1
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Effects of Neutral, Anionic and Cationic Polymer Brushes Grafted from Poly(para-phenylene vinylene) and Poly(para-phenylene ethynylene) on the Polymer’s Photoluminescent Properties. Polymers (Basel) 2022; 14:polym14142767. [PMID: 35890546 PMCID: PMC9322352 DOI: 10.3390/polym14142767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 11/17/2022] Open
Abstract
The conformation of a fluorescent polymer, in the solid state or in solution, plays a critical role in the polymer’s fluorescent properties. Thus, grafted side chains on a fluorescent polymer can directly influence its optical properties. In this study, the effect of grafted polymeric side chains on the photoluminescent properties of poly(para-phenylene vinylene) (PPV) and poly(para-phenylene ethynylene) (PPE) were investigated. Low- and high-molecular-weight grafts of neutral poly(n-butyl acrylate), cationic poly(trimethylaminoethyl methacrylate) and anionic poly(sulfopropyl acrylate) were grafted onto PPVs and PPEs, and the effect of the grafting on the graft copolymer’s absorption and emission wavelengths, the fluorescence intensity and the quantum yield were studied. The results indicate that in the case of the ionic grafts, contrary to the expectations, the polymers have a reduced quantum yield. This contrasts with the copolymers with uncharged side chains (PnBA), where a major increase in the quantum yield is seen for the self-quenching conjugated pristine polymers. These results reinforce that the molecular conformation of the polymer in a solid or solution plays a critical role in fluorescent polymers photoluminescent properties.
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2
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Faikhruea K, Choopara I, Somboonna N, Assavalapsakul W, Kim BH, Vilaivan T. Enhancing Peptide Nucleic Acid-Nanomaterial Interaction and Performance Improvement of Peptide Nucleic Acid-Based Nucleic Acid Detection by Using Electrostatic Effects. ACS APPLIED BIO MATERIALS 2022; 5:789-800. [PMID: 35119822 DOI: 10.1021/acsabm.1c01177] [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] [Indexed: 12/25/2022]
Abstract
Single-stranded peptide nucleic acid (PNA) probes interact strongly with several nanomaterials, and the interaction was diminished in the presence of complementary nucleic acid targets which forms the basis of many nucleic acid sensing platforms. As opposed to the negatively charged DNA probes, the charges on the PNA probes may be fine-tuned by incorporating amino acids with charged side chains. The contribution of electrostatic effects to the interaction between PNA probes and nanomaterials has been largely overlooked. This work reveals that electrostatic effects substantially enhanced the quenching of dye-labeled conformationally constrained pyrrolidinyl PNA probes by several nanomaterials including graphene oxide (GO), reduced graphene oxide, gold nanoparticles (AuNPs), and silver nanoparticles. The fluorescence quenching and the color change from red to purple in the case of AuNPs because of aggregation were inhibited in the presence of complementary nucleic acid targets. Thus, fluorescence and colorimetric assays for DNA and RNA that can distinguish even single-base-mismatched nucleic acids with improved sensitivity over conventional DNA probes were established. Both the GO- and AuNP-based sensing platforms have been successfully applied for the detection of real DNA and RNA samples in vitro and in living cells. This study emphasizes the active roles of electrostatic effects in the PNA-nanomaterial interactions, which paves the way toward improving the performance of PNA-nanomaterial based assays of nucleic acids.
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Affiliation(s)
- Kriangsak Faikhruea
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Ilada Choopara
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Naraporn Somboonna
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Wanchai Assavalapsakul
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Byeang Hyean Kim
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok 10330, Thailand
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3
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Teengam P, Nisab N, Chuaypen N, Tangkijvanich P, Vilaivan T, Chailapakul O. Fluorescent paper-based DNA sensor using pyrrolidinyl peptide nucleic acids for hepatitis C virus detection. Biosens Bioelectron 2021; 189:113381. [PMID: 34090155 DOI: 10.1016/j.bios.2021.113381] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 05/07/2021] [Accepted: 05/17/2021] [Indexed: 12/17/2022]
Abstract
A novel fluorescent paper-based DNA sensor employing a highly specific pyrrolidinyl peptide nucleic acid (acpcPNA) probe was developed for the sensitive and selective detection of hepatitis C virus (HCV). The acpcPNA was covalently immobilized onto partially oxidized cellulose paper via reductive alkylation between the amine and the aldehyde groups. The fluorescence-based detection was performed by monitoring the fluorescence signal response of a fluorescent dye that selectively binds to the single-strand region of the DNA target over the PNA probe employing a custom-made portable fluorescent camera gadget in combination with a smartphone camera. Under the optimal conditions, a linear relationship between the fluorescence change in the green channel and the amount of HCV DNA from 5 to 100 pmol with a correlation coefficient of 0.9956, and the limit of detection of 5 pmol were obtained for short synthetic oligonucleotides. The acpcPNA probe exhibited very high selectivity for the complementary oligonucleotides over the single-base-mismatched, two-base-mismatched, and non-complementary DNA targets. Benefitting from the signal amplification achieved through the numerous binding sites for the dye provided by the overhanging tail of long ssDNA target sequences, this system was successfully applied to detect the HCV complementary DNA (cDNA) obtained from clinical samples with satisfactory results. The proposed fluorescent paper-based sensor demonstrated a great potential to be used as a low-cost, simple, label-free, sensitive, and selective DNA sensor for point-of-care applications.
