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Szczepaniak O, Ligaj M. May DNA analyses be biased by hidden oxidative damage? Voltammetric study of temperature and oxidation stress effect. PLoS One 2024; 19:e0305590. [PMID: 38875261 PMCID: PMC11178200 DOI: 10.1371/journal.pone.0305590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 06/01/2024] [Indexed: 06/16/2024] Open
Abstract
The analysis of nucleic acids is one of the fundamental parts of modern molecular biology and molecular diagnostics. The information collected predominantly depends on the condition of the genetic material. All potential damage induced by oxidative stress may affect the final results of the analysis of genetic material obtained using commonly used techniques such as polymerase chain reaction or sequencing. The aim of this work was to evaluate the effects of high temperature and pH on DNA structure in the context of the occurrence of oxidative damage, using square-wave voltammetry and two independent research protocols. We resulted in visible oxidation damage registered in acidic conditions after the thermal denaturation process (pH 4.7) with changes in the intensity of guanine and adenine signals. However, using phosphate buffer (pH 7.0) for DNA denaturation negatively affected the DNA structure, but without any oxidized derivatives present. This leads to the conclusion that oxidation occurring in the DNA melting process results in the formation of various derivatives of nucleobases, both electrochemically active and inactive. These derivatives may distort the results of molecular tests due to the possibility of forming complementary bonds with various nucleobases. For example, 8-oxoguanine can form pairs with both cytosine and adenine.
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Affiliation(s)
- Oskar Szczepaniak
- Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Poznań, Poland
| | - Marta Ligaj
- Department of Industrial Products and Packaging Quality, Poznań University of Economics and Business, Poznań, Poland
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Abdul Rashid JI, Yusof NA, Abdullah J, Shomiad Shueb RH. Strategies in the optimization of DNA hybridization conditions and its role in electrochemical detection of dengue virus (DENV) using response surface methodology (RSM). RSC Adv 2023; 13:18748-18759. [PMID: 37362605 PMCID: PMC10286818 DOI: 10.1039/d3ra00216k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/28/2023] [Indexed: 06/28/2023] Open
Abstract
In recent years, limited research has been conducted on enhancing DNA hybridization-based biosensor approaches using statistical models. This study explores the application of response surface methodology (RSM) to improve the performance of a DNA hybridization biosensor for dengue virus (DENV) detection. The biosensor is based on silicon nanowires decorated with gold nanoparticles (SiNWs/AuNPs) and utilizes methylene blue as a redox indicator. The DNA hybridization process between the immobilized DNA probe and the target DENV gene was monitored using differential pulse voltammetry (DPV) based on the reduction of methylene blue. Fourier-transform infrared spectroscopy (FTIR) and electrochemical impedance spectroscopy (EIS) were employed to confirm successful DNA hybridization events on the modified screen-printed gold electrode (SPGE) surface. Several parameters, including pH buffer, NaCl concentration, temperature, and hybridization time, were simultaneously optimized, with NaCl concentration having the most significant impact on DNA hybridization events. This study enhances the understanding of the role of each parameter in influencing DNA hybridization detection in electrochemical biosensors. The optimized biosensor demonstrated the ability to detect complementary oligonucleotide and amplified DENV gene concentrations as low as 0.0891 ng µL-1 (10 pM) and 2.8 ng µL-1, respectively. The developed biosensor shows promise for rapid clinical diagnosis of dengue virus infection.
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Affiliation(s)
- Jahwarhar Izuan Abdul Rashid
- Department of Chemistry and Biology, Centre for Defence Foundation Studies, National Defence University of Malaysia Sungai Besi Camp 57000 Kuala Lumpur Malaysia
| | - Nor Azah Yusof
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia Serdang Selangor 43400 Malaysia
| | - Jaafar Abdullah
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia Serdang Selangor 43400 Malaysia
| | - Rafidah Hanim Shomiad Shueb
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia 16150 Kubang Kerian Kelantan Malaysia
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Taufiq S, Waqar M, Sharif MN, Abbas SR. Towards portable rapid TB biosensor: Detecting Mycobacterium tuberculosis in raw sputum samples using functionalized screen printed electrodes. Bioelectrochemistry 2023; 150:108353. [PMID: 36603412 DOI: 10.1016/j.bioelechem.2022.108353] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Due to lack of robust, sensitive and low cost detection strategies, Tuberculosis (TB) remains a significant global health issue. WHO reports 1.5 million deaths per year, ∼80 % cases occur in low- to middle-income countries, where resource limitations complicate the diagnosis. Robust detection of TB infection is important to contain the spread and treat disease. We developed a label-free DNA biosensor based on commercially available screen printed electrodes (SPEs) (DropSens and Zensors) that can detect TB robustly, sensitively, and specifically via DNA hybridization with its IS6110 gene marker, in purified DNA and raw sputum samples. The fabricated biosensor was morphologically characterized by scanning electron microscopy coupled with energy dispersive X-ray spectroscopy. Cyclic voltammetry and Differential Pulse Voltammetry was used for electrochemical analysis of the modified electrode. The fabricated biosensor demonstrated satisfactory selectivity for Mycobacterium tuberculosis (MTB) against Salmonella typhimurium and Escherichia coli and was able to detect MTB; the limit of detection (LOD) of 1.90 nM with R2 = 0.993, when analyzed over a range of concentrations of DNA (0.5-10 nM). It is being exploited to detect target MTB from clinical samples, without DNA purification. The approach is robust, sensitive, and specific, requires low sample volume and can be extended towards portable point of care diagnosis of TB.
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Affiliation(s)
- Saman Taufiq
- Department of Industrial Biotechnology, Atta ur Rahman School of Applied Biosciences, National University of Science and Technology (NUST), Islamabad, Pakistan; Biosensors and Therapeutics Lab, School of Interdisciplinary Engineering and Sciences (SINES), NUST, Islamabad, Pakistan.
| | - Muhammad Waqar
- Department of Industrial Biotechnology, Atta ur Rahman School of Applied Biosciences, National University of Science and Technology (NUST), Islamabad, Pakistan
| | - Muhammad Nauman Sharif
- Department of Industrial Biotechnology, Atta ur Rahman School of Applied Biosciences, National University of Science and Technology (NUST), Islamabad, Pakistan; Biosensors and Therapeutics Lab, School of Interdisciplinary Engineering and Sciences (SINES), NUST, Islamabad, Pakistan.
| | - Shah Rukh Abbas
- Department of Industrial Biotechnology, Atta ur Rahman School of Applied Biosciences, National University of Science and Technology (NUST), Islamabad, Pakistan; Biosensors and Therapeutics Lab, School of Interdisciplinary Engineering and Sciences (SINES), NUST, Islamabad, Pakistan.
