mutational alteration of the polymerase can overcome the inhibition to the extent that no DNA purification is now required. An N-terminal deletion (Klentaq1) is some 10–100-fold inhibition resistant to whole blood compared to full-length, wild-type (w.t.) Taq, which is strongly inhibited by 0.1–1% blood. Further mutations at codon 708, both in Klentaq 1 and Taq, confer enhanced resistance to various inhibitors of PCR reactions, including whole blood, plasma, hemoglobin, lactoferrin, serum IgG, soil extracts and humic acid, as well as high concentrations of intercalating dyes. Blood PCR inhibitors can predominantly reduce the DNA extension speed of the w.t. Taq polymerase as compared to the mutant enzymes. Single-copy human genomic targets are readily amplified from whole blood or crude soil extract, without pretreatment to purify the template DNA, and the allowed increase in dye concentration overcomes fluorescence background and quenching in real-time PCR of blood.
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Zhang X, Liu S, Jiao K, Gao H, Shi Y. Rapid and cost-effective detection of sequence-specific DNA by monitoring the electrochemical response of 2'-deoxyguanosine 5'-triphosphate in a PCR sample. Analyst 2008; 133:1729-35. [PMID: 19082076 DOI: 10.1039/b808880b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This study describes a novel strategy for rapid and cost-effective detection of sequence-specific DNA based upon the essential utility of the polymerase chain reaction (PCR) and electrochemical technologies. A dramatic enhancement of the anodic peak current (i(pa)) and a visible decrease of overpotential towards free 2'-deoxyguanosine 5'-triphosphate (dGTP) could be realized on a glassy carbon electrode modified with short single-walled carbon nanotubes (S-SWNT/GCE). Thereby, the concentration of the free dGTP in the PCR sample mixture could be determined sensitively. The i(pa) of the free dGTP decreased remarkably after a successful PCR amplification owing to the participation of the free dGTP as one of the reactive substrates for the PCR products, namely dsDNA. Based upon this response change of the free dGTP before and after incorporation in PCR, a novel method aiming at detecting PCR results was established. One transgenic maize sample as a model was successfully detected by employing the specific sequences of 35S promoter from cauliflower mosaic virus (CaMV35S) gene and nopaline synthase (NOS) gene as markers. The result was in good accordance with that obtained with gel electrophoresis.
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Affiliation(s)
- Xuzhi Zhang
- Key Laboratory of Eco-Chemical Engineering of Ministry of Education, College of Chemistry & Molecular Engineering, Qingdao University of Science & Technology, Qingdao, PR China
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Shaik GM, Dráberová L, Dráber P, Boubelík M, Dráber P. Tetraalkylammonium derivatives as real-time PCR enhancers and stabilizers of the qPCR mixtures containing SYBR Green I. Nucleic Acids Res 2008; 36:e93. [PMID: 18606615 PMCID: PMC2528177 DOI: 10.1093/nar/gkn421] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Tetraalkylammonium (TAA) derivatives have been reported to serve as stabilizers of asymmetrical cyanine dyes in aqueous solutions and to increase the yield and efficiency of polymerase chain reaction (PCR) detected by end-point analysis. In this study, we compared the ability of various TAA derivatives (with alkyl chain ranging from 1 to 5 carbons) and some other compounds to serve as enhancers of real-time PCR based on fluorescence detection from intercalating dye SYBR Green I (SGI). Our data indicate that TAA chlorides and some other TAA derivatives serve as potent enhancers of SGI-monitored real-time PCR. Optimal results were obtained with 10-16 mM tetrapropylammonium chloride. The effect of TAA compounds was dependent on the nature of counter ions present and composition of the reaction mixtures used. Based on measurements of SGI-generated fluorescence signal in the presence of PCR-amplified DNA fragments, oligonucleotide primers and/or various additives, we propose that TAA-derivatives reduce the binding of SGI to oligonucleotide primers and thus enhance primer-template interactions during annealing phase. Furthermore, these compounds serve as stabilizers of SGI-containing PCR mixtures. The combined data indicate that TAA derivatives might be a new class of additives contributing to robustness of real-time PCR monitored by asymmetrical cyanine dye SGI.