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Affiliation(s)
- Prinjaporn Teengam
- Electrochemistry and Optical Spectroscopy Center of Excellence, Department of Chemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand
| | - Narathorn Nisab
- Electrochemistry and Optical Spectroscopy Center of Excellence, Department of Chemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand
| | - Natthaya Chuaypen
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand
| | - Pisit Tangkijvanich
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand.
| | - Orawon Chailapakul
- Electrochemistry and Optical Spectroscopy Center of Excellence, Department of Chemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand.
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4
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Karunakaran I, Angamuthu A, Gopalan P. Impact of N-(2-aminoethyl) Glycine Unit on Watson-Crick Base Pairs. Z PHYS CHEM 2019. [DOI: 10.1515/zpch-2017-1095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Abstract
We aim to understand the structure and stability of the backbone tailored Watson-Crick base pairs, Guanine-Cytosine (GC), Adenine-Thymine (AT) and Adenine-Uracil (AU) by incorporating N-(2-aminoethyl) glycine units (linked by amide bonds) at the purine and pyrimidine sites of the nucleobases. Density functional theory (DFT) is employed in which B3LYP/6-311++G∗
∗ level of theory has been used to optimize all the structures. The peptide attached base pairs are compared with the natural deoxyribose nucleic acid (DNA)/ribonucleic acid (RNA) base pairs and the calculations are carried out in both the gas and solution phases. The structural propensities of the optimized base pairs are analyzed using base pair geometries, hydrogen bond distances and stabilization energies and, compared with the standard reference data. The structural parameters were found to correlate well with the available data. The addition of peptide chain at the back bone of the DNA/RNA base pairs results only with a minimal distortion and hence does not alter the structural configuration of the base pairs. Also enhanced stability of the base pairs is spotted while adding peptidic chain at the purine site rather than the pyrimidine site of the nucleobases. The stability of the complexes is further interpreted by considering the hydrogen bonded N–H stretching frequencies of the respective base pairs. The discrimination in the interaction energies observed in both gas and solution phases are resulted due to the existence of distinct lowest unoccupied molecular orbitals (LUMO) in the solution phase. The reactivity of the base pairs is also analyzed through the in-depth examinations on the highest occupied molecular orbital (HOMO)-LUMO orbitals.
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Affiliation(s)
- Indumathi Karunakaran
- Department of Physics , PSGR Krishnammal College for Women , Coimbatore 641004, Tamilnadu , India
| | - Abiram Angamuthu
- Department of Physics , Karunya Institute of Technology and Sciences , Coimbatore 641114, Tamilnadu , India
| | - Praveena Gopalan
- Department of Physics , PSGR Krishnammal College for Women , Coimbatore 641004, Tamilnadu , India , Tel.: +91-7812844344
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5
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Abstract
Fluorogenic oligonucleotide probes that can produce a change in fluorescence signal upon binding to specific biomolecular targets, including nucleic acids as well as non-nucleic acid targets, such as proteins and small molecules, have applications in various important areas. These include diagnostics, drug development and as tools for studying biomolecular interactions in situ and in real time. The probes usually consist of a labeled oligonucleotide strand as a recognition element together with a mechanism for signal transduction that can translate the binding event into a measurable signal. While a number of strategies have been developed for the signal transduction, relatively little attention has been paid to the recognition element. Peptide nucleic acids (PNA) are DNA mimics with several favorable properties making them a potential alternative to natural nucleic acids for the development of fluorogenic probes, including their very strong and specific recognition and excellent chemical and biological stabilities in addition to their ability to bind to structured nucleic acid targets. In addition, the uncharged backbone of PNA allows for other unique designs that cannot be performed with oligonucleotides or analogues with negatively-charged backbones. This review aims to introduce the principle, showcase state-of-the-art technologies and update recent developments in the areas of fluorogenic PNA probes during the past 20 years.
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Affiliation(s)
- Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
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6
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Al Sulaiman D, Chang JYH, Ladame S. Subnanomolar Detection of Oligonucleotides through Templated Fluorogenic Reaction in Hydrogels: Controlling Diffusion to Improve Sensitivity. Angew Chem Int Ed Engl 2017; 56:5247-5251. [PMID: 28382640 PMCID: PMC5502887 DOI: 10.1002/anie.201701356] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/02/2017] [Indexed: 02/06/2023]
Abstract
Oligonucleotide-templated reactions are valuable tools for nucleic acid sensing both in vitro and in vivo. They are typically carried out under conditions that make any reaction in the absence of template highly unfavorable (most commonly by using a low concentration of reactants), which has a negative impact on the detection sensitivity. Herein, we report a novel platform for fluorogenic oligonucleotide-templated reactions between peptide nucleic acid probes embedded within permeable agarose and alginate hydrogels. We demonstrate that under conditions of restricted mobility (that is, limited diffusion), non-specific interactions between probes are prevented, thus leading to lower background signals. When applied to nucleic acid sensing, this accounts for a significant increase in sensitivity (that is, lower limit of detection). Optical nucleic acid sensors based on fluorogenic peptide nucleic acid probes embedded in permeable, physically crosslinked, alginate beads were also engineered and proved capable of detecting DNA concentrations as low as 100 pm.