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Mehrannia L, Khalilzadeh B, Rahbarghazi R, Milani M, Saydan Kanberoglu G, Yousefi H, Erk N. Electrochemical Biosensors as a Novel Platform in the Identification of Listeriosis Infection. BIOSENSORS 2023; 13:216. [PMID: 36831982 PMCID: PMC9954029 DOI: 10.3390/bios13020216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/17/2023] [Accepted: 01/29/2023] [Indexed: 06/18/2023]
Abstract
Listeria monocytogenes (L.M.) is a gram-positive bacillus with wide distribution in the environment. This bacterium contaminates water sources and food products and can be transmitted to the human population. The infection caused by L.M. is called listeriosis and is common in pregnant women, immune-deficient patients, and older adults. Based on the released statistics, listeriosis has a high rate of hospitalization and mortality; thus, rapid and timely detection of food contamination and listeriosis cases is necessary. During the last few decades, biosensors have been used for the detection and monitoring of varied bacteria species. These devices are detection platforms with great sensitivity and low detection limits. Among different types of biosensors, electrochemical biosensors have a high capability to circumvent several drawbacks associated with the application of conventional laboratory techniques. In this review article, different electrochemical biosensor types used for the detection of listeriosis were discussed in terms of actuators, bioreceptors, specific working electrodes, and signal amplification. We hope that this review will facilitate researchers to access a complete and comprehensive template for pathogen detection based on the different formats of electrochemical biosensors.
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Affiliation(s)
- Leila Mehrannia
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz 51666-14733, Iran
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz 51666-14733, Iran
| | - Balal Khalilzadeh
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz 51666-14733, Iran
| | - Reza Rahbarghazi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz 51666-14733, Iran
- Department of Applied Cell Sciences, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz 51666-14733, Iran
| | - Morteza Milani
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz 51666-14733, Iran
| | | | - Hadi Yousefi
- Department of Basic Medical Sciences, Khoy University of Medical Sciences, Khoy 58167-53464, Iran
| | - Nevin Erk
- Department of Analytical Chemistry, Faculty of Pharmacy, Ankara University, Ankara 06560, Turkey
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5
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Büyüksünetçi YT, Anık Ü. Electro-Nano Diagnostic Platform Based on Antibody-Antigen Interaction: An Electrochemical Immunosensor for Influenza A Virus Detection. BIOSENSORS 2023; 13:176. [PMID: 36831942 PMCID: PMC9953406 DOI: 10.3390/bios13020176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/16/2023] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
H1N1 is a kind of influenza A virus that causes serious health issues throughout the world. Its symptoms are more serious than seasonal flu and can sometimes be lethal. For this reason, rapid, accurate, and effective diagnostic tests are needed. In this study, an electrochemical immunosensor for the sensitive, selective, and practical detection of the H1N1 virus was developed. The sensor platform included multi-walled carbon nanotube gold-platinum (MWCNT-Au-Pt) hybrid nanomaterial and anti-hemagglutinin (anti-H1) monoclonal antibody. For the construction of this biosensor, a gold screen-printed electrode (AuSPE) was used as a transducer. Firstly, AuSPE was modified with MWCNT-Au-Pt hybrid nanomaterial via drop casting. Anti-H1 antibody was immobilized onto the electrode surface after the modification process with cysteamine was applied. Then, the effect of the interaction time with cysteamine for surface modification was investigated. Following that, the experimental parameters, such as the amount of hybrid nanomaterial and the concentration of anti-H1 were optimized. Under the optimized conditions, the analytical characteristics of the developed electrochemical immunosensor were investigated for the H1N1 virus by using electrochemical impedance spectroscopy. As a result, a linear range was obtained between 2.5-25.0 µg/mL with a limit of the detection value of 3.54 µg/mL. The relative standard deviation value for 20 µg/mL of the H1N1 virus was also calculated and found as 0.45% (n = 3). In order to determine the selectivity of the developed anti-H1-based electrochemical influenza A immunosensor, the response of this system towards the H3N2 virus was investigated. The matrix effect was also investigated by using synthetic saliva supplemented with H1N1 virus.
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Affiliation(s)
- Yudum Tepeli Büyüksünetçi
- Sensors, Biosensors and Nano-Diagnostic Laboratory, Research Laboratory Center, Mugla Sitki Kocman University, Kotekli, 48000 Mugla, Turkey
| | - Ülkü Anık
- Sensors, Biosensors and Nano-Diagnostic Laboratory, Research Laboratory Center, Mugla Sitki Kocman University, Kotekli, 48000 Mugla, Turkey
- Chemistry Department, Faculty of Science, Mugla Sitki Kocman University, Kotekli, 48000 Mugla, Turkey
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Szczepaniak O, Ligaj M, Stuper-Szablewska K, Kobus-Cisowska J. Genoprotective effect of cornelian cherry (Cornus mas L.) phytochemicals, electrochemical and ab initio interaction study. Biomed Pharmacother 2022; 152:113216. [PMID: 35665669 DOI: 10.1016/j.biopha.2022.113216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/24/2022] [Accepted: 05/26/2022] [Indexed: 11/02/2022] Open
Abstract
Cornelian cherry (Cornus mas L.) has broad and multidimensional potential in preventing civilisational diseases. Part of these diseases results from DNA oxidative mutations. Thus, the paper aimed to predict how phenolics present in C. mas may interact with dsDNA in ab initio experiment and to check the effect of different cornelian cherry extracts on DNA structure and DNA oxidation. A special research model was designed using biosensor with a carbonpaste electrode. We resulted in various effects observed for phenolics and the extracts. Flavonoids, but of vitexin interacted with declining energy of the DNA models and liability of DNA oxidation. However, for 8-oxoguaniosine the trend was the opposite. Among the evaluated extracts, water-ethanolic extracts caused decline in adenine and guanine signals after dsDNA exposition on the extract. Principal component analysis showed that alcoholic extracts of cv. Szafer and Słowianin, which were rich in apigenin and kaempferol exhibit mild genoprotective effect.
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Affiliation(s)
- Oskar Szczepaniak
- Department of Gastronomy Sciences and Functional Foods, Poznań University of Life Sciences, Poland.
| | - Marta Ligaj
- Department of Non-Food Products Quality and Packaging Development, Poznań University of Economics and Business, Poland
| | | | - Joanna Kobus-Cisowska
- Department of Gastronomy Sciences and Functional Foods, Poznań University of Life Sciences, Poland
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Kanapathy S, Obande GA, Chuah C, Shueb RH, Yean CY, Banga Singh KK. Sequence-Specific Electrochemical Genosensor for Rapid Detection of blaOXA-51-like Gene in Acinetobacter baumannii. Microorganisms 2022; 10:1413. [PMID: 35889132 PMCID: PMC9322073 DOI: 10.3390/microorganisms10071413] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/04/2022] [Accepted: 07/07/2022] [Indexed: 11/26/2022] Open
Abstract
Acinetobacter baumannii (A. baumannii) are phenotypically indistinguishable from the Acinetobacter calcoaceticus−A. baumannii (ACB) complex members using routine laboratory methods. Early diagnosis plays an important role in controlling A. baumannii infections and this could be assisted by the development of a rapid, yet sensitive diagnostic test. In this study, we developed an enzyme-based electrochemical genosensor for asymmetric PCR (aPCR) amplicon detection of the blaOXA-51-like gene in A. baumannii. A. baumanniiblaOXA-51-like gene PCR primers were designed, having the reverse primer modified at the 5′ end with FAM. A blaOXA-51-like gene sequence-specific biotin labelled capture probe was designed and immobilized using a synthetic oligomer (FAM-labelled) deposited on the working electrode of a streptavidin-modified, screen-printed carbon electrode (SPCE). The zot gene was used as an internal control with biotin and FAM labelled as forward and reverse primers, respectively. The blaOXA-51-like gene was amplified using asymmetric PCR (aPCR) to generate single-stranded amplicons that were detected using the designed SPCE. The amperometric current response was detected with a peroxidase-conjugated, anti-fluorescein antibody. The assay was tested using reference and clinical A. baumannii strains and other nosocomial bacteria. The analytical sensitivity of the assay at the genomic level and bacterial cell level was 0.5 pg/mL (1.443 µA) and 103 CFU/mL, respectively. The assay was 100% specific and sensitive for A. baumannii. Based on accelerated stability performance, the developed genosensor was stable for 1.6 years when stored at 4 °C and up to 28 days at >25 °C. The developed electrochemical genosensor is specific and sensitive and could be useful for rapid, accurate diagnosis of A. baumannii infections even in temperate regions.
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Affiliation(s)
- Swarnaletchumi Kanapathy
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia; (S.K.); (C.C.); (R.H.S.); (C.Y.Y.)
| | - Godwin Attah Obande
- Department of Microbiology, Faculty of Science, Federal University of Lafia, Lafia 950101, Nasarawa State, Nigeria;
| | - Candy Chuah
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia; (S.K.); (C.C.); (R.H.S.); (C.Y.Y.)
- Faculty of Health Sciences, Universiti Teknologi MARA, Kampus Bertam, Kepala Batas 13200, Penang, Malaysia
| | - Rafidah Hanim Shueb
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia; (S.K.); (C.C.); (R.H.S.); (C.Y.Y.)
| | - Chan Yean Yean
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia; (S.K.); (C.C.); (R.H.S.); (C.Y.Y.)
| | - Kirnpal Kaur Banga Singh
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia; (S.K.); (C.C.); (R.H.S.); (C.Y.Y.)
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8
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Advances in Electrochemical Techniques for the Detection and Analysis of Genetically Modified Organisms: An Analysis Based on Bibliometrics. CHEMOSENSORS 2022. [DOI: 10.3390/chemosensors10050194] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Since the first successful transgenic plants obtained in 1983, dozens of plants have been tested. On the one hand, genetically modified plants solve the problems of agricultural production. However, due to exogenous genes of transgenic plants, such as its seeds or pollen drift, diffusion between populations will likely lead to superweeds or affect the original traits. The detection technology of transgenic plants and their products have received considerable attention. Electrochemical sensing technology is a fast, low-cost, and portable analysis technology. This review interprets the application of electrochemical technology in the analysis and detection of transgenic products through bibliometrics. A total of 83 research articles were analyzed, spanning 2001 to 2021. We described the different stages in the development history of the subject and the contributions of countries and institutions to the topic. Although there were more annual publications in some years, there was no explosive growth in any period. The lack of breakthroughs in this technology is a significant factor in the lack of experts from other fields cross-examining the subject. Through keyword co-occurrence analysis, different research directions on this topic were discussed. The use of nanomaterials with excellent electrical conductivity allows for more sensitive detection of GM crops by electrochemical sensors. Furthermore, co-citation analysis was used to interpret the most popular reports on the topic. In the end, we predict the future development of this topic according to the analysis results.
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Mahadhy A, Mattiasson B, StåhlWernersson E, Hedström M. Evaluation of Polytyramine Film and 6-Mercaptohexanol Self-Assembled Monolayers as the Immobilization Layers for a Capacitive DNA Sensor Chip: A Comparison. SENSORS 2021; 21:s21238149. [PMID: 34884153 PMCID: PMC8662409 DOI: 10.3390/s21238149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 11/16/2022]
Abstract
The performance of a biosensor is associated with the properties of an immobilization layer on a sensor chip. In this study, gold sensor chips were modified with two different immobilization layers, polytyramine film and 6-mercaptohexanol self-assembled monolayer. The physical, electrochemical and analytical properties of polytyramine film and mercaptohexanol self-assembled monolayer modified gold sensor chips were studied and compared. The study was conducted using atomic force microscopy, cyclic voltammetry and a capacitive DNA-sensor system (CapSenze™ Biosystem). The results obtained by atomic force microscopy and cyclic voltammetry indicate that polytyramine film on the sensor chip surface possesses better insulating properties and provides more spaces for the immobilization of the capture probe than a mercaptohexanol self-assembled monolayer. A capacitive DNA sensor hosting a polytyramine single-stranded DNA-modified sensor chip displayed higher sensitivity and larger signal amplitude than that of a mercaptohexanol single-stranded DNA-modified sensor chip. The linearity responses for polytyramine single-stranded DNA- and mercaptohexanol single-stranded DNA-modified sensor chips were obtained at log concentration ranges, equivalent to 10-12 to 10-8 M and 10-10 to 10-8 M, with detection limits of 4.0 × 10-13 M and 7.0 × 10-11 M of target complementary single-stranded DNA, respectively. Mercaptohexanol single-stranded DNA- and polytyramine single-stranded DNA-modified sensor chips exhibited a notable selectivity at an elevated hybridization temperature of 50 °C, albeit the signal amplitudes due to the hybridization of the target complementary single-stranded DNA were reduced by almost 20% and less than 5%, respectively.
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Affiliation(s)
- Ally Mahadhy
- Department of Biotechnology, Lund University, 22100 Lund, Sweden; (A.M.); (E.S.); (M.H.)
- Department of Molecular Biology and Biotechnology, University of Dar es Salaam, Dar es Salaam 16103, Tanzania
| | - Bo Mattiasson
- Department of Biotechnology, Lund University, 22100 Lund, Sweden; (A.M.); (E.S.); (M.H.)
- CapSenze Biosystem AB, Värmö 5520, 26873 Billeberga, Sweden
- Correspondence: ; Tel.: +46-46-222-8264 or +46-70-605-9830
| | - Eva StåhlWernersson
- Department of Biotechnology, Lund University, 22100 Lund, Sweden; (A.M.); (E.S.); (M.H.)
| | - Martin Hedström
- Department of Biotechnology, Lund University, 22100 Lund, Sweden; (A.M.); (E.S.); (M.H.)
- CapSenze Biosystem AB, Värmö 5520, 26873 Billeberga, Sweden
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Starodub TN, Fenske D, Fuhr O, Miskiewicz S, Kazheva ON, Starodub VA. Structure and Properties of Anion-Radical Salt of 7,7,8,8-Tetracyanoquinodimethane with N-Methyl-2,2'-dipyridyl Cation. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521030251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Hrbek V, Zdenkova K, Jilkova D, Cermakova E, Jiru M, Demnerova K, Pulkrabova J, Hajslova J. Authentication of Meat and Meat Products Using Triacylglycerols Profiling and by DNA Analysis. Foods 2020; 9:foods9091269. [PMID: 32927765 PMCID: PMC7555453 DOI: 10.3390/foods9091269] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 09/06/2020] [Accepted: 09/08/2020] [Indexed: 11/16/2022] Open
Abstract
Two alternative, complementary analytical strategies were successfully used to identify the most common meat species—beef, pork and chicken—in meat products. The first innovative high-throughput approach was based on triacylglycerols fingerprinting by direct analysis in real time coupled with high-resolution mass spectrometry (DART–HRMS). The second was the classic commonly used DNA analysis based on the use of nuclear or mitochondrial DNA in multiplex polymerase chain reaction (mPCR). The DART–HRMS method represents a rapid, high throughput screening method and was shown to have a good potential for the authentication of meat products. Nevertheless, it should be noted that due to a limited number of samples in this pilot study, we present here a proof of concept. More samples must be analyzed by DART–HRMS to build a robust classification model applicable for reliable authentication. To verify the DART–HRMS results, all samples were analyzed by PCRs. Good compliance in samples classification was documented. In routine practice under these conditions, screening based on DART–HRMS could be used for identification of suspect samples, which could be then examined and validated by accurate PCRs. In this way, saving of both labor and cost could be achieved. In the final phase, commercially available meat products from the Czech market were tested using this new strategy. Canned meats—typical Czech sausages and luncheon meats, all with declared content of beef, pork and chicken meat—were used. Compliance with the label declaration was confirmed and no adulteration was found.
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Affiliation(s)
- Vojtech Hrbek
- Department of Food Analysis and Nutrition, University of Chemistry and Technology, Technicka 5, 166 28 Prague 6, Czech Republic; (V.H.); (M.J.); (J.P.); (J.H.)
| | - Kamila Zdenkova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Technicka 5, 166 28 Prague 6, Czech Republic; (E.C.); (K.D.)
- Correspondence:
| | - Diliara Jilkova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Technicka 5, 166 28 Prague 6, Czech Republic; (E.C.); (K.D.)
- Research Department, Food Research Institute Prague, Radiová 1285/7, 10231 Prague 10, Czech Republic;
| | - Eliska Cermakova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Technicka 5, 166 28 Prague 6, Czech Republic; (E.C.); (K.D.)
| | - Monika Jiru
- Department of Food Analysis and Nutrition, University of Chemistry and Technology, Technicka 5, 166 28 Prague 6, Czech Republic; (V.H.); (M.J.); (J.P.); (J.H.)
| | - Katerina Demnerova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Technicka 5, 166 28 Prague 6, Czech Republic; (E.C.); (K.D.)
| | - Jana Pulkrabova
- Department of Food Analysis and Nutrition, University of Chemistry and Technology, Technicka 5, 166 28 Prague 6, Czech Republic; (V.H.); (M.J.); (J.P.); (J.H.)
| | - Jana Hajslova
- Department of Food Analysis and Nutrition, University of Chemistry and Technology, Technicka 5, 166 28 Prague 6, Czech Republic; (V.H.); (M.J.); (J.P.); (J.H.)
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12
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Zhou L, Arugula MA, Chin BA, Simonian AL. Simultaneous Surface Plasmon Resonance/Fluorescence Spectroelectrochemical in Situ Monitoring of Dynamic Changes on Functional Interfaces: A Study of the Electrochemical Proximity Assay Model System. ACS APPLIED MATERIALS & INTERFACES 2018; 10:41763-41772. [PMID: 30379060 DOI: 10.1021/acsami.8b13993] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Understanding the chemical composition and morphology of interfaces plays a vital role in the development of sensors, drug delivery systems, coatings for biomedical implants, and so forth. In many cases, the interface characterization can be performed by a combination of electrochemical and one of the optical techniques. In this study, we further enhanced capabilities in probing interfaces by combining electrochemical characterization with multiple optical techniques, that is, surface plasmon resonance (SPR) and fluorescence spectroscopy. This new combination was utilized to study the electrochemical proximity assay (ECPA)-a recently developed protein recognition strategy for the point-of-care test. The SPR/fluorescence spectroelectrochemical technique has achieved not only recognition of binding components involved in the ECPA model system, estimation of their thicknesses and surface coverages, but more importantly, highly reliable in situ monitoring of dynamic changes of components involved in interfacial binding via cross-validation and confirmation from three simultaneously generated signals-SPR, fluorescence, and electrochemistry. In addition, the obtained corresponding proportions among magnitudes of three signals provide crucial information for future studies on simultaneous characterization of multiple components in one step and differentiation of nonspecific binding events. Another advantage using this technique is that the excitation of fluorescence is not only confined by surface plasmons, but by photons, so the fluorescence information can be also gained as the distance of fluorophores from the surface exceeds the decay length of surface plasmons.
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Affiliation(s)
- Lang Zhou
- Materials Research and Education Center, Department of Mechanical Engineering , Auburn University , Auburn , Alabama 36849 , United States
| | - Mary A Arugula
- Materials Research and Education Center, Department of Mechanical Engineering , Auburn University , Auburn , Alabama 36849 , United States
| | - Bryan A Chin
- Materials Research and Education Center, Department of Mechanical Engineering , Auburn University , Auburn , Alabama 36849 , United States
| | - Aleksandr L Simonian
- Materials Research and Education Center, Department of Mechanical Engineering , Auburn University , Auburn , Alabama 36849 , United States
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Spychaj A, Pospiech E, Iwańska E, Montowska M. Detection of allergenic additives in processed meat products. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2018; 98:4807-4815. [PMID: 29675958 DOI: 10.1002/jsfa.9083] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 03/13/2018] [Accepted: 04/15/2018] [Indexed: 06/08/2023]
Abstract
Allergic responses to food components are an increasing problem all over the world. It is therefore important to protect people who are vulnerable to food allergens against accidental and unintended consumption of products containing allergic ingredients. The meat industry commonly uses various allergic additives in the production of processed products, such as legumes (soy, peas, beans), milk and egg preparations, cereals containing gluten (wheat, rye, barley and oats), and spices (celery and mustard). These meat additives have specific technological properties, which help to create a texture or flavor profile, or affect the nutritional value, although some of them, such as soy, mustard, milk and egg white proteins, can cause severe allergic reactions. The aim of this paper is to discuss the application of various recently established methods of detection of allergenic additives in processed meat products - for instance cold cuts and sausages. The new methods are based mainly on protein, DNA, and isoflavones or phytic acid analysis. The article also characterizes the latest trends in the development of research on methods that would enable quick and reliable identification of targeted allergens in meat products. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Anita Spychaj
- Faculty of Food Science and Nutrition, Department of Meat Technology, Poznan University of Life Sciences, Poznan, Poland
| | - Edward Pospiech
- Faculty of Food Science and Nutrition, Department of Meat Technology, Poznan University of Life Sciences, Poznan, Poland
| | - Ewa Iwańska
- Faculty of Food Science and Nutrition, Department of Meat Technology, Poznan University of Life Sciences, Poznan, Poland
| | - Magdalena Montowska
- Faculty of Food Science and Nutrition, Department of Meat Technology, Poznan University of Life Sciences, Poznan, Poland
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Sánchez-Paniagua López M, Manzanares-Palenzuela CL, López-Ruiz B. Biosensors for GMO Testing: Nearly 25 Years of Research. Crit Rev Anal Chem 2018; 48:391-405. [DOI: 10.1080/10408347.2018.1442708] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Marta Sánchez-Paniagua López
- Sección Departamental de Química Analítica, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
| | | | - Beatriz López-Ruiz
- Sección Departamental de Química Analítica, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
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15
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Lo YT, Shaw PC. DNA-based techniques for authentication of processed food and food supplements. Food Chem 2018; 240:767-774. [DOI: 10.1016/j.foodchem.2017.08.022] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 07/07/2017] [Accepted: 08/03/2017] [Indexed: 12/31/2022]
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16
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Dutta G, Lillehoj PB. An ultrasensitive enzyme-free electrochemical immunosensor based on redox cycling amplification using methylene blue. Analyst 2017; 142:3492-3499. [PMID: 28831485 PMCID: PMC5600201 DOI: 10.1039/c7an00789b] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We report a new enzyme-free electrochemical sensor for ultrasensitive measurements of protein biomarkers in plasma and whole blood samples based on a unique electrochemical-chemical-chemical (ECC) redox cycling signal amplification scheme. This scheme uses methylene blue (MB) as a redox indicator which undergoes an endergonic reaction with Ru(NH3)63+ and a highly exergonic reaction with tris(2-carboxyethyl)phosphine (TCEP). This approach offers improved detection sensitivity and sensor stability compared with enzyme-based ECC redox cycling techniques, while involving a simpler sensor modification process and detection protocol. This redox cycling scheme was combined with a robust immunosandwich assay for quantitative measurements of protein biomarkers. For proof of principle, Plasmodium falciparum histidine-rich protein 2 (PfHRP2) was measured in human plasma and whole blood samples, which could be detected down to 10 fg mL-1 and 18 fg mL-1, respectively. Furthermore, this immunosensor exhibits high selectivity, excellent reproducibility and good stability for up to 2 weeks, making it a promising platform for point-of-care testing, especially for detecting extremely low biomarker concentrations in raw biofluids.
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Affiliation(s)
- Gorachand Dutta
- Department of Mechanical Engineering, Michigan State University, East Lansing, MI 48824, USA.
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17
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Computational Biosensors: Molecules, Algorithms, and Detection Platforms. MODELING, METHODOLOGIES AND TOOLS FOR MOLECULAR AND NANO-SCALE COMMUNICATIONS 2017. [PMCID: PMC7123247 DOI: 10.1007/978-3-319-50688-3_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Advanced nucleic acid-based sensor-applications require computationally intelligent biosensors that are able to concurrently perform complex detection and classification of samples within an in vitro platform. Realization of these cutting-edge computational biosensor systems necessitates innovation and integration of three key technologies: molecular probes with computational capabilities, algorithmic methods to enable in vitro computational post processing and classification, and immobilization and detection approaches that enable the realization of deployable computational biosensor platforms. We provide an overview of current technologies, including our contributions towards the development of computational biosensor systems.
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Çakir Ö, Meriç S, Meriç S, Ari Ş. GMO Analysis Methods for Food: From Today to Tomorrow. Food Saf (Tokyo) 2016. [DOI: 10.1002/9781119160588.ch5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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Rehosek M, Mitoraj D, Bledowski M, Beranek R. PhotoelectrochemicalversusElectrochemical Detection of H2O2Using an All-inorganic Sensor Based on Nanostructured Copper Oxide. ELECTROANAL 2016. [DOI: 10.1002/elan.201600227] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Marco Rehosek
- Faculty of Chemistry and Biochemistry; Ruhr University Bochum; Universitätsstr. 150 44780 Bochum Germany
- Max-Planck-Institut für Kohlenforschung; Kaiser-Wilhelm-Platz 1 D-45470 Mülheim an der Ruhr Germany
| | - Dariusz Mitoraj
- Faculty of Chemistry and Biochemistry; Ruhr University Bochum; Universitätsstr. 150 44780 Bochum Germany
- Institute of Electrochemistry; Ulm University; Albert-Einstein-Allee 47 89069 Ulm Germany
| | - Michal Bledowski
- Faculty of Chemistry and Biochemistry; Ruhr University Bochum; Universitätsstr. 150 44780 Bochum Germany
| | - Radim Beranek
- Faculty of Chemistry and Biochemistry; Ruhr University Bochum; Universitätsstr. 150 44780 Bochum Germany
- Institute of Electrochemistry; Ulm University; Albert-Einstein-Allee 47 89069 Ulm Germany
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20
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Karaballi RA, Nel A, Krishnan S, Blackburn J, Brosseau CL. Development of an electrochemical surface-enhanced Raman spectroscopy (EC-SERS) aptasensor for direct detection of DNA hybridization. Phys Chem Chem Phys 2016; 17:21356-63. [PMID: 25780805 DOI: 10.1039/c4cp05077k] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Rapid detection of disease biomarkers at the patient point-of-care is essential to timely and effective treatment. The research described herein focuses on the development of an electrochemical surface-enhanced Raman spectroscopy (EC-SERS) DNA aptasensor capable of direct detection of tuberculosis (TB) DNA. Specifically, a plausible DNA biomarker present in TB patient urine was chosen as the model target for detection. Cost-effective screen printed electrodes (SPEs) modified with silver nanoparticles (AgNP) were used as the aptasensor platform, onto which the aptamer specific for the target DNA was immobilized. Direct detection of the target DNA was demonstrated through the appearance of SERS peaks characteristic for adenine, present only in the target strand. Modulation of the applied potential allowed for a sizeable increase in the observed SERS response and the use of thiol back-filling prevented non-specific adsorption of non-target DNA. To our knowledge, this work represents the first EC-SERS study of an aptasensor for the direct, label-free detection of DNA hybridization. Such a technology paves the way for rapid detection of disease biomarkers at the patient point-of-care.
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Affiliation(s)
- R A Karaballi
- Department of Chemistry, Saint Mary's University, Halifax, Nova Scotia B3H 3C3, Canada.
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Das R, Goel AK, Sharma MK, Upadhyay S. Electrochemical DNA sensor for anthrax toxin activator gene atxA-detection of PCR amplicons. Biosens Bioelectron 2015; 74:939-46. [DOI: 10.1016/j.bios.2015.07.066] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 07/15/2015] [Accepted: 07/28/2015] [Indexed: 02/08/2023]
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22
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Martín-Fernández B, Manzanares-Palenzuela CL, Sánchez-Paniagua López M, de-los-Santos-Álvarez N, López-Ruiz B. Electrochemical genosensors in food safety assessment. Crit Rev Food Sci Nutr 2015; 57:2758-2774. [DOI: 10.1080/10408398.2015.1067597] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Begoña Martín-Fernández
- Sección Departamental de Química Analítica, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
| | | | - Marta Sánchez-Paniagua López
- Sección Departamental de Química Analítica, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
| | | | - Beatriz López-Ruiz
- Sección Departamental de Química Analítica, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
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Oliveira N, Souza E, Ferreira D, Zanforlin D, Bezerra W, Borba MA, Arruda M, Lopes K, Nascimento G, Martins D, Cordeiro M, Lima-Filho J. A Sensitive and Selective Label-Free Electrochemical DNA Biosensor for the Detection of Specific Dengue Virus Serotype 3 Sequences. SENSORS 2015; 15:15562-77. [PMID: 26140346 PMCID: PMC4541844 DOI: 10.3390/s150715562] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 06/13/2015] [Accepted: 06/23/2015] [Indexed: 11/16/2022]
Abstract
Dengue fever is the most prevalent vector-borne disease in the world, with nearly 100 million people infected every year. Early diagnosis and identification of the pathogen are crucial steps for the treatment and for prevention of the disease, mainly in areas where the co-circulation of different serotypes is common, increasing the outcome of dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). Due to the lack of fast and inexpensive methods available for the identification of dengue serotypes, herein we report the development of an electrochemical DNA biosensor for the detection of sequences of dengue virus serotype 3 (DENV-3). DENV-3 probe was designed using bioinformatics software and differential pulse voltammetry (DPV) was used for electrochemical analysis. The results showed that a 22-m sequence was the best DNA probe for the identification of DENV-3. The optimum concentration of the DNA probe immobilized onto the electrode surface is 500 nM and a low detection limit of the system (3.09 nM). Moreover, this system allows selective detection of DENV-3 sequences in buffer and human serum solutions. Therefore, the application of DNA biosensors for diagnostics at the molecular level may contribute to future advances in the implementation of specific, effective and rapid detection methods for the diagnosis dengue viruses.
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Affiliation(s)
- Natália Oliveira
- Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco-UFPE, Av. Prof. Moraes Rego, s/n, Campus da UFPE, 50670-901 Recife, PE, Brazil.
| | - Elaine Souza
- Universidade Federal de Alagoas (UFAL), Campus Arapiraca, Av. Manoel Severino Barbosa, s/n, Bom Sucesso, 57.309-005 Arapiraca, AL, Brazil.
| | - Danielly Ferreira
- Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco-UFPE, Av. Prof. Moraes Rego, s/n, Campus da UFPE, 50670-901 Recife, PE, Brazil.
| | - Deborah Zanforlin
- Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco-UFPE, Av. Prof. Moraes Rego, s/n, Campus da UFPE, 50670-901 Recife, PE, Brazil.
| | - Wessulla Bezerra
- Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco-UFPE, Av. Prof. Moraes Rego, s/n, Campus da UFPE, 50670-901 Recife, PE, Brazil.
| | - Maria Amélia Borba
- Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco-UFPE, Av. Prof. Moraes Rego, s/n, Campus da UFPE, 50670-901 Recife, PE, Brazil.
| | - Mariana Arruda
- Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco-UFPE, Av. Prof. Moraes Rego, s/n, Campus da UFPE, 50670-901 Recife, PE, Brazil.
| | - Kennya Lopes
- Departamento de Virologia e Terapia Experimental (LAVITE), Centro de Pesquisas Aggeu Magalhães (CPqAM), Fundação Oswaldo Cruz (Fiocruz)-Pernambuco, Av. Professor Moraes Rego, s/n, Campus da UFPE, 50.670-420 Recife, PE, Brazil.
| | - Gustavo Nascimento
- Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco-UFPE, Av. Prof. Moraes Rego, s/n, Campus da UFPE, 50670-901 Recife, PE, Brazil.
| | - Danyelly Martins
- Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco-UFPE, Av. Prof. Moraes Rego, s/n, Campus da UFPE, 50670-901 Recife, PE, Brazil.
- Departamento de Bioquímica, Universidade Federal de Pernambuco-UFPE, Av. Professor Moraes Rego, s/n, Campus da UFPE, CEP: 50670-901 Recife, PE, Brazil.
| | - Marli Cordeiro
- Departamento de Bioquímica, Universidade Federal de Pernambuco-UFPE, Av. Professor Moraes Rego, s/n, Campus da UFPE, CEP: 50670-901 Recife, PE, Brazil.
| | - José Lima-Filho
- Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco-UFPE, Av. Prof. Moraes Rego, s/n, Campus da UFPE, 50670-901 Recife, PE, Brazil.
- Departamento de Bioquímica, Universidade Federal de Pernambuco-UFPE, Av. Professor Moraes Rego, s/n, Campus da UFPE, CEP: 50670-901 Recife, PE, Brazil.
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Electrochemical genosensors as innovative tools for detection of genetically modified organisms. Trends Analyt Chem 2015. [DOI: 10.1016/j.trac.2014.10.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Rahman MM, Li XB, Lopa NS, Ahn SJ, Lee JJ. Electrochemical DNA hybridization sensors based on conducting polymers. SENSORS (BASEL, SWITZERLAND) 2015; 15:3801-29. [PMID: 25664436 PMCID: PMC4367386 DOI: 10.3390/s150203801] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 01/27/2015] [Indexed: 02/07/2023]
Abstract
Conducting polymers (CPs) are a group of polymeric materials that have attracted considerable attention because of their unique electronic, chemical, and biochemical properties. This is reflected in their use in a wide range of potential applications, including light-emitting diodes, anti-static coating, electrochromic materials, solar cells, chemical sensors, biosensors, and drug-release systems. Electrochemical DNA sensors based on CPs can be used in numerous areas related to human health. This review summarizes the recent progress made in the development and use of CP-based electrochemical DNA hybridization sensors. We discuss the distinct properties of CPs with respect to their use in the immobilization of probe DNA on electrode surfaces, and we describe the immobilization techniques used for developing DNA hybridization sensors together with the various transduction methods employed. In the concluding part of this review, we present some of the challenges faced in the use of CP-based DNA hybridization sensors, as well as a future perspective.
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Affiliation(s)
- Md Mahbubur Rahman
- Nanotechnology Research Center and Department of Applied Life Science, College of Biomedical and Health Science, Konkuk University, Chungju 380-701, Korea.
| | - Xiao-Bo Li
- Nanotechnology Research Center and Department of Applied Life Science, College of Biomedical and Health Science, Konkuk University, Chungju 380-701, Korea.
| | - Nasrin Siraj Lopa
- Nanotechnology Research Center and Department of Applied Life Science, College of Biomedical and Health Science, Konkuk University, Chungju 380-701, Korea.
| | - Sang Jung Ahn
- Center for Advanced Instrumentation, Korea Research Institute of Standards and Science (KRISS), Daejeon 305-340, Korea.
| | - Jae-Joon Lee
- Nanotechnology Research Center and Department of Applied Life Science, College of Biomedical and Health Science, Konkuk University, Chungju 380-701, Korea.
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Coupling electrochemical response of a DNA biosensor with PCR for Neisseria gonorrhoeae detection. Diagn Microbiol Infect Dis 2014; 78:16-23. [DOI: 10.1016/j.diagmicrobio.2013.09.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 09/10/2013] [Accepted: 09/15/2013] [Indexed: 12/20/2022]
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28
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Campos-Ferreira DS, Nascimento GA, Souza EV, Souto-Maior MA, Arruda MS, Zanforlin DM, Ekert MH, Bruneska D, Lima-Filho JL. Electrochemical DNA biosensor for human papillomavirus 16 detection in real samples. Anal Chim Acta 2013; 804:258-63. [DOI: 10.1016/j.aca.2013.10.038] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 10/08/2013] [Accepted: 10/16/2013] [Indexed: 12/21/2022]
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29
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Arugula MA, Zhang Y, Simonian AL. Biosensors as 21st Century Technology for Detecting Genetically Modified Organisms in Food and Feed. Anal Chem 2013; 86:119-29. [DOI: 10.1021/ac402898j] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mary A. Arugula
- Department of Materials Engineering, Auburn University, Auburn, Alabama 36849, United States
| | - Yuanyuan Zhang
- Department of Materials Engineering, Auburn University, Auburn, Alabama 36849, United States
| | - Alex L. Simonian
- Department of Materials Engineering, Auburn University, Auburn, Alabama 36849, United States
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Chen WT, Huang MF, Chang HT. Using surface-assisted laser desorption/ionization mass spectrometry to detect ss- and ds-oligodeoxynucleotides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:877-883. [PMID: 23539494 DOI: 10.1007/s13361-013-0595-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 01/22/2013] [Accepted: 01/28/2013] [Indexed: 06/02/2023]
Abstract
We applied surface-assisted laser desorption/ionization mass spectrometry (SALDI-MS) with HgTe nanostructures as the matrix for the detection of single- and double-stranded oligodeoxynucleotides (ss-ODNs and ds-ODNs). The concentrations of surfactant and additives (metal ions, an amine) and the pH and ionic strength of the sample matrix played significantly different roles in the detection of ss- and ds-ODNs with various sequences. In the presence of Brij 76 (1.5 %), Hg(2+) (7.5 μM), and cadaverine (10 μM) at pH 5.0, this SALDI-MS approach allowed the simultaneous detection of T15, T20, T33, and T40, with limits of detection at the femtomole-to-picomole level and sample-to-sample intensity variation <23 %. In the presence of Ag(+) (1 μM) and cadaverine (10 μM) at pH 7.0, this technique allowed the detection of randomly sequenced ss- and ds-ODNs at concentrations down to the femtomole level. To the best of our knowledge, this paper is the first to report the detection of ss-ODNs (up to 50-mer) and ds-ODNs (up to 30 base pairs) through the combination of SALDI-MS with HgTe nanostructures as matrices. We demonstrated the practicality of this approach through analysis of a single nucleotide polymorphism that determines the fate of the valine residue in the β-globin of sickle cell megaloblasts.
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Affiliation(s)
- Wen-Tsen Chen
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
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31
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Genetically modified crops: detection strategies and biosafety issues. Gene 2013; 522:123-32. [PMID: 23566850 DOI: 10.1016/j.gene.2013.03.107] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 01/19/2013] [Accepted: 03/10/2013] [Indexed: 11/23/2022]
Abstract
Genetically modified (GM) crops are increasingly gaining acceptance but concurrently consumers' concerns are also increasing. The introduction of Bacillus thuringiensis (Bt) genes into the plants has raised issues related to its risk assessment and biosafety. The International Regulations and the Codex guidelines regulate the biosafety requirements of the GM crops. In addition, these bodies synergize and harmonize the ethical issues related to the release and use of GM products. The labeling of GM crops and their products are mandatory if the genetically modified organism (GMO) content exceeds the levels of a recommended threshold. The new and upcoming GM crops carrying multiple stacked traits likely to be commercialized soon warrant sensitive detection methods both at the DNA and protein levels. Therefore, traceability of the transgene and its protein expression in GM crops is an important issue that needs to be addressed on a priority basis. The advancement in the area of molecular biology has made available several bioanalytical options for the detection of GM crops based on DNA and protein markers. Since the insertion of a gene into the host genome may even cause copy number variation, this may be uncovered using real time PCR. Besides, assessing the exact number of mRNA transcripts of a gene, correlation between the template activity and expressed protein may be established. Here, we present an overview on the production of GM crops, their acceptabilities, detection strategies, biosafety issues and potential impact on society. Further, overall future prospects are also highlighted.
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32
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Porous silicon biosensor: Current status. Biosens Bioelectron 2013; 41:54-64. [DOI: 10.1016/j.bios.2012.09.045] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 09/13/2012] [Accepted: 09/22/2012] [Indexed: 01/10/2023]
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33
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Huang J, Su X, Li Z. Enzyme-Free and Amplified Fluorescence DNA Detection Using Bimolecular Beacons. Anal Chem 2012; 84:5939-43. [DOI: 10.1021/ac3004727] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Jiahao Huang
- Department of Mechanical Engineering, The Hong Kong University of Science and Technology,
Clear Water Bay, Kowloon, Hong Kong
| | - Xuefen Su
- School of Public Health and
Primary Care, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, New Territories,
Hong Kong
| | - Zhigang Li
- Department of Mechanical Engineering, The Hong Kong University of Science and Technology,
Clear Water Bay, Kowloon, Hong Kong
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Thipmanee O, Samanman S, Sankoh S, Numnuam A, Limbut W, Kanatharana P, Vilaivan T, Thavarungkul P. Label-free capacitive DNA sensor using immobilized pyrrolidinyl PNA probe: effect of the length and terminating head group of the blocking thiols. Biosens Bioelectron 2012; 38:430-5. [PMID: 22770826 DOI: 10.1016/j.bios.2012.06.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 06/13/2012] [Indexed: 10/28/2022]
Abstract
This paper reports, for the first time, the influence of the length and the terminating head group of blocking thiols on the sensitivity and specificity of a label-free capacitive DNA detection system using immobilized pyrrolidinyl peptide nucleic acid (acpcPNA) probes. A C-terminal lysine-modified acpcPNA was immobilized through four different alkanethiol self-assembled monolayers (SAMs), i.e., 3-mercaptopropionic acid (MPA), thioctic acid (TA), thiourea (TU) and mercaptosuccinic acid (MSA). The hybridization between the acpcPNA probes and the target DNA was directly measured using the capacitive system. Five blocking thiols of various lengths (C=3, 6, 8, 9 and 11), with the -OH terminating head group, i.e., 3-mercapto-1-propanol (3-MPL), 6-mercapto-1-hexanol (6-MHL), 8-mercapto-1-octanol (8-MOL), 9-mercapto-1-nonanol (9-MNL), 11-mercapto-1-undecanol (11-MUL) and another blocking thiol (C=11) with a -CH(3) terminating head group, and 1-dodecanethiol (1-DDT) were investigated. The blocking thiol with the same length as the total spacer of the immobilized acpcPNA gave the highest sensitivity and specificity with the -OH terminating head group providing a slightly better signal than the -CH(3) group. Under the optimized conditions, the immobilized acpcPNA probes provided a wide linear range for DNA detection (1.0 × 10(-11)-1.0 × 10(-8)M) with a very low detection limit in the picomolar range. The modified acpcPNA electrode could be reused through at least 58 cycles. The high sensitivity and very low detection limits are potentially useful for the analysis of ultra-trace levels of DNA in samples. Preliminary studies were also performed to see the effect of probe concentration and target length.
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Affiliation(s)
- Orawan Thipmanee
- Trace Analysis and Biosensor Research Center, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand
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Ahmed T, Kilina S, Das T, Haraldsen JT, Rehr JJ, Balatsky AV. Electronic fingerprints of DNA bases on graphene. NANO LETTERS 2012; 12:927-931. [PMID: 22257137 DOI: 10.1021/nl2039315] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We calculate the electronic local density of states (LDOS) of DNA nucleotide bases (A,C,G,T), deposited on graphene. We observe significant base-dependent features in the LDOS in an energy range within a few electronvolts of the Fermi level. These features can serve as electronic fingerprints for the identification of individual bases in scanning tunneling spectroscopy (STS) experiments that perform image and site dependent spectroscopy on biomolecules. Thus the fingerprints of DNA-graphene hybrid structures may provide an alternative route to DNA sequencing using STS.
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Affiliation(s)
- Towfiq Ahmed
- Department of Physics, University of Washington, Seattle, Washington 98195, USA.
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Mandler D, Kraus-Ophir S. Self-assembled monolayers (SAMs) for electrochemical sensing. J Solid State Electrochem 2011. [DOI: 10.1007/s10008-011-1493-6] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Tichoniuk M, Gwiazdowska D, Ligaj M, Filipiak M. Electrochemical detection of foodborne pathogen Aeromonas hydrophila by DNA hybridization biosensor. Biosens Bioelectron 2010; 26:1618-23. [PMID: 20829023 DOI: 10.1016/j.bios.2010.08.030] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Revised: 07/17/2010] [Accepted: 08/12/2010] [Indexed: 12/01/2022]
Abstract
The paper describes an electrochemical DNA biosensor used for the detection of Aeromonas hydrophila. This opportunistic pathogen is recognized as an emerging foodborne hazard and is associated with a variety of virulence factors including production of cytotoxic enterotoxin aerolysin. The genosensor recognition layer was prepared using mixed self-assembled monolayer (SAM) consisting of thiolated single-stranded DNA probe (ssDNA) and diluent molecules--mercaptoalcohol: mercaptoethanol (MCE) or mercaptohexanol (MCH) or mercaptononanol (MCN). The voltammetric examination of double-layer capacitance of biosensor recognition interface supported by chronocoulometric quantitation of DNA present on the electrode surface showed that mixed ssDNA and MCH monolayer revealed the lowest defectiveness. Its double-layer capacitance equaled 4.0 μF cm(-2) and ssDNA probe surface coverage reached 8.5×10(11) molecules cm(-2) of gold electrode surface. Chronocoulometric quantitation of DNA and square wave voltammetry (SWV) measurements of electroactive indicator, methylene blue (MB) were performed to investigate the influence of hybridization reaction time, concentration of target DNA fragments, and presence of non-complementary DNA on the electrochemical response of genosensor recognition interface. The biosensor enabled distinction between the DNA samples isolated from A. hydrophila (present at the concentration of 2.5 μg cm(-3)) and other microbial DNA.
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Affiliation(s)
- M Tichoniuk
- Poznan University of Economics, Al. Niepodleglosci 10, 61-875 Poznan, Poland.
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Xu K, Huang J, Ye Z, Ying Y, Li Y. Recent development of nano-materials used in DNA biosensors. SENSORS 2009; 9:5534-57. [PMID: 22346713 PMCID: PMC3274166 DOI: 10.3390/s90705534] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Revised: 07/06/2009] [Accepted: 07/08/2009] [Indexed: 01/24/2023]
Abstract
As knowledge of the structure and function of nucleic acid molecules has increased, sequence-specific DNA detection has gained increased importance. DNA biosensors based on nucleic acid hybridization have been actively developed because of their specificity, speed, portability, and low cost. Recently, there has been considerable interest in using nano-materials for DNA biosensors. Because of their high surface-to-volume ratios and excellent biological compatibilities, nano-materials could be used to increase the amount of DNA immobilization; moreover, DNA bound to nano-materials can maintain its biological activity. Alternatively, signal amplification by labeling a targeted analyte with nano-materials has also been reported for DNA biosensors in many papers. This review summarizes the applications of various nano-materials for DNA biosensors during past five years. We found that nano-materials of small sizes were advantageous as substrates for DNA attachment or as labels for signal amplification; and use of two or more types of nano-materials in the biosensors could improve their overall quality and to overcome the deficiencies of the individual nano-components. Most current DNA biosensors require the use of polymerase chain reaction (PCR) in their protocols. However, further development of nano-materials with smaller size and/or with improved biological and chemical properties would substantially enhance the accuracy, selectivity and sensitivity of DNA biosensors. Thus, DNA biosensors without PCR amplification may become a reality in the foreseeable future.
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Affiliation(s)
- Kai Xu
- School of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, Zhejiang Province, China, 310029; E-Mails: (K.X.); (J.H.); (Z.Y.)
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences; Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong Province, 266101, China
| | - Junran Huang
- School of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, Zhejiang Province, China, 310029; E-Mails: (K.X.); (J.H.); (Z.Y.)
| | - Zunzhong Ye
- School of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, Zhejiang Province, China, 310029; E-Mails: (K.X.); (J.H.); (Z.Y.)
| | - Yibin Ying
- School of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, Zhejiang Province, China, 310029; E-Mails: (K.X.); (J.H.); (Z.Y.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +86-571-869 718 85; Fax: +86-571-869 718 85
| | - Yanbin Li
- Department of Biological & Agricultural Engineering, University of Arkansas, Fayetteville, AR 72701, USA; E-Mail:
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Valério E, Abrantes L, Viana A. 4-Aminothiophenol Self-Assembled Monolayer for the Development of a DNA Biosensor Aiming the Detection of Cylindrospermopsin Producing Cyanobacteria. ELECTROANAL 2008. [DOI: 10.1002/elan.200804350] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Marmiroli N, Maestri E, Gullì M, Malcevschi A, Peano C, Bordoni R, De Bellis G. Methods for detection of GMOs in food and feed. Anal Bioanal Chem 2008; 392:369-84. [DOI: 10.1007/s00216-008-2303-6] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Revised: 07/14/2008] [Accepted: 07/17/2008] [Indexed: 12/17/2022]
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