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Affiliation(s)
- Gouse M Shaik
- Department of Signal Transduction, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídenská 1083, 14220 Prague 4, Czech Republic
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Mao F, Leung WY, Xin X. Characterization of EvaGreen and the implication of its physicochemical properties for qPCR applications. BMC Biotechnol 2007; 7:76. [PMID: 17996102 PMCID: PMC2213645 DOI: 10.1186/1472-6750-7-76] [Citation(s) in RCA: 185] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Accepted: 11/09/2007] [Indexed: 11/19/2022] Open
Abstract
Background EvaGreen (EG) is a newly developed DNA-binding dye that has recently been used in quantitative real-time PCR (qPCR), post-PCR DNA melt curve analysis and several other applications. However, very little is known about the physicochemical properties of the dye and their relevance to the applications, particularly to qPCR and post PCR DNA melt curve analysis. In this paper, we characterized EG along with a widely used qPCR dye, SYBR Green I (SG), for their DNA-binding properties and stability, and compared their performance in qPCR under a variety of conditions. Results This study systematically compared the DNA binding profiles of the two dyes under different conditions and had these findings: a) EG had a lower binding affinity for both double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) than SG; b) EG showed no apparent preference for either GC- or AT-rich sequence while SG had a slight preference for AT-rich sequence; c) both dyes showed substantially lower affinity toward ssDNA than toward dsDNA and even lower affinity toward shorter ssDNA fragments except that this trend was more pronounced for EG. Our results also demonstrated that EG was stable both under PCR condition and during routine storage and handling. In the comparative qPCR study, both EG and SG exhibited PCR interference when used at high dye concentration, as evident from delayed Ct and/or nonspecific product formation. The problem worsened when the chain extension time was shortened or when the amplicon size was relatively long (>500 bp). However, qPCR using EG tolerated a significantly higher dye concentration, thus permitting a more robust PCR signal as well as a sharper and stronger DNA melt peak. These differences in qPCR performance between the two dyes are believed to be attributable to their differences in DNA binding profiles. Conclusion These findings suggest that an ideal qPCR dye should possess several DNA-binding characteristics, including a "just right" affinity for dsDNA and low or no affinity for ssDNA and short DNA fragments. The favorable DNA-binding profile of EG, coupled with its good stability and instrument-compatibility, should make EG a promising dye for qPCR and related applications.
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Affiliation(s)
- Fei Mao
- Biotium, Inc. Hayward, California, USA.
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Gudnason H, Dufva M, Bang D, Wolff A. Comparison of multiple DNA dyes for real-time PCR: effects of dye concentration and sequence composition on DNA amplification and melting temperature. Nucleic Acids Res 2007; 35:e127. [PMID: 17897966 PMCID: PMC2095797 DOI: 10.1093/nar/gkm671] [Citation(s) in RCA: 196] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The importance of real-time polymerase chain reaction (PCR) has increased steadily in clinical applications over the last decade. Many applications utilize SYBR Green I dye to follow the accumulation of amplicons in real time. SYBR Green I has, however, a number of limitations that include the inhibition of PCR, preferential binding to GC-rich sequences and effects on melting curve analysis. Although a few alternative dyes without some of these limitations have been recently proposed, no large-scale investigation into the properties of intercalating dyes has been performed. In this study, we investigate 15 different intercalating DNA dyes for their inhibitory effects on PCR, effects on DNA melting temperature and possible preferential binding to GC-rich sequences. Our results demonstrated that in contrast to the results of SYBR Green I, two intercalating dyes SYTO-13 and SYTO-82 do not inhibit PCR, show no preferential binding to GC rich sequences and do not influence melting temperature, Tm, even at high concentrations. In addition, SYTO-82 demonstrated a 50-fold lower detection limit in a dilution series assay. In conclusion, the properties of SYTO-82 and SYTO-13 will simplify the development of multiplex assays and increase the sensitivity of real-time PCR.