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Affiliation(s)
- Dana Al Sulaiman
- Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Jason Y H Chang
- Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Sylvain Ladame
- Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
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7
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Al Sulaiman D, Chang JYH, Ladame S. Subnanomolar Detection of Oligonucleotides through Templated Fluorogenic Reaction in Hydrogels: Controlling Diffusion to Improve Sensitivity. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701356] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Dana Al Sulaiman
- Department of Bioengineering; Imperial College London; South Kensington Campus London SW7 2AZ UK
| | - Jason Y. H. Chang
- Department of Bioengineering; Imperial College London; South Kensington Campus London SW7 2AZ UK
| | - Sylvain Ladame
- Department of Bioengineering; Imperial College London; South Kensington Campus London SW7 2AZ UK
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8
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Thivaios I, Kakogianni S, Bokias G. A Library of Quinoline-Labeled Water-Soluble Copolymers with pH-Tunable Fluorescence Response in the Acidic pH Region. Macromolecules 2016. [DOI: 10.1021/acs.macromol.6b00258] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ioannis Thivaios
- Department
of Chemistry, University of Patras, University Campus, Rio-Patras GR26504, Greece
| | - Sofia Kakogianni
- Department
of Chemistry, University of Patras, University Campus, Rio-Patras GR26504, Greece
| | - Georgios Bokias
- Department
of Chemistry, University of Patras, University Campus, Rio-Patras GR26504, Greece
- Foundation for
Research and Technology Hellas/Institute of Chemical Engineering Sciences
(FORTH/ICE-HT), Platani Str., Patras GR26504, Greece
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9
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Sengupta PP, Gloria JN, Amato DN, Amato DV, Patton DL, Murali B, Flynt AS. Utilizing Intrinsic Properties of Polyaniline to Detect Nucleic Acid Hybridization through UV-Enhanced Electrostatic Interaction. Biomacromolecules 2015; 16:3217-25. [PMID: 26388289 PMCID: PMC4822489 DOI: 10.1021/acs.biomac.5b00935] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Detection of specific RNA or DNA molecules by hybridization to "probe" nucleic acids via complementary base-pairing is a powerful method for analysis of biological systems. Here we describe a strategy for transducing hybridization events through modulating intrinsic properties of the electroconductive polymer polyaniline (PANI). When DNA-based probes electrostatically interact with PANI, its fluorescence properties are increased, a phenomenon that can be enhanced by UV irradiation. Hybridization of target nucleic acids results in dissociation of probes causing PANI fluorescence to return to basal levels. By monitoring restoration of base PANI fluorescence as little as 10(-11) M (10 pM) of target oligonucleotides could be detected within 15 min of hybridization. Detection of complementary oligos was specific, with introduction of a single mismatch failing to form a target-probe duplex that would dissociate from PANI. Furthermore, this approach is robust and is capable of detecting specific RNAs in extracts from animals. This sensor system improves on previously reported strategies by transducing highly specific probe dissociation events through intrinsic properties of a conducting polymer without the need for additional labels.
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Affiliation(s)
- Partha Pratim Sengupta
- Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Jared N. Gloria
- Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Dahlia N. Amato
- School of Polymers and High Performance Materials, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Douglas V. Amato
- School of Polymers and High Performance Materials, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Derek L. Patton
- School of Polymers and High Performance Materials, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Beddhu Murali
- School of Computing, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Alex S. Flynt
- Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
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10
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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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11
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Zhu X, Wang X, He F, Tang F, Li L. Self-assembled nanocomposite film with tunable enhanced fluorescence for the detection of DNA. ACS APPLIED MATERIALS & INTERFACES 2015; 7:1334-1339. [PMID: 25539666 DOI: 10.1021/am507772e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In this study, a simple and environmentally friendly, silver nanocomposite film was prepared via the in situ reduction of silver ions in self-assembled chitosan (CS)/sodium alginate film matrixes. Negatively charged DNA containing the fluorescent intercalator acriflavine (Acf) was assembled on the surface of the silver nanocomposite film, to facilitate the detection of DNA. A tunable fluorescence enhancement was achieved for the Acf in the silver nanocomposite film simply by changing the thickness of the interlayer between the DNA and the silver nanocomposite film. Using the interlayer prepared by an assembly of poly(acrylic acid) and CS, a significant enhancement in the fluorescence of Acf was obtained. Owing to the ability of Acf to intercalate into DNA, this hybrid system with an enhanced Acf fluorescence could be used to monitor the template-independent DNA elongation process in a facile, high-efficiency, label-free fashion.
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Affiliation(s)
- Xi Zhu
- School of Materials Science and Engineering, University of Science and Technology Beijing , Beijing 100083, P. R. China
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12
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Artificial Nucleic Acid Probes and Their Applications in Clinical Microbiology. METHODS IN MICROBIOLOGY 2015. [DOI: 10.1016/bs.mim.2015.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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13
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Wang X, He F, Zhu X, Tang F, Li L. Hybrid silver nanoparticle/conjugated polyelectrolyte nanocomposites exhibiting controllable metal-enhanced fluorescence. Sci Rep 2014; 4:4406. [PMID: 24638208 PMCID: PMC3957278 DOI: 10.1038/srep04406] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 03/03/2014] [Indexed: 02/04/2023] Open
Abstract
Metal-enhanced fluorescence of conjugated polyelectrolytes (CPs) is realized using a simple, green hybrid Ag nanocomposite film. Ag nanoparticles (Ag NPs) are pre-prepared by sodium citrate reduction and incorporated into agarose by mixing to form an Ag-containing agarose film (Ag@agarose). Through variation of the amount of Ag NPs in the Ag@agarose film as well as the thickness of the interlayer between CPs and the Ag@agarose film prepared of layer-by-layer assembly of chitosan and sodium alginate, a maximum 8.5-fold increase in the fluorescence of CPs is obtained. After introducing tyrosinase, this system also can be used to detect phenolic compounds with high sensitivity and good visualization under ultraviolet light.
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Affiliation(s)
- Xiaoyu Wang
- State Key Laboratory for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China
| | - Fang He
- State Key Laboratory for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China
| | - Xi Zhu
- State Key Laboratory for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China
| | - Fu Tang
- State Key Laboratory for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China
| | - Lidong Li
- State Key Laboratory for Advanced Metals and Materials, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China
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14
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Bissonnette L, Bergeron MG. Next revolution in the molecular theranostics of infectious diseases: microfabricated systems for personalized medicine. Expert Rev Mol Diagn 2014; 6:433-50. [PMID: 16706745 DOI: 10.1586/14737159.6.3.433] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The molecular diagnosis of infectious diseases is currently going through a revolution sustained by the regulatory approval of amplification tests that have been shown to be equivalent or superior to existing gold standard methods. The recent approval of a microarray system for the pharmacogenomic profiling of cytochrome P450-mediated drug metabolism is paving the way to novel, rapid, sensitive, robust and economical microfabricated systems for point-of-care diagnostics, which are utilized closer and closer to the patient's bedside. These systems will enable the multiparametric genetic evaluation of several medical conditions, including infectious diseases. This forecoming revolution will position molecular theranostics in a broader integrated view of personalized medicine, which exploits genetic information from microbes and human hosts to optimize patient management and disease treatment.
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Affiliation(s)
- Luc Bissonnette
- Département de Biologie Médicale (Microbiologie), Faculté de Médecine, Université Laval, Québec City, Canada.
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15
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Gnapareddy B, Kim JA, Dugasani SR, Tandon A, Kim B, Bashar S, Choi JA, Joe GH, Kim T, Ha TH, Park SH. Fabrication and characterization of PNA–DNA hybrid nanostructures. RSC Adv 2014. [DOI: 10.1039/c4ra04751f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The feasibility of constructing PNA–DNA hybrid nanostructures by conventional free solution annealing and substrate assisted growth methods was studied.
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Affiliation(s)
- Bramaramba Gnapareddy
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT)
- Sungkyunkwan University
- Suwon 440-746, Korea
- Department of Physics
- Sungkyunkwan University
| | - Jang Ah Kim
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT)
- Sungkyunkwan University
- Suwon 440-746, Korea
- School of Mechanical Engineering
- Sungkyunkwan University
| | - Sreekantha Reddy Dugasani
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT)
- Sungkyunkwan University
- Suwon 440-746, Korea
- Department of Physics
- Sungkyunkwan University
| | - Anshula Tandon
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT)
- Sungkyunkwan University
- Suwon 440-746, Korea
- Department of Physics
- Sungkyunkwan University
| | - Byeonghoon Kim
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT)
- Sungkyunkwan University
- Suwon 440-746, Korea
- Department of Physics
- Sungkyunkwan University
| | - Saima Bashar
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT)
- Sungkyunkwan University
- Suwon 440-746, Korea
- Department of Physics
- Sungkyunkwan University
| | | | | | - Taesung Kim
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT)
- Sungkyunkwan University
- Suwon 440-746, Korea
- School of Mechanical Engineering
- Sungkyunkwan University
| | - Tai Hwan Ha
- Research Center of Integrative Cellulomics
- Korea Research Institute of Bioscience and Biotechnology (KRIBB)
- Daejeon 305-806, Korea
| | - Sung Ha Park
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT)
- Sungkyunkwan University
- Suwon 440-746, Korea
- Department of Physics
- Sungkyunkwan University
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16
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Sun J, Cai M, Lavigne JJ. Supramolecular Chemistry in In VitroBiosensors. Supramol Chem 2012. [DOI: 10.1002/9780470661345.smc177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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17
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Wang X, He F, Tang F, Li L. Optically amplified DNA detection on self-assembled solid films using conjugated polyelectrolytes. ACTA ACUST UNITED AC 2012. [DOI: 10.1039/c2jm32534a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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18
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Lepage PH, Peytavi R, Bergeron MG, Leclerc M. Amplification strategy using aggregates of ferrocene-containing cationic polythiophene for sensitive and specific electrochemical detection of DNA. Anal Chem 2011; 83:8086-92. [PMID: 21932839 DOI: 10.1021/ac200713f] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report a new electrochemical amplification strategy for an ultrasensitive electrochemical detection of DNA sequences using aggregates composed of a water-soluble, ferrocene-functionalized polythiophene. A two-step hybridization is performed at one addressing surface with PNA capture probes whereas the electrochemical detection is done on an electrode nearby. Specific and quantitative detection of DNA targets with a detection limit of 4 × 10(-16) M (about 4 zeptomoles or about 2500 copies of oligonucleotides) was achieved.
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Affiliation(s)
- Patricia Harding Lepage
- Canada Research Chair on Electroactive and Photoactive Polymers, Département de Chimie, Université Laval, Québec City, Québec, Canada
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Tedeschi T, Calabretta A, Bencivenni M, Manicardi A, Corrado G, Caramante M, Corradini R, Rao R, Sforza S, Marchelli R. A PNA microarray for tomato genotyping. MOLECULAR BIOSYSTEMS 2011; 7:1902-7. [PMID: 21465054 DOI: 10.1039/c1mb05048f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The design and development of a PNA microarray designed for the simultaneous identification of several SNPs characteristic of seven different tomato varieties is described. Highly selective arginine-based monomer containing PNAs (Arg-PNAs) have been used in order to obtain very selective probes. Seven modified PNA probes were synthesised and their binding properties in solution were studied. PNA-microarrays based on these probes were prepared and applied to SNP discrimination in model experiments using oligonucleotide mixtures simulating the different sequences of the seven tomato varieties. The strength and the limitations of such a system for SNP recognition are thoroughly discussed.
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Affiliation(s)
- Tullia Tedeschi
- Dipartimento di Chimica Organica e Industriale, University of Parma, Parco Area delle Scienze 17a, I-43124, Parma, Italy
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20
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Klingstedt T, Nilsson KPR. Conjugated polymers for enhanced bioimaging. Biochim Biophys Acta Gen Subj 2011; 1810:286-96. [DOI: 10.1016/j.bbagen.2010.05.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Revised: 04/22/2010] [Accepted: 05/05/2010] [Indexed: 10/19/2022]
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21
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Optical detection systems using immobilized aptamers. Biosens Bioelectron 2011; 26:3725-36. [PMID: 21419619 DOI: 10.1016/j.bios.2011.02.031] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 02/16/2011] [Accepted: 02/18/2011] [Indexed: 11/24/2022]
Abstract
Advances in the development and the applications of optical biosensing systems based on immobilized aptamers are presented. These nucleic acid sequences have been used as new molecular recognition elements to develop heterogeneous assays, biosensors and microarrays. Among different detection modes that have been employed, optical ones which are described here are among the most used. Since their first report in 1996, numerous optical detection systems using aptamers and mainly based on fluorescence have been developed. Two main approaches have been used: label-based (using fluorophore, luminophore, enzyme, nanoparticles) or aptamer label-free detection systems (e.g. surface plasmon resonance, optical resonance). Most methods are based on a labeling approach. Some targets can be optically detected using not only colorimetry, chemiluminescence or the most developed fluorescence mode but also more recent non conventional optical methods such as surface plasmon-coupled directional emission (SPCDE). The first SPCDE-based aptasensor for thrombin detection has recently been reported in 2009. Aptasensors based on surface-enhanced Raman scattering spectroscopy (SERS) which presents advantages compared to fluorescence have also been described. Different label-free techniques have recently been shown to be suitable for developing performant aptasensors or aptamer-based microarrays, such as surface plasmon resonance (SPR), diffraction grating, evanescent-field-coupled (EFC) waveguide-mode, optical resonance or Brewster angle straddle interferometry (BASI). Important advances have been realized on optical aptamer-based detection systems that appear as highly efficient devices with enormous potential.
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22
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Liu X, Fan Q, Huang W. DNA biosensors based on water-soluble conjugated polymers. Biosens Bioelectron 2011; 26:2154-64. [DOI: 10.1016/j.bios.2010.09.025] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 09/06/2010] [Accepted: 09/14/2010] [Indexed: 01/22/2023]
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23
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Bae SW, Cho MS, Hur SS, Chae CB, Chung DS, Yeo WS, Hong JI. A Doubly Signal-Amplified DNA Detection Method Based on Pre-Complexed [Ru(bpy)3]2+-Doped Silica Nanoparticles. Chemistry 2010; 16:11572-5. [DOI: 10.1002/chem.201001255] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Indexed: 11/10/2022]
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24
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Kanjanawarut R, Su X. Colorimetric detection of DNA using unmodified metallic nanoparticles and peptide nucleic acid probes. Anal Chem 2010; 81:6122-9. [PMID: 20337394 DOI: 10.1021/ac900525k] [Citation(s) in RCA: 182] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have developed a colorimetric assay for DNA detection based on the aggregation of unmodified metallic nanoparticles. Charge neutral peptide nucleic acids (PNA) are used as a "coagulant" of citrate anion-coated particles and as hybridization probe. In the absence of a complementary target DNA, free PNA molecules in solution induce aggressive particle aggregation because of the removal of charge repulsion as a result of PNA coating on nanoparticles. When a complementary DNA is present and PNA-DNA complexes are formed, the particles remain stable because the negative charges of the DNA strands in the complexes adsorbed on the particle surface ensure sufficient charge repulsions. In this method, no probe immobilization is needed and PNA-DNA hybridization occurs in a homogeneous phase. The assay results are displayed as rapidly as the changes in color and/or in UV-vis adsorption spectra of the colloidal solutions. We have validated the assay principle using gold- and silver-nanoparticles (AuNPs and AgNPs), with the involvement of a shorter (13 mer) and a longer (22 mer) probe sequences. A specific DNA can be detected in the presence of at least 10 times of interference DNA, and the detection limit is at a DNA/PNA ratio of 0.05. When NaCl is added to accelerate the particle aggregation, the selectivity is further improved, and single-base-mismatch discrimination is achieved. A two-component assay using a mixture of AuNPs and AgNPs has also been constituted, aiming to improve the result accuracy by making use of the multiple aggregation signatures from the two types of particles. For single-base-mismatch discrimination, the AgNPs offer a higher sensitivity than AuNPs by showing more obvious spectra and color alternation, and the two-component assay offers three parameters in the UV-vis adsorption spectra.
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Affiliation(s)
- Roejarek Kanjanawarut
- Institute of Materials Research and Engineering, ASTAR (Agency for Science, Technology and Research), 3 Research Link, Singapore 117602
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25
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26
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Tang Y, Achyuthan KE, Whitten DG. Label-free and real-time sequence specific DNA detection based on supramolecular self-assembly. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:6832-6837. [PMID: 20030336 DOI: 10.1021/la904008v] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A new label-free, optical method was developed to detect sequence-specific DNA based on supramolecular self-assembly. A cationic phenylene ethynylene oligomer with two pairs of positively charged side chains (OPE-2) can form a J-dimer or J-aggregate with negatively charged DNA by a combination of electrostatic and hydrophobic interactions. At microM concentrations of dsDNA (number of bases in ssDNA ranges from 8 to 32), the optimum supramolecular self-assembly occurs between OPE-2 and dsDNA and is characterized by a new absorption peak emerging at 418 nm and an increase in fluorescence intensity (about 4.5-fold for dsDNA(1)). In contrast, the self-assembled complexes between OPE-2 and ssDNA are less readily formed under the same conditions. Interestingly, the induced circular dichroism (CD) signal for OPE-2/ssDNA is quite strong, likely owing to the self-assembly onto ssDNA simultaneously templating helix formation. In contrast, the induced CD signal for OPE-2/dsDNA is weak, likely because the dsDNA is in a double helix conformation, and OPE-2 associated with the dsDNA should be outside of the helix. In fact, there is a steady decrease in the induced CD signal for ssDNA with the addition of equimolar complementary ssDNA over time that allows the monitoring of DNA hybridization in real time. Introduction of mismatched bases into the target DNA sequence prevents the full hybridization between ssDNA and the target DNA. For these cases, the decrease in the induced CD signals occurs more slowly and to a lesser extent, as some of the unhybridized portions may remain in helical association with OPE-2. In view of these observed signal changes, sequence specific DNA and single nucleotide mismatch can be detected in a very simple and sensitive manner without any modification of the DNA.
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Affiliation(s)
- Yanli Tang
- Center for Biomedical Engineering and Department of Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, New Mexico 87131, USA
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27
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Aneja A, Mathur N, Bhatnagar PK, Mathur PC. Detection of known mutations for medical diagnostics by FRET spectroscopy. JOURNAL OF BIOMATERIALS SCIENCE-POLYMER EDITION 2010; 20:1823-30. [PMID: 19793441 DOI: 10.1163/156856208x386426] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A rapid, simple and low-cost method for the detection of known mutations in DNA oligonucleotide in a biothreat agent, Bacillus anthracis, has been reported. The technique is based on fluorescence resonance energy transfer (FRET), that utilizes a cationic conjugated polymer and a PNA probe labeled with Fluorescein dye (PNAC*). When the PNA probe is hybridized with a complementary target ssDNA and its mutated sequences separately, the energy transfer from polymer to PNAC*/ssDNA complex decreases with increasing number of mutations. It means that the efficiency of FRET or the degree of hybridization depends on the extent of mutations in the DNA sequence. The method is sensitive enough to detect upto 4 bases mismatch. We have, thus, explored a possible application of fluorescence-based technology for medical diagnostics.
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Affiliation(s)
- Anamika Aneja
- Department of Electronic Science, University of Delhi South Campus, New Delhi-110021, India.
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28
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Lee K, Povlich LK, Kim J. Recent advances in fluorescent and colorimetric conjugated polymer-based biosensors. Analyst 2010; 135:2179-89. [DOI: 10.1039/c0an00239a] [Citation(s) in RCA: 146] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Reppy MA. Structure, Emissive Properties, and Reporting Abilities of Conjugated Polymers. ADVANCED FLUORESCENCE REPORTERS IN CHEMISTRY AND BIOLOGY II 2010. [DOI: 10.1007/978-3-642-04701-5_12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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30
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Feng X, Xu Q, Liu L, Wang S. A new light-harvesting conjugated polyelectrolyte microgel for DNA and enzyme detections. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:13737-13741. [PMID: 19527041 DOI: 10.1021/la901444c] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A new fluorescent microgel containing the CP moiety (PFP-NIPAm) was prepared with the size within 100 nm. Covalent linking of the conjugated polyelectrolyte moiety into the microgel prevents leakage of the fluorophore while keeping its fluorescence property. The new fluorescent microgel can be used as an optical platform to detect DNA and enzyme. More importantly, because the electrostatic attraction dominates the interactions between cationic PFP-NIPAm microgel and negatively charged target, washing with high ionic strength aqueous solution can block their interactions and displace the target from the PFP-NIPAm microgel. Thus, PFP-NIPAm can be readily reusable for detection. Another unique feature is that the PFP-NIPAm microgel extends the detection media from homogeneous solution to solid phase, which shows great potential for biodetection in the real world using conjugated polymers. Furthermore, the detection can be carried out under UV light, and no expensive detection instrumentation is needed. In principle, such an assay system could be expanded to a high-throughput assay.
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Affiliation(s)
- Xuli Feng
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, PR China
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31
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Calabretta A, Tedeschi T, Di Cola G, Corradini R, Sforza S, Marchelli R. Arginine-based PNA microarrays for APOE genotyping. MOLECULAR BIOSYSTEMS 2009; 5:1323-30. [PMID: 19823748 DOI: 10.1039/b909912n] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Four modified PNAs containing one chiral monomer bearing two arginine-derived side chains, with the correct configuration for specific and stable DNA binding, were synthesized, complementary to two DNA tracts in the APOE gene containing SNPs related to the insurgence of Alzheimer's disease. PNA binding performances were first tested in solution against complementary and mismatched oligonucleotides by measuring melting temperatures, and showed high specificity in SNP recognition. In order to set up a new diagnostic platform for APOE genotyping, PNA microarrays were then developed with the synthesized modified PNAs. PNA probe deposition protocols on microarrays were optimized in order to minimize cross-contamination due to carry over. The microarrays obtained by arginine-based PNA deposition were incubated with complementary and mismatched oligonucleotides, showing excellent mismatch recognition on the microarray platform. The specificity of the microarrays was finally tested with oligonucleotide mixtures simulating the real genotype profiles. Six different hybridisation patterns related to six different genotypes in the APOE gene were found to be clearly distinct in microarray experiments, demonstrating the potential of this approach for highly specific genetic analysis.
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Affiliation(s)
- Alessandro Calabretta
- Department of Organic and Industrial Chemistry, University of Parma, Viale G.P. Usberti 17a, I-43100, Parma, Italy
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32
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Russ Algar W, Massey M, Krull UJ. The application of quantum dots, gold nanoparticles and molecular switches to optical nucleic-acid diagnostics. Trends Analyt Chem 2009. [DOI: 10.1016/j.trac.2008.11.012] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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33
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Zheng W, He L. Label-Free, Real-Time Multiplexed DNA Detection Using Fluorescent Conjugated Polymers. J Am Chem Soc 2009; 131:3432-3. [DOI: 10.1021/ja809175q] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Weiming Zheng
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695
| | - Lin He
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695
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34
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Fang Z, Kelley SO. Direct electrocatalytic mRNA detection using PNA-nanowire sensors. Anal Chem 2009; 81:612-7. [PMID: 19086897 DOI: 10.1021/ac801890f] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report an electrochemical nucleic acids sensing system that exhibits high sensitivity and specificity when challenged with heterogeneous samples of RNA. The platform directly detects specific RNA sequences in cellular and clinical samples without any sample labeling or PCR amplification. The sensor features an electrode platform consisting of three-dimensional gold nanowires, and DNA or RNA hybridization is detected using an electrocatalytic reporter system. In this study, probes made of peptide nucleic acid (PNA) are used to detect a newly identified cancer biomarkera gene fusion recently associated with prostate cancer. The system is able to detect the fusion sequence with 100 fM sensitivity, and retains high sensitivity even in the presence of a large excess of non-complementary sequences. Moreover, the sensor is able to detect the fusion sequence in as little as 10 ng of mRNA isolated from cell lines or 100 ng total RNA from patient tissue samples. The PNA-nanowire nucleic acids sensor described is one of the first electrochemical sensors to directly detect specific mRNAs in unamplified patient samples.
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Affiliation(s)
- Zhichao Fang
- Leslie Dan Faculty of Pharmacy, Department of Pharmaceutical Sciences, and Faculty of Medicine, Department of Biochemistry, University of Toronto, Ontario M5S 3M2, Canada
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35
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Joung HA, Lee NR, Lee SK, Ahn J, Shin YB, Choi HS, Lee CS, Kim S, Kim MG. High sensitivity detection of 16s rRNA using peptide nucleic acid probes and a surface plasmon resonance biosensor. Anal Chim Acta 2008; 630:168-73. [PMID: 19012828 DOI: 10.1016/j.aca.2008.10.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2008] [Revised: 09/29/2008] [Accepted: 10/01/2008] [Indexed: 11/18/2022]
Abstract
A signal enhancing method allowing highly sensitive detection of E. coli 16s rRNA was developed using peptide nucleic acid (PNA) as a capture probe and a surface plasmon resonance (SPR) sensor as a detector. 16s rRNA has been used as a genetic marker for identification of organisms, and can be analyzed directly without PCR amplification due to the relatively high number of copies. PNA has a neutral backbone structure, therefore hybridization with 16s rRNA results in the ionic condition being changed from neutral to negative. A cationic Au nanoparticle was synthesized and used for signal amplification by ionic interaction with 16s rRNA hybridized on the PNA probe-immobilized SPR sensor chip. This method resulted in a detection limit of E. coli rRNA of 58.2+/-1.37 pg mL(-1). Using this analytical method, Staphylococcus aureus was detected without purification of rRNA.
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Affiliation(s)
- Hyou-Arm Joung
- BioNanotechnology Research Center, KRIBB, Daejeon, Republic of Korea
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36
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Chiari M, Cretich M, Damin F, Di Carlo G, Oldani C. Advanced polymers for molecular recognition and sensing at the interface. J Chromatogr B Analyt Technol Biomed Life Sci 2008; 866:89-103. [DOI: 10.1016/j.jchromb.2008.01.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2007] [Revised: 12/07/2007] [Accepted: 01/04/2008] [Indexed: 11/29/2022]
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37
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Ho HA, Najari A, Leclerc M. Optical detection of DNA and proteins with cationic polythiophenes. Acc Chem Res 2008; 41:168-78. [PMID: 18198841 DOI: 10.1021/ar700115t] [Citation(s) in RCA: 387] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In recent years, intense research has been carried out worldwide with the goal of developing simple, sensitive, and specific detection tools for biomedical applications. Along these lines, we reported in 2002 on cationic polythiophene derivatives able to provide ultrasensitive detection levels and the capability to distinguish perfect matches from oligonucleotides having as little as a single base mismatch. It was shown that the intrinsic fluorescence of the random-coil polymers quenches as a result of the planar, highly conjugated conformation adopted by the polymers when complexed with a single-strand DNA (ssDNA) capture probe but increases again after hybridization with the perfectly matched complementary strand. This change in fluorescence intensity is mainly due to a modification in the delocalization of pi electrons along the carbon chain backbone that occurs when switching between the two conformations. Thus, by monitoring, via the change in fluorescence intensity, the hybridization of the complementary ssDNA target with the "duplex", one could detect as little as 220 complementary target molecules in a 150 microL sample volume (0.36 zmol) in less than 1 hour. Building on this initial concept, we then reported that tagging the DNA probe with a suitable fluorophore dramatically increases the detection sensitivity. This novel molecular system involves the self-assembly of aggregates of duplexes in solution, prior to the introduction of the target, which allows a highly efficient resonance energy transfer (RET) between a "donor" (being the complex formed of the DNA double helix and the polymer chain wrapped around it) and a large number of neighboring "acceptors" (the fluorophores attached to the DNA probes). The massive intrinsic signal amplification (fluorescence chain reaction or FCR) provided by this novel integrated molecular system allows the specific detection of as little as five dsDNA copies in a 3 mL sample volume in only 5 minutes, without the need for prior amplification of the target. Clearly, direct and reliable detection of DNA hybridization without prior PCR amplification or chemical tagging of the genetic target is now possible with this methodology. We have also shown that proteins can be detected following a similar strategy. Impressive results have also been reported by direct and specific staining of targeted proteins. All these features have recently allowed the development of responsive polymeric supports for the detection of DNA and proteins. All these assays that do not require any chemical manipulation of the biological targets or sophisticated experimental procedures should soon lead to major advances in genomics and proteomics.
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Affiliation(s)
- Hoang-A. Ho
- Canada Research Chair on Electroactive and Photoactive Polymers, Department of Chemistry, Université Laval, Quebec City, Quebec G1K 7P4, Canada
| | - Ahmed Najari
- Canada Research Chair on Electroactive and Photoactive Polymers, Department of Chemistry, Université Laval, Quebec City, Quebec G1K 7P4, Canada
| | - Mario Leclerc
- Canada Research Chair on Electroactive and Photoactive Polymers, Department of Chemistry, Université Laval, Quebec City, Quebec G1K 7P4, Canada
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38
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He F, Feng F, Wang S. Conjugated polyelectrolytes for label-free DNA microarrays. Trends Biotechnol 2008; 26:57-9. [PMID: 18191257 DOI: 10.1016/j.tibtech.2007.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2007] [Revised: 10/23/2007] [Accepted: 10/24/2007] [Indexed: 10/22/2022]
Abstract
Classical strategies for gene microarrays require labeling of probes or target nucleic acids with signaling molecules, a process that is expensive, time consuming and not always reliable. Bazan and colleagues showed that a nucleic acid-binding cationic conjugated polyelectrolyte can be used in label-free DNA microarrays based on surfaces modified with neutral peptide nucleic acid (PNA) probes. This technique provides a simple and sensitive method for DNA detection without the need for covalent labeling of target DNA.
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Affiliation(s)
- Fang He
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100080, People's Republic of China
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39
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Sun C, Gaylord BS, Hong JW, Liu B, Bazan GC. Application of cationic conjugated polymers in microarrays using label-free DNA targets. Nat Protoc 2007; 2:2148-51. [PMID: 17853870 DOI: 10.1038/nprot.2007.307] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A fluorescence-based microarray technique that does not require target DNA labeling is detailed. This 'label-free' approach utilizes a cationic, water-soluble conjugated polymer PFBT (poly[9,9'-bis(6''-(N,N,N-trimethylammonium)hexyl)fluorene-co-alt-4,7-(2,1,3-benzothiadiazole) dibromide]), and neutral PNA (peptide nucleic acid) hybridization probes. DNA hybridization to immobilized PNA spots results in a change in the net charge at that particular surface. Electrostatic interactions between the cationic polymer and negatively charged DNA bind the polymer to the hybrid DNA/PNA complex. By exciting the conjugated polymer at 488 nm on a commercial microarray scanner, the presence of the target is directly indicated by the fluorescence emission of the polymer. This feature eliminates the necessity of target labeling required in traditional microarray protocols. There are five steps involved in the procedure before scanning or imaging the array: (i) slide hydration, (ii) target hybridization, (iii) post-hybridization washing, (iv) polymer application and (v) polymer washing. Each step takes 20 min to 1 h. The overall protocol requires approximately 2-3 h.
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Affiliation(s)
- ChengJun Sun
- Sirigen Inc., Santa Barbara, California 93111, USA
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40
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Su X, Teh HF, Lieu X, Gao Z. Enzyme-based colorimetric detection of nucleic acids using peptide nucleic acid-immobilized microwell plates. Anal Chem 2007; 79:7192-7. [PMID: 17708676 DOI: 10.1021/ac0709403] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The development of label-free or nonlabeling assays for nucleic acids is important in basic biological research and biomedical diagnosis. In this study, we have developed an enzyme-based colorimetric assay for nucleic acids, which combines the robustness of nonlabeling of DNA and RNA samples and the adequate sensitivity of enzymatic reactions. The core of this assay is the use of neutral peptide nucleic acid (PNA) as capture probe and the electrostatic adsorption of horseradish peroxidase (HRP) on hybridized, negatively charged nucleic acids to report the hybridization events, through HRP-catalyzed color reactions of 3,3',5,5'-tetramethylbenzidine and H(2)O(2). The proposed assay has been validated with fully complementary and single base-mismatched DNAs of different chain lengths. The proposed assay has also been validated with total RNA samples extracted from two human cancer cell lines (A 549 lung cancer cell and HeLa cell) for microRNA detection in real samples. Through extensive optimizations of HRP adsorption and nucleic acid hybridization conditions, detection limits of 0.1-0.2 nM for DNA (depending on chain length) and approximately 2 microg of total RNA have been achieved. Surface plasmon resonance spectroscopy has been used to elucidate the HRP adsorption and PNA-nucleic acid hybridizations through real-time measurements and to provide guidance for the development of the colorimetