1
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Algama CH, Basir J, Wijesinghe KM, Dhakal S. Fluorescence-Based Multimodal DNA Logic Gates. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:1185. [PMID: 39057862 PMCID: PMC11280116 DOI: 10.3390/nano14141185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 07/02/2024] [Accepted: 07/03/2024] [Indexed: 07/28/2024]
Abstract
The use of DNA structures in creating multimodal logic gates bears high potential for building molecular devices and computation systems. However, due to the complex designs or complicated working principles, the implementation of DNA logic gates within molecular devices and circuits is still quite limited. Here, we designed simple four-way DNA logic gates that can serve as multimodal platforms for simple to complex operations. Using the proximity quenching of the fluorophore-quencher pair in combination with the toehold-mediated strand displacement (TMSD) strategy, we have successfully demonstrated that the fluorescence output, which is a result of gate opening, solely relies on the oligonucleotide(s) input. We further demonstrated that this strategy can be used to create multimodal (tunable displacement initiation sites on the four-way platform) logic gates including YES, AND, OR, and the combinations thereof. The four-way DNA logic gates developed here bear high promise for building biological computers and next-generation smart molecular circuits with biosensing capabilities.
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Affiliation(s)
| | | | | | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284, USA
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2
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Liu J, Zhang T, Liu X, Lam JWY, Tang BZ, Chau Y. Molecular logic operations from complex coacervation with aggregation-induced emission characteristics. MATERIALS HORIZONS 2022; 9:2443-2449. [PMID: 35856292 DOI: 10.1039/d2mh00537a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Leveraging complex coacervation of a polycation and a bivalent anion with aggregation-induced emission characteristics, we accomplish eight basic logic operations with environmental stimuli as inputs, producing Boolean-like fluorescence intensity or turbidity 'outputs' with contrast higher than one order of magnitude. Storage of information of a fluorescent pattern and thermo-sensor applications are also demonstrated.
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Affiliation(s)
- Jianhui Liu
- Department of Chemical and Biological Engineering, the Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China.
| | - Tianfu Zhang
- Department of Chemistry and Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, the Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Xiaolin Liu
- Department of Chemistry and Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, the Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Jacky W Y Lam
- Department of Chemistry and Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, the Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Ben Zhong Tang
- Department of Chemistry and Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, the Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
- School of Science and Engineering, Shenzhen Key Laboratory of Functional Aggregate Materials, the Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Ying Chau
- Department of Chemical and Biological Engineering, the Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China.
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3
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Lan Y, Wei Y, Wei Y, Wang L, Dong C. Versatile Triple-Output Molecular Logic Gate for Cysteine and Silver (I) in Foods and the Environment Based on I-Motif DNA Modulation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:3608-3617. [PMID: 35289171 DOI: 10.1021/acs.jafc.1c07469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
DNA-based molecular logic gates have been developed rapidly but most of them have a single output mode. This study is to develop a triple-output label-free fluorescent DNA-based multifunctional molecular logic gate with berberine as a fluorescent signal and a Ag+-aptamer as a recognition matrix. The Ag+-aptamer has been identified to switch from a random coil to an i-motif structure of C-Ag+-C from a Ag+-induced responsive conformational change. As a fluorescent probe, berberine is ultrasensitive to the changes of microenvironments, and the binding to i-motif DNA's more rigid structure causes a significant increase in fluorescence, anisotropy, and lifetime. The addition of cysteine to the berberine/C-Ag+-C system disintegrates the i-motif DNA structure because of the strong coordination between Ag+ and cysteine, and then the triple-output signals are almost retrieved. Given this, a highly sensitive triple-output molecular logic gate for the analyses of Ag+ and cysteine is constructed with high specificity. Moreover, this simple and cost-effective molecular logic gate has been applied for the detection of cysteine and Ag+ in various real environmental samples including river water, PM2.5, soil, and food samples with satisfactory recoveries from 89.83 to 106.04%.
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Affiliation(s)
- Yifeng Lan
- Shanxi Laboratory for Yellow River, Institute of Environmental Science, Shanxi University, Taiyuan 030006, P. R. China
| | - Yuxin Wei
- Shanxi Laboratory for Yellow River, Institute of Environmental Science, Shanxi University, Taiyuan 030006, P. R. China
| | - Yanli Wei
- Shanxi Laboratory for Yellow River, Institute of Environmental Science, Shanxi University, Taiyuan 030006, P. R. China
| | - Li Wang
- Shanxi Laboratory for Yellow River, Institute of Environmental Science, Shanxi University, Taiyuan 030006, P. R. China
| | - Chuan Dong
- Shanxi Laboratory for Yellow River, Institute of Environmental Science, Shanxi University, Taiyuan 030006, P. R. China
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4
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Liu L, Liu P, Ga L, Ai J. Advances in Applications of Molecular Logic Gates. ACS OMEGA 2021; 6:30189-30204. [PMID: 34805654 PMCID: PMC8600522 DOI: 10.1021/acsomega.1c02912] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 10/05/2021] [Indexed: 05/21/2023]
Abstract
Logic gates are devices that can perform Boolean logic operations and are the basic components of integrated circuits for information processing and storage. In recent years, molecular logic gates are gradually replacing traditional silicon-based electronic computers with their significant advantages and are used in research in water quality monitoring, heavy metal ion detection, disease diagnosis and treatment, food safety detection, and biological sensors. Logic gates at the molecular level have broad development prospects and huge development potential. In this review, the development and application of logic gates in various fields are used as the entry point to discuss the research progress of logic gates and logic circuits. At the same time, the application of logic gates in quite a few emerging fields is briefly summarized and predicted.
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Affiliation(s)
- Lijun Liu
- College
of Chemistry and Environmental Science, Inner Mongolian Key Laboratory
for Enviromental Chemistry, Inner Mongolia
Normal University, 81 Zhaowudalu, Hohhot 010022, People’s Republic of China
| | - Pingping Liu
- College
of Chemistry and Environmental Science, Inner Mongolian Key Laboratory
for Enviromental Chemistry, Inner Mongolia
Normal University, 81 Zhaowudalu, Hohhot 010022, People’s Republic of China
| | - Lu Ga
- College
of Pharmacy, Inner Mongolia Medical University, Jinchuankaifaqu, Hohhot 010110, People’s Republic of China
| | - Jun Ai
- College
of Chemistry and Environmental Science, Inner Mongolian Key Laboratory
for Enviromental Chemistry, Inner Mongolia
Normal University, 81 Zhaowudalu, Hohhot 010022, People’s Republic of China
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5
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Cui X, Abd El-Aty AM, Zhang C, Xu L, Liu H, Jia H, Wang Y, Cao Z, Salvador JP, She Y, Jin F, Wang J, Jin M, Hammock BD. Enhanced Bio-Barcode Immunoassay Using Droplet Digital PCR for Multiplex Detection of Organophosphate Pesticides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:11131-11141. [PMID: 34494438 DOI: 10.1021/acs.jafc.1c03216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A bio-barcode immunoassay based on droplet digital polymerase chain reaction (ddPCR) was developed to simultaneously quantify triazophos, parathion, and chlorpyrifos in apple, cucumber, cabbage, and pear. Three gold nanoparticle (AuNP) probes and magnetic nanoparticle (MNP) probes were prepared, binding through their antibodies with the three pesticides in the same tube. Three groups of primers, probes, templates, and three antibodies were designed to ensure the specificity of the method. Under the optimal conditions, the detection limits (expressed as IC10) of triazophos, parathion, and chlorpyrifos were 0.22, 0.45, and 4.49 ng mL-1, respectively. The linear ranges were 0.01-20, 0.1-100, and 0.1-500 ng mL-1, and the correlation coefficients (R2) were 0.9661, 0.9834, and 0.9612, respectively. The recoveries and relative standard deviations (RSDs) were in the ranges of 75.5-98.9 and 8.3-16.7%. This study provides the first insights into the ddPCR for the determination of organophosphate pesticides. It also laid the foundation for high-throughput detection of other small molecules.
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Affiliation(s)
- Xueyan Cui
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - A M Abd El-Aty
- State Key Laboratory of Biobased Material and Green Papermaking, College of Food Science and Engineering, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, P. R. China
- Department of Pharmacology, Faculty of Veterinary Medicine, Cairo University, 12211 Giza, Egypt
- Department of Medical Pharmacology, Medical Faculty, Ataturk University, Erzurum 25240, Turkey
| | - Chan Zhang
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - Lingyuan Xu
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - Haijin Liu
- Inspection and Testing Center of Agricultural and Livestock Products of Tibet, Lhasa 850000, P. R. China
| | - Huiyan Jia
- Ningbo Academy of Agricultural Sciences, Ningbo 315040, Zhengjiang, P. R. China
| | - Yuanshang Wang
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - Zhen Cao
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - J-Pablo Salvador
- Nanobiotechnology for Diagnostics Group, Instituto de Química Avanzada de Cataluña, IQAC-CSIC, C/ Jordi Girona, 18-26, 08034 Barcelona, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Avenida Monforte de Lemos, 3-5, Pavillion 11, Floor 0, 28029 Madrid, Spain
| | - Yongxin She
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - Fen Jin
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - Jing Wang
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - Maojun Jin
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - Bruce D Hammock
- Department of Entomology & Nematology and the UC Davis Comprehensive Cancer Center, University of California, Davis, Davis, California 95616, United States
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6
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Chen W, Cheng CA, Xiang D, Zink JI. Expanding nanoparticle multifunctionality: size-selected cargo release and multiple logic operations. NANOSCALE 2021; 13:5497-5506. [PMID: 33687426 DOI: 10.1039/d1nr00642h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Physically stimulated nanoparticles that deliver size-selected cargo and function as logic gates are reported. To achieve this goal the particle requires multiple components, and we recognized early on that the components, not just the released cargo, could be used to demonstrate logic operations (OR and AND logic). For stimuli, we chose two non-invasive types, red light and alternating magnetic fields (AMF), because they both have potential biological relevance. To realize cargo delivery with size selection and logic operations, we mechanized the surface of core@shell nanoparticles with a superparamagnetic core that generates localized heating when exposed to an AMF, and a mesoporous silica shell into which cargo molecules with different sizes were loaded. We demonstrate the core@shell nanoparticles can load the dual cargos with different sizes and subsequently release the smaller (∼0.5 nm) and bigger (∼2 nm) cargos in succession when stimulated by a red light followed by an AMF. Finally, we demonstrate that the multi-component nanoparticles could function as nanoparticle-based Boolean logic gates where AMF and red light served as the two inputs and the release of small cargo, and free cyclodextrin served as the outputs. The construction of two Boolean logic gates (OR, and AND) was realized.
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Affiliation(s)
- Wei Chen
- Department of Chemistry & Biochemistry, University of California Los Angeles, Los Angeles, California, 90095, USA. and California NanoSystems Institute, University of California Los Angeles, Los Angeles, California, 90095, USA
| | - Chi-An Cheng
- California NanoSystems Institute, University of California Los Angeles, Los Angeles, California, 90095, USA and Department of Bioengineering, University of California Los Angeles, Los Angeles, California, 90095, USA
| | - Danlei Xiang
- Department of Chemistry & Biochemistry, University of California Los Angeles, Los Angeles, California, 90095, USA.
| | - Jeffrey I Zink
- Department of Chemistry & Biochemistry, University of California Los Angeles, Los Angeles, California, 90095, USA. and California NanoSystems Institute, University of California Los Angeles, Los Angeles, California, 90095, USA
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7
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Nakagawa O, Aoyama H, Fujii A, Kishimoto Y, Obika S. Crystallographic Structure of Novel Types of Ag I -Mediated Base Pairs in Non-canonical DNA Duplex Containing 2'-O,4'-C-Methylene Bridged Nucleic Acids. Chemistry 2021; 27:3842-3848. [PMID: 33274789 DOI: 10.1002/chem.202004819] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/04/2020] [Indexed: 11/08/2022]
Abstract
Metal-mediated base pairs have widespread applications, such as in DNA-metal nanodevices and sensors. Here, we focused on their sugar conformation in duplexes and observed the crystallographic structure of the non-canonical DNA/DNA duplex containing 2'-O,4'-C-methylene bridged nucleic acid in the presence of AgI ions. The X-ray crystallographic structure was successfully obtained at a resolution of 1.5 Å. A novel type of AgI -mediated base pair between the N1 positions of anti-conformation of adenines in the duplex was observed. In the central non-canonical region, a hexad nucleobase structure containing AgI -mediated base pairs between the N7 positions of guanines was formed. A highly bent non-canonical structure was formed at the origin of AgI -mediated base pairs in the central region. The bent duplex structure induced by the addition of AgI ions might become a powerful tool for dynamic structural changes in DNA nanotechnology applications.
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Affiliation(s)
- Osamu Nakagawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan.,Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihamahoji, Yamashiro-cho, Tokushima, 770-8514, Japan
| | - Hiroshi Aoyama
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Akane Fujii
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Yuki Kishimoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
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8
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Funai T, Tagawa C, Nakagawa O, Wada SI, Ono A, Urata H. Enzymatic formation of consecutive thymine–HgII–thymine base pairs by DNA polymerases. Chem Commun (Camb) 2020; 56:12025-12028. [DOI: 10.1039/d0cc04423g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Ten consecutive T–HgII–T base pairs were successfully formed by DNA polymerase-catalyzed primer extension reactions.
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Affiliation(s)
- Tatsuya Funai
- Department of Bioorganic Chemistry
- Osaka University of Pharmaceutical Sciences
- 4-20-1 Nasahara
- Takatsuki
- Japan
| | - Chizuko Tagawa
- Department of Bioorganic Chemistry
- Osaka University of Pharmaceutical Sciences
- 4-20-1 Nasahara
- Takatsuki
- Japan
| | - Osamu Nakagawa
- Department of Bioorganic Chemistry
- Osaka University of Pharmaceutical Sciences
- 4-20-1 Nasahara
- Takatsuki
- Japan
| | - Shun-ichi Wada
- Department of Bioorganic Chemistry
- Osaka University of Pharmaceutical Sciences
- 4-20-1 Nasahara
- Takatsuki
- Japan
| | - Akira Ono
- Department of Material & Life Chemistry
- Faculty of Engineering, Kanagawa University
- 3-27-1 Rokkakubashi
- Kanagawa-ku
- Japan
| | - Hidehito Urata
- Department of Bioorganic Chemistry
- Osaka University of Pharmaceutical Sciences
- 4-20-1 Nasahara
- Takatsuki
- Japan
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9
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Tian J, Chu H, Zhang Y, Li K, Tian H, Zhang X, Xu W. TiO 2 Nanoparticle-Enhanced Linker Recombinant Strand Displacement Amplification (LRSDA) for Universal Label-Free Visual Bioassays. ACS APPLIED MATERIALS & INTERFACES 2019; 11:46504-46514. [PMID: 31755686 DOI: 10.1021/acsami.9b16314] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The influence of nanomaterials on dynamic isothermal amplification and their morphology regulated by bionic biological reactions in vitro remain unknown. From a theoretical perspective, TiO2 nanoparticles enhance the amplification efficiency and reaction specificity of recombinase polymerase amplification (RPA). These nanoparticles aggregated into larger nanoclusters by adsorbing RPA components, termed nanoscale RPA factories, which increased their local concentrations to enhance RPA. Following the nick/extension cycles mediated by a bifunctional linker located at the 5' end of the forward primers, the TiO2 nanoparticle-enhanced LRSDA process produces single-stranded products, constituting the G-quadruplex DNAzymes and catalyzing the chromogenic substrate to facilitate colorimetric analysis for on-site bioassays. Salmonella spp. and genetically modified maize MON810 could be detected with a detection limit of 4 cfu/mL and 0.1% transgenic components, respectively. Briefly, TiO2-assisted isothermal molecular amplification addressed the demands of practical on-site applications.
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Affiliation(s)
- Jingjing Tian
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering , China Agricultural University , Beijing 100083 , People's Republic of China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety) , Ministry of Agriculture , Beijing 100083 , People's Republic of China
| | - Huashuo Chu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering , China Agricultural University , Beijing 100083 , People's Republic of China
| | - Yuan Zhang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering , China Agricultural University , Beijing 100083 , People's Republic of China
- College of Food Science and Technology , Agricultural University of Hebei , Baoding , Hebei 071001 , People's Republic of China
| | - Kai Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering , China Agricultural University , Beijing 100083 , People's Republic of China
| | - Hongtao Tian
- College of Food Science and Technology , Agricultural University of Hebei , Baoding , Hebei 071001 , People's Republic of China
| | - Xiujie Zhang
- Department Center of Science and Technology , Ministry of Agriculture and Rural Affairs , Beijing 100176 , People's Republic of China
| | - Wentao Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering , China Agricultural University , Beijing 100083 , People's Republic of China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety) , Ministry of Agriculture , Beijing 100083 , People's Republic of China
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10
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Guo M, Wang J, Du R, Liu Y, Chi J, He X, Huang K, Luo Y, Xu W. A test strip platform based on a whole-cell microbial biosensor for simultaneous on-site detection of total inorganic mercury pollutants in cosmetics without the need for predigestion. Biosens Bioelectron 2019; 150:111899. [PMID: 31767350 DOI: 10.1016/j.bios.2019.111899] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/05/2019] [Accepted: 11/14/2019] [Indexed: 12/23/2022]
Abstract
Mercury pollutants such as mercuric chloride (HgCl2), mercurous chloride (Hg2Cl2) and mercuric ammonium chloride (Hg(NH2)Cl) are often found in cosmetics. Previous attempts at the on-site detection of mercury were hindered by the complicated and dangerous pretreatment procedure of converting various forms of mercury to Hg (II) ions. In this study, a test strip platform was developed based on a whole-cell microbial biosensor for the simultaneous detection of soluble and insoluble inorganic mercury pollutants in cosmetics without the need for predigestion. The genetic circuits with constitutively expressed MerR as sensor proteins and inducible red fluorescent protein (RFP) as the reporter were introduced into Escherichia coli to construct the mercury detection biosensor. The RFP fluorescence intensity of this biosensor showed a excellent linear relationship (R2 = 0.9848) with the Hg (II) concentration ranging from 50 nM to 10 μM in Luria-Bertani (LB) broth. Further research indicated that this biosensor could respond not only to Hg (II) ions but also to insoluble Hg2Cl2 and Hg2Cl2. The transcriptomic results confirmed the mercury conversion ability of the whole-cell biosensor from a gene expression perspective. This biosensor was embedded on filter paper to form a test strip, which could be used to determine whether the total inorganic mercury pollutants in cosmetics exceeded 1 mg/kg. Therefore, this strip provided a low cost, easy-to-use, and instrument-independent method for the detection of mercury pollution in cosmetics, while this study revealed the unique advantages of microbial biosensors in the automatic bioconversion of targets.
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Affiliation(s)
- Mingzhang Guo
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing, 100083, China
| | - Jili Wang
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing, 100083, China
| | - Ruoxi Du
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing, 100083, China
| | - Yanger Liu
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing, 100083, China
| | - Jiani Chi
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing, 100083, China
| | - Xiaoyun He
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing, 100083, China
| | - Kunlun Huang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing, 100083, China
| | - Yunbo Luo
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing, 100083, China
| | - Wentao Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing, 100083, China.
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11
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Funai T, Aotani M, Kiriu R, Nakamura J, Miyazaki Y, Nakagawa O, Wada S, Torigoe H, Ono A, Urata H. Silver(I)‐Ion‐Mediated Cytosine‐Containing Base Pairs: Metal Ion Specificity for Duplex Stabilization and Susceptibility toward DNA Polymerases. Chembiochem 2019; 21:517-522. [DOI: 10.1002/cbic.201900450] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Tatsuya Funai
- Department of Bioorganic ChemistryOsaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
| | - Megumi Aotani
- Department of Bioorganic ChemistryOsaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
| | - Risa Kiriu
- Department of Bioorganic ChemistryOsaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
| | - Junko Nakamura
- Department of Bioorganic ChemistryOsaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
| | - Yuki Miyazaki
- Department of Bioorganic ChemistryOsaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
| | - Osamu Nakagawa
- Department of Bioorganic ChemistryOsaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
- Present address: Graduate School of Pharmaceutical SciencesOsaka University 1–6 Yamadaoka, Suita Osaka 565-0871 Japan
| | - Shun‐ichi Wada
- Department of Bioorganic ChemistryOsaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
| | - Hidetaka Torigoe
- Department of Applied ChemistryFaculty of ScienceTokyo University of Science 1-3 Kagurazaka, Shinjuku-ku Tokyo 162-8601 Japan
| | - Akira Ono
- Department of Material and Life ChemistryFaculty of EngineeringKanagawa University 3-27-1 Rokkakubashi Kanagawa-ku, Yokohama 221-8686 Japan
| | - Hidehito Urata
- Department of Bioorganic ChemistryOsaka University of Pharmaceutical Sciences 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan
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12
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Funai T, Adachi N, Aotani M, Wada SI, Urata H. Effects of metal ions on thermal stabilities of DNA duplexes containing homo- and heterochiral mismatched base pairs: comparison of internal and terminal substitutions. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 39:310-321. [PMID: 31514571 DOI: 10.1080/15257770.2019.1658116] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The effects of metal ions on the stabilities of duplexes containing a D-homochiral and heterochiral mismatched base pairs were studied. In some duplexes containing an internal mismatched base pair, significant stabilization by HgII and AgI ions was observed. While, in duplexes containing a terminal mismatched base pair, only the duplexes containing T-T and LT-T mispairs were significantly stabilized by HgII ions, and the stabilities of the duplexes containing T-T and LT-T mispairs exceeded those of the corresponding homochiral matched duplex. The results suggest that the formation of homo- and heterochiral T-HgII-T base pairs at duplex termini would be useful for the thermal and enzymatic stabilization of DNA-based nanodevice.
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Affiliation(s)
- Tatsuya Funai
- Department of Bioorganic Chemistry, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan
| | - Nahomi Adachi
- Department of Bioorganic Chemistry, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan
| | - Megumi Aotani
- Department of Bioorganic Chemistry, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan
| | - Shun-Ichi Wada
- Department of Bioorganic Chemistry, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan
| | - Hidehito Urata
- Department of Bioorganic Chemistry, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan
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Fujii A, Nakagawa O, Kishimoto Y, Okuda T, Nakatsuji Y, Nozaki N, Kasahara Y, Obika S. 1,3,9-Triaza-2-oxophenoxazine: An Artificial Nucleobase Forming Highly Stable Self-Base Pairs with Three Ag I Ions in a Duplex. Chemistry 2019; 25:7443-7448. [PMID: 30843298 DOI: 10.1002/chem.201900373] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Indexed: 12/23/2022]
Abstract
Metal-mediated base pairs (MMBPs) formed by natural or artificial nucleobases have recently been developed. The metal ions can be aligned linearly in a duplex by MMBP formation. The development of a three- or more-metal-coordinated MMBPs has the potential to improve the conductivity and enable the design of metal ion architectures in a duplex. This study aimed to develop artificial self-bases coordinated by three linearly aligned AgI ions within an MMBP. Thus, artificial nucleic acids with a 1,3,9-triaza-2-oxophenoxazine (9-TAP) nucleobase were designed and synthesized. In a DNA/DNA duplex, self-base pairs of 9-TAP could form highly stable MMBPs with three AgI ions. Nine equivalents of AgI led to the formation of three consecutive 9-TAP self-base pairs with extremely high stability. The complex structures of 9-TAP MMBPs were determined by using electrospray ionization mass spectrometry and UV titration experiments. Highly stable self-9-TAP MMBPs with three AgI ions are expected to be applicable to new DNA nanotechnologies.
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Affiliation(s)
- Akane Fujii
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Osamu Nakagawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Yuki Kishimoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Takumi Okuda
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Yusuke Nakatsuji
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Natsumi Nozaki
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Yuuya Kasahara
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan
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14
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Entering the Pantheon of 21 st Century Molecular Biology Tools: A Perspective on Digital PCR. Methods Mol Biol 2019; 1768:3-10. [PMID: 29717434 DOI: 10.1007/978-1-4939-7778-9_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
After several decades of relatively modest use, in the last several years digital PCR (dPCR) has grown to become the new gold standard for nucleic acid quantification. This coincides with the commercial availability of scalable, affordable, and reproducible droplet-based dPCR platforms in the past five years and has led to its rapid dissemination into diverse research fields and testing applications. Among these, it has been adopted most vigorously into clinical oncology where it is beginning to be used for plasma genotyping in cancer patients undergoing treatment. Additionally, innovation across the scientific community has extended the benefits of reaction partitioning beyond DNA and RNA quantification alone, and demonstrated its usefulness in evaluating DNA size and integrity, the physical linkage of colocalized markers, levels of enzyme activity and specific cation concentrations in a sample, and more. As dPCR technology gains in popularity and breadth, its power and simplicity can often be taken for granted; thus, the reader is reminded that due diligence must be exercised in order to make claims not only of precision but also of accuracy in their measurements.
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15
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Zhong W, Tang W, Tan Y, Fan J, Huang Q, Zhou D, Hong W, Liu Y. A DNA arithmetic logic unit for implementing data backtracking operations. Chem Commun (Camb) 2019; 55:842-845. [DOI: 10.1039/c8cc08441f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A data backtracking operation was successfully realized by adding redundant modules to the circuit, greatly improving the system reliability.
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Affiliation(s)
- Weiye Zhong
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen
- P. R. China
| | - Weiyang Tang
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen
- P. R. China
| | - Yun Tan
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen
- P. R. China
| | - Jin Fan
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen
- P. R. China
| | - Qichen Huang
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen
- P. R. China
| | - Danli Zhou
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen
- P. R. China
| | - Weimin Hong
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen
- P. R. China
| | - Yizhen Liu
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen
- P. R. China
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16
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Nakagawa O, Fujii A, Kishimoto Y, Nakatsuji Y, Nozaki N, Obika S. 2'-O,4'-C-Methylene-Bridged Nucleic Acids Stabilize Metal-Mediated Base Pairing in a DNA Duplex. Chembiochem 2018; 19:2372-2379. [PMID: 30168891 DOI: 10.1002/cbic.201800448] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Indexed: 11/08/2022]
Abstract
The 2'-O,4'-C-methylene-bridged or locked nucleic acid (2',4'-BNA/LNA), with an N-type sugar conformation, effectively improves duplex-forming ability. 2',4'-BNA/LNA is widely used to improve gene knockdown in nucleic acid based therapies and is used in gene diagnosis. Metal-mediated base pairs (MMBPs), such as thymine (T)-HgII -T and cytosine (C)-AgI -C have been developed and used as attractive tools in DNA nanotechnology studies. This study aimed to investigate the application of 2',4'-BNA/LNA in the field of MMBPs. 2',4'-BNA/LNA with 5-methylcytosine stabilized the MMBP of C with AgI ions. Moreover, the 2',4'-BNA/LNA sugar significantly improved the duplex-forming ability of the DNA/DNA complex, relative to that by the unmodified sugar. These results suggest that the sugar conformation is important for improving the stability of duplex-containing MMBPs. The results indicate that 2',4'-BNA/LNA can be applied not only to nucleic acid based therapies, but also to MMBP technologies.
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Affiliation(s)
- Osamu Nakagawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Akane Fujii
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Yuki Kishimoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Yusuke Nakatsuji
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Natsumi Nozaki
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka Suita, Osaka, 565-0871, Japan
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17
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Construction of a Preoperative Radiologic-Risk Signature for Predicting the Pathologic Status of Prostate Cancer at Radical Prostatectomy. AJR Am J Roentgenol 2018; 211:805-811. [PMID: 29995494 DOI: 10.2214/ajr.17.19360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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18
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Wang J, Wu CJ, Bao ML, Zhang J, Shi HB, Zhang YD. Using support vector machine analysis to assess PartinMR: A new prediction model for organ-confined prostate cancer. J Magn Reson Imaging 2018; 48:499-506. [PMID: 29437268 DOI: 10.1002/jmri.25961] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 01/19/2018] [Indexed: 12/17/2022] Open
Affiliation(s)
- Jing Wang
- Center for Medical Device Evaluation, CFDA; Beijing China
| | - Chen-Jiang Wu
- Department of Radiology; First Affiliated Hospital with Nanjing Medical University; Nanjing China
| | - Mei-Ling Bao
- Department of Pathology; First Affiliated Hospital with Nanjing Medical University; Nanjing China
| | - Jing Zhang
- Department of Radiology; First Affiliated Hospital with Nanjing Medical University; Nanjing China
| | - Hai-Bin Shi
- Department of Radiology; First Affiliated Hospital with Nanjing Medical University; Nanjing China
| | - Yu-Dong Zhang
- Department of Radiology; First Affiliated Hospital with Nanjing Medical University; Nanjing China
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19
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Wang C, Cheng N, Zhu L, Xu Y, Huang K, Zhu P, Zhu S, Fu W, Xu W. Colorimetric biosensor based on a DNAzyme primer and its application in logic gate operations for DNA screening. Anal Chim Acta 2017; 987:111-117. [DOI: 10.1016/j.aca.2017.08.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 07/07/2017] [Accepted: 08/03/2017] [Indexed: 10/19/2022]
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20
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Spectroscopic and TDDFT investigation on highly selective fluorogenic chemosensor and construction of molecular logic gates. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2017; 72:667-675. [DOI: 10.1016/j.msec.2016.11.131] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 11/18/2016] [Accepted: 11/26/2016] [Indexed: 11/23/2022]
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21
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Gao H, Yu X, Deng T, Sun M, Xiao X, Huang X, Chen Y, Li R. Event-specific detection of transgenic potato AV43-6-G7 using real-time and digital PCR methods. BMC Biotechnol 2016; 16:74. [PMID: 27784303 PMCID: PMC5081928 DOI: 10.1186/s12896-016-0303-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 10/13/2016] [Indexed: 01/09/2023] Open
Abstract
Background The isolation of unknown DNA sequences flanked by known sequences is an important task in the event-specific detection of GMOs. None of event-specific detection method was developed based on the junction sequence of an exogenous integrant in the transgenic potato AV43-6-G7. Results The flanking sequence between the exogenous fragment and recombinant chromosome of this potato was successfully acquired through exogenous gene 5′-RACE. The event-specific primers and Taqman probe were designed to amplify fragments spanning the exogenous DNA and potato genomic DNA. The specific real-time PCR and digital PCR detection methods for AV43-6-G7 potato were established based on primers designed according to the flanking sequences. The detection limit of the qualitative PCR assay was 0.01 % for AV43-6-G7 potato in 100 ng of potato genomic DNA, corresponding to approximately 11.6 copies of the potato haploid genome. The ddPCR assays for Potato AV43-6-G7 achieved a limit of quantification of approximately 58 target copies, with RSD ≤ 25 %. The aLOQ of this system was approximately 1.2 copies. Conclusions These results indicated that these event-specific methods would be useful for the identification of potato AV43-6-G7. Electronic supplementary material The online version of this article (doi:10.1186/s12896-016-0303-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongwei Gao
- Shandong Entry-Exit Inspection and Quarantine Bureau of People's Republic of China, Qingdao, China.
| | - Xiaofan Yu
- Qingdao University Medical College, Qingdao, China
| | - Tingting Deng
- Chinese Academy of Inspection and Quarantine Institute, Beijing, China
| | - Min Sun
- Shandong Entry-Exit Inspection and Quarantine Bureau of People's Republic of China, Qingdao, China
| | - Xizhi Xiao
- Shandong Entry-Exit Inspection and Quarantine Bureau of People's Republic of China, Qingdao, China
| | - Xin Huang
- Chinese Academy of Inspection and Quarantine Institute, Beijing, China
| | - Ying Chen
- Chinese Academy of Inspection and Quarantine Institute, Beijing, China
| | - Ronggui Li
- Qingdao University Medical College, Qingdao, China
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