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Affiliation(s)
- Haukur Gudnason
- Department of Micro- and Nanotechnology, Technical University of Denmark, bldg. 345, DK-2800 Lyngby and Laboratory of Applied Micro-nanotechnology, Department of Poultry, Fish, and Fur Animals, The National Veterinary Institute, Technical University of Denmark, Hangovej 2, DK-8200 Aarhus N, Denmark
| | - Martin Dufva
- Department of Micro- and Nanotechnology, Technical University of Denmark, bldg. 345, DK-2800 Lyngby and Laboratory of Applied Micro-nanotechnology, Department of Poultry, Fish, and Fur Animals, The National Veterinary Institute, Technical University of Denmark, Hangovej 2, DK-8200 Aarhus N, Denmark
| | - D.D. Bang
- Department of Micro- and Nanotechnology, Technical University of Denmark, bldg. 345, DK-2800 Lyngby and Laboratory of Applied Micro-nanotechnology, Department of Poultry, Fish, and Fur Animals, The National Veterinary Institute, Technical University of Denmark, Hangovej 2, DK-8200 Aarhus N, Denmark
| | - Anders Wolff
- Department of Micro- and Nanotechnology, Technical University of Denmark, bldg. 345, DK-2800 Lyngby and Laboratory of Applied Micro-nanotechnology, Department of Poultry, Fish, and Fur Animals, The National Veterinary Institute, Technical University of Denmark, Hangovej 2, DK-8200 Aarhus N, Denmark
- *To whom correspondence should be addressed. Tel:+45 45256305 +45 45887762
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Hou CSJ, Milovic N, Godin M, Russo PR, Chakrabarti R, Manalis SR. Label-free microelectronic PCR quantification. Anal Chem 2007; 78:2526-31. [PMID: 16615760 DOI: 10.1021/ac0520689] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a robust and simple method for direct, label-free PCR product quantification using an integrated microelectronic sensor. The field-effect sensor can sequentially detect the intrinsic charge of multiple unprocessed PCR products and does not require sample processing or additional reagents in the PCR mixture. The sensor measures nucleic acid concentration in the PCR relevant range and specifically detects the PCR products over reagents such as Taq polymerase and nucleotide monomers. The sensor can monitor the product concentration at various stages of PCR and can generate a readout that resembles that of a real-time fluorescent measurement using an intercalating dye but without its potential inhibition artifacts. The device is mass-produced using standard semiconductor processes, can be reused for months, and integrates all sensing components directly on-chip. As such, our approach establishes a foundation for the direct integration of PCR-based in vitro biotechnologies with microelectronics.
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Affiliation(s)
- Chih-Sheng Johnson Hou
- Department of Electrical Engineering and Computer Science, Biological Engineering Division, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Hou CSJ, Godin M, Payer K, Chakrabarti R, Manalis SR. Integrated microelectronic device for label-free nucleic acid amplification and detection. LAB ON A CHIP 2007; 7:347-54. [PMID: 17330166 DOI: 10.1039/b617082j] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
We present an integrated microelectronic device for amplification and label-free detection of nucleic acids. Amplification by polymerase chain reaction (PCR) is achieved with on-chip metal resistive heaters, temperature sensors, and microfluidic valves. We demonstrate a rapid thermocycling with rates of up to 50 degrees C s(-1) and a PCR product yield equivalent to that of a bench-top system. Amplicons within the PCR product are detected by their intrinsic charge with a silicon field-effect sensor. Similar to existing optical approaches with intercalators such as SYBR Green, our sensing approach can directly detect standard double-stranded PCR product, while in contrast, our sensor does not require labeling reagents. By combining amplification and detection on the same device, we show that the presence or absence of a particular DNA sequence can be determined by converting the analog surface potential output of the field-effect sensor to a simple digital true/false readout.
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Affiliation(s)
- Chih-Sheng Johnson Hou
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Vianna ME, Horz HP, Gomes BPFA, Conrads G. In vivo evaluation of microbial reduction after chemo-mechanical preparation of human root canals containing necrotic pulp tissue. Int Endod J 2006; 39:484-92. [PMID: 16674744 DOI: 10.1111/j.1365-2591.2006.01121.x] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
AIM To determine in vivo, the degree of microbial reduction after chemo-mechanical preparation of human root canals containing necrotic pulp tissue when using two endodontic irrigating reagents, sodium hypochlorite (NaOCl) or chlorhexidine gel (CHX). METHODOLOGY Thirty-two single rooted teeth with necrotic pulp were divided into two groups. One group (n=16) was irrigated with 2.5% NaOCl, whilst the other group (n=16) was irrigated with 2% CHX gel. Assessment of the bacterial load was accomplished by use of real-time quantitative-polymerase chain reaction (RTQ-PCR) directed against the small subunit ribosomal DNA using the SYBRGreen and TaqMan formats. Statistical analysis was performed using the Mann-Whitney test. For contrast, bacterial load was also determined by traditional culture techniques. RESULTS The bacterial load was reduced substantially in both groups (over 96%). However, using RTQ-PCR the bacterial load before and after chemo-mechanical preparation was greater when compared with evaluation using colony forming units (CFU). Furthermore, as measured by RTQ-PCR, the bacterial reduction in the NaOCl-group (SYBRGreen 99.99%; TaqMan: 99.63%) was significantly greater (P<0.01) than in the CHX-group (SYBRGreen 96.62%; TaqMan: 96.60%). According to culture technique 75% of cases were free of bacteria after chemo-mechanical preparation in the NaOCl-group, whilst 50% of cases were bacteria free in the CHX-group. CONCLUSION NaOCl has not only a higher capacity to kill microorganisms but is also more able to remove cells from the root canal.
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Affiliation(s)
- M E Vianna
- Endodontic Area, Department of Restorative Dentistry, Piracicaba Dental School, State University of Campinas, Piracicaba, SP, Brazil, and Department of Medical Microbiology, RWTH Aachen University Hospital, Germany
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Renouf V, Claisse O, Lonvaud-Funel A. rpoB gene: a target for identification of LAB cocci by PCR-DGGE and melting curves analyses in real time PCR. J Microbiol Methods 2006; 67:162-70. [PMID: 16626824 DOI: 10.1016/j.mimet.2006.03.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2005] [Revised: 03/06/2006] [Accepted: 03/07/2006] [Indexed: 11/25/2022]
Abstract
Lactic acid bacteria (LAB) are essential in the quality of many fermented beverages like beer, cider and wine. In the two later cases, they convert malic acid into lactic acid during the malolactic fermentation. After fermentation, microbial stabilization is needed to prevent the development of spoilage bacteria species. Among them, cocci lead to different alterations: Pediococcus sp., and some strains of Leuconostoc mesenteroides and Oenococcus oeni can produce exopolysaccharides which modify wine viscosity and lead to ropiness. They also can produce acetic acid, biogenic amine, ethyl carbamate and volatile phenols. Therefore detection and identification are crucial. Results of phenotypic tests and DNA-DNA probes are not accurate enough. 16S RNA gene which is currently used for bacterial species identification presents intraspecies heterogeneity. The rpoB gene is an alternative to this limitation. However previous PCR targeting partial sequence of rpoB gene could not delimit cocci species. Therefore we compared the rpoB gene sequence of the six main cocci species found in fermented beverages: P. damnosus, P. dextrinicus, P. parvulus, P. pentosaceus, L. mesenteroides and O. oeni. The most discriminating partial sequence of the rpoB gene was chosen for designing primers. By PCR-DGGE the reliability of these primers was verified. It was controlled in a mixture of several cocci and other lactic acid bacteria (Lactobacillus sp.). Then we adapted the primers and the PCR conditions in order to achieve the identification of cocci species by real time PCR program including the fluorescent dye SYBR Green I, which gives faster results. PCR melt curves were established and a specific T(m) was attributed to each species.
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Affiliation(s)
- Vincent Renouf
- UMR oenologie-ampélologie, INRA-Université Victor Segalen Bordeaux2, 351 cours de la libération, 33405 Talence cedex, France
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Horz HP, Vianna ME, Gomes BPFA, Conrads G. Evaluation of universal probes and primer sets for assessing total bacterial load in clinical samples: general implications and practical use in endodontic antimicrobial therapy. J Clin Microbiol 2005; 43:5332-7. [PMID: 16208011 PMCID: PMC1248440 DOI: 10.1128/jcm.43.10.5332-5337.2005] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
By re-examining 10 previously published "universal" PCR assays using the ARB phylogenetic software package and database with 41,000 16S rRNA gene sequences, we found that they differed considerably in their coverage of the domain Bacteria. We evaluated the broadest-range real-time quantitative PCR protocol for its efficacy in measuring the antimicrobial effects of endodontic treatments.
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Affiliation(s)
- H P Horz
- Division of Oral Microbiology and Immunology, Department of Operative and Preventive Dentistry & Peridontology, RWTH Aachen University Hospital, Aachen, Germany
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Monis PT, Giglio S, Saint CP. Comparison of SYTO9 and SYBR Green I for real-time polymerase chain reaction and investigation of the effect of dye concentration on amplification and DNA melting curve analysis. Anal Biochem 2005; 340:24-34. [PMID: 15802126 DOI: 10.1016/j.ab.2005.01.046] [Citation(s) in RCA: 222] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2004] [Indexed: 12/11/2022]
Abstract
Following the initial report of the use of SYBR Green I for real-time polymerase chain reaction (PCR) in 1997, little attention has been given to the development of alternative intercalating dyes for this application. This is surprising considering the reported limitations of SYBR Green I, which include limited dye stability, dye-dependent PCR inhibition, and selective detection of amplicons during DNA melting curve analysis of multiplex PCRs. We have tested an alternative to SYBR Green I and report the first detailed evaluation of the intercalating dye SYTO9. Our findings demonstrate that SYTO9 produces highly reproducible DNA melting curves over a broader range of dye concentrations than does SYBR Green I, is far less inhibitory to PCR than SYBR Green I, and does not appear to selectively detect particular amplicons. The low inhibition and high melting curve reproducibility of SYTO9 means that it can be readily incorporated into a conventional PCR at a broad range of concentrations, allowing closed tube analysis by DNA melting curve analysis. These features simplify the use of intercalating dyes in real-time PCR and the improved reproducibility of DNA melting curve analysis will make SYTO9 useful in a diagnostic context.
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Affiliation(s)
- Paul T Monis
- Microbiology Unit, Australian Water Quality Centre, Private Mail Bag 3, Salisbury, SA 5108, Australia.
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Monis PT, Giglio S. Nucleic acid amplification-based techniques for pathogen detection and identification. INFECTION GENETICS AND EVOLUTION 2005; 6:2-12. [PMID: 16169776 PMCID: PMC7106022 DOI: 10.1016/j.meegid.2005.08.004] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2005] [Revised: 07/29/2005] [Accepted: 08/01/2005] [Indexed: 11/28/2022]
Abstract
Nucleic acid amplification techniques have revolutionised diagnostic and research industries. Current technologies that allow the detection of amplification in real-time are fast becoming industry standards, particularly in a diagnostic context. In this review, we describe and explore the application of numerous real-time detection chemistries and amplification techniques for pathogen detection and identification, including the polymerase chain reaction, nucleic acid sequence-based amplification, strand displacement amplification and the ligase chain reaction. The emergence of newer technologies, such as lab-on-a-chip devices and photo-cleavable linkers, is also discussed.
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Affiliation(s)
- Paul T Monis
- Australian Water Quality Centre, South Australian Water Corporation, Microbiology Unit, Salisbury, SA 5108, Australia.
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Monis PT, Giglio S, Keegan AR, Andrew Thompson RC. Emerging technologies for the detection and genetic characterization of protozoan parasites. Trends Parasitol 2005; 21:340-6. [PMID: 15925542 DOI: 10.1016/j.pt.2005.05.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2005] [Revised: 04/04/2005] [Accepted: 05/10/2005] [Indexed: 11/21/2022]
Abstract
The development and adaptation of new technologies for the genetic characterization and identification of parasites continue to accelerate, providing an increasing number of research and analytical tools. We review emerging technologies that have applications in this area, including real-time PCR and microarrays, and discuss the fundamental principles of some of these technologies and how they are applied to characterize parasites. We give special consideration to the application of genetic data to biological questions, where selection of the most appropriate technique depends on the biological question posed by the investigator.
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Affiliation(s)
- Paul T Monis
- Australian Water Quality Centre, South Australian Water Corporation, Private Mail Bag 3, Salisbury, South Australia 5108, Australia.
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Pickett MA, Everson JS, Pead PJ, Clarke IN. The plasmids of Chlamydia trachomatis and Chlamydophila pneumoniae (N16): accurate determination of copy number and the paradoxical effect of plasmid-curing agents. Microbiology (Reading) 2005; 151:893-903. [PMID: 15758234 DOI: 10.1099/mic.0.27625-0] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A 7·5 kbp cryptic plasmid is found in almost all isolates of Chlamydia trachomatis. Real-time PCR assays, using TaqMan chemistry, were set up to quantify accurately both the chlamydial plasmid and the single copy, chromosomal omcB gene in the infectious, elementary bodies (EBs) of C. trachomatis L1 440. Plasmid copy number was also determined in the EBs of six other lymphogranuloma venereum (LGV) isolates (serovars L1–L3), ten trachoma isolates (serovars A–C) and nine urogenital isolates (serovars D–J). The results indicated an average plasmid copy number of 4·0±0·8 (mean±95 % confidence interval) plasmids per chromosome. During the chlamydial developmental cycle, up to 7·6 plasmids per chromosome were detected, indicating an increased plasmid copy number in the actively replicating reticulate bodies. Attempts to eliminate the plasmid from strain L1 440 using the plasmid-curing agents ethidium bromide, acridine orange or imipramine/novobiocin led to a paradoxical increase in plasmid copy number. It is speculated that the stress induced by chemical curing agents may stimulate the activity of plasmid-encoded replication (Rep) proteins. In contrast to C. trachomatis, only a single isolate of Chlamydophila pneumoniae bears a plasmid. C. pneumoniae strain N16 supports a 7·4 kbp plasmid in which ORF1, encoding one of the putative Rep proteins, is disrupted by a deletion and split into two smaller ORFs. Similar assay techniques revealed 1·3±0·2 plasmids per chromosome (mean±95 % confidence interval) in EBs of this strain. These findings are in agreement with the hypothesis that the ORF1-encoded protein is involved in, but not essential for, plasmid replication and control of copy number.
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Affiliation(s)
- Mark A Pickett
- Molecular Microbiology Group, University of Southampton Medical School, MP814, Southampton General Hospital, Hampshire SO16 6YD, UK
| | - J Sylvia Everson
- Molecular Microbiology Group, University of Southampton Medical School, MP814, Southampton General Hospital, Hampshire SO16 6YD, UK
| | - Patrick J Pead
- Molecular Microbiology Group, University of Southampton Medical School, MP814, Southampton General Hospital, Hampshire SO16 6YD, UK
| | - Ian N Clarke
- Molecular Microbiology Group, University of Southampton Medical School, MP814, Southampton General Hospital, Hampshire SO16 6YD, UK
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Dehainault C, Laugé A, Caux-Moncoutier V, Pagès-Berhouet S, Doz F, Desjardins L, Couturier J, Gauthier-Villars M, Stoppa-Lyonnet D, Houdayer C. Multiplex PCR/liquid chromatography assay for detection of gene rearrangements: application to RB1 gene. Nucleic Acids Res 2004; 32:e139. [PMID: 15477586 PMCID: PMC524313 DOI: 10.1093/nar/gnh137] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Screening for large gene rearrangements is established as an important part of molecular medicine but is also challenging. A variety of robust methods can detect whole-gene deletions, but will fail to detect more subtle rearrangements that may involve a single exon. In this paper, we describe a new, versatile and robust method to assess exon copy number, called multiplex PCR/liquid chromatography assay (MP/LC). Multiple exons are amplified using unlabeled primers, then separated by ion-pair reversed-phase high-performance liquid chromatography (IP-RP-HPLC), and quantitated by fluorescent detection using a post-column intercalation dye. The relative peak intensities for each target directly reflect exon copy number. This novel technique was used to screen a panel of 121 unrelated retinoblastoma patients who were tested previously using a reference strategy. MP/LC correctly scored all deletions and demonstrated a previously undetected RB1 duplication, the first to be described. MP/LC appears to be an easy, versatile, and cost-effective method, which is particularly relevant to denaturing HPLC (DHPLC) users since it broadens the spectrum of available applications on a DHPLC system.
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Affiliation(s)
- C Dehainault
- Service de Génétique Oncologique, Pathologie Moléculaire des Cancers, Institut Curie, Paris, France
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48
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Zipper H, Brunner H, Bernhagen J, Vitzthum F. Investigations on DNA intercalation and surface binding by SYBR Green I, its structure determination and methodological implications. Nucleic Acids Res 2004; 32:e103. [PMID: 15249599 PMCID: PMC484200 DOI: 10.1093/nar/gnh101] [Citation(s) in RCA: 479] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The detection of double-stranded (ds) DNA by SYBR Green I (SG) is important in many molecular biology methods including gel electrophoresis, dsDNA quantification in solution and real-time PCR. Biophysical studies at defined dye/base pair ratios (dbprs) were used to determine the structure-property relationships that affect methods applying SG. These studies revealed the occurrence of intercalation, followed by surface binding at dbprs above approximately 0.15. Only the latter led to a significant increase in fluorescence. Studies with poly(dA)* poly(dT) and poly(dG)* poly(dC) homopolymers showed sequence-specific binding of SG. Also, salts had a marked impact on SG fluorescence. We also noted binding of SG to single-stranded (ss) DNA, although SG/ssDNA fluorescence was at least approximately 11-fold lower than with dsDNA. To perform these studies, we determined the structure of SG by mass spectrometry and NMR analysis to be [2-[N-(3-dimethylaminopropyl)-N-propylamino]-4-[2,3-dihydro-3-methyl-(benzo-1,3-thiazol-2-yl)-methylidene]-1-phenyl-quinolinium]. For comparison, the structure of PicoGreen (PG) was also determined and is [2-[N-bis-(3-dimethylaminopropyl)-amino]-4-[2,3-dihydro-3-methyl-(benzo-1,3-thiazol-2-yl)-methylidene]-1-phenyl-quinolinium]+. These structure-property relationships help in the design of methods that use SG, in particular dsDNA quantification in solution and real-time PCR.
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Affiliation(s)
- Hubert Zipper
- Laboratory of Biochemistry, Institute for Interfacial Engineering, University of Stuttgart, 70569 Stuttgart, Germany
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49
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Rose'Meyer RB, Mellick AS, Garnham BG, Harrison GJ, Massa HM, Griffiths LR. The measurement of adenosine and estrogen receptor expression in rat brains following ovariectomy using quantitative PCR analysis. BRAIN RESEARCH. BRAIN RESEARCH PROTOCOLS 2003; 11:9-18. [PMID: 12697258 DOI: 10.1016/s1385-299x(02)00219-2] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In our laboratory we have developed a quantitative-polymerase chain reaction (Q-PCR) strategy to examine the differential expression of adenosine receptor (ADOR), A(1), A(2A), A(2B) and A(3), and estrogen receptors (ER) alpha and beta. Brain and uterine mRNA were first used to optimise specific amplification conditions prior to SYBR Green I real time analysis of receptor subtype expression. SYBR Green I provided a convenient and sensitive means of examining specific PCR amplification product in real time, and allowed the generation of standard curves from which relative receptor abundance could be determined. Real time Q-PCR analysis was then performed, to examine changes in receptor expression levels in brains of adult female Wistar rats 3-month post ovariectomy. Comparison with sham-operated age-matched control rats demonstrated both comparative and absolute-copy number changes in receptor levels. Evaluation of both analytical methods investigated 18S rRNA as an internal reference for comparative gene expression analysis in the brain. The results of this study revealed preferential repression of ADORA(2A) (>4-fold down) and consistent (>2-fold) down-regulation of ADORA(1), ADORA(3), and ER-beta, following ovariectomy. No change was found in ADORA(2B) or ER-alpha. Analysis of absolute copy number in this study revealed a correlation between receptor expression in response to ovariectomy, and relative receptor subtype abundance in the brain.
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MESH Headings
- Animals
- Brain/metabolism
- Down-Regulation/genetics
- Estrogen Receptor beta
- Estrogens/deficiency
- Female
- Gene Expression Regulation/genetics
- Ovariectomy
- Polymerase Chain Reaction/methods
- RNA, Messenger/analysis
- RNA, Messenger/metabolism
- RNA, Ribosomal, 18S/analysis
- RNA, Ribosomal, 18S/genetics
- Rats
- Rats, Wistar
- Receptor, Adenosine A2A
- Receptor, Adenosine A3
- Receptors, Estrogen/genetics
- Receptors, Purinergic P1/genetics
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Affiliation(s)
- Roselyn B Rose'Meyer
- School of Health Sciences, Griffith University, GCMC PMB 50, Gold Coast, QLD 9726, Australia.
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50
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Bahrami AR, Dickman MJ, Matin MM, Ashby JR, Brown PE, Conroy MJ, Fowler GJS, Rose JP, Sheikh QI, Yeung AT, Hornby DP. Use of fluorescent DNA-intercalating dyes in the analysis of DNA via ion-pair reversed-phase denaturing high-performance liquid chromatography. Anal Biochem 2002; 309:248-52. [PMID: 12413458 DOI: 10.1016/s0003-2697(02)00306-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
SYBR Green 1 is an asymmetrical cyanine DNA-binding dye that provides an opportunity for increasing the sensitivity of nucleic acid detection when used in conjunction with gel electrophoresis. In this paper, we summarize the general properties and specific uses of SYBR green 1 in ion-pair reversed-phase denaturing high-performance liquid chromatography (IP DHPLC). We describe several applications for the WAVE DHPLC platform that illustrate the generic potential of such intercalating dyes in mutation detection and gene expression profiling. We show that SYBR Green 1 obviates the need to use end-labeled oligodeoxynucleotides for the sensitive detection of nucleic acids during chromatography. Moreover the incorporation of SYBR Green 1 into samples and elution buffers does not impair resolution and has no significant effect on the retention times of DNA fragments compared with dye-free DHPLC.
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Affiliation(s)
- Ahmad R Bahrami
- Department of Molecular Biology, The Transgenomic Research Laboratory, Krebs Institute, Firth Court, Western Bank, Sheffield S10 2TN, UK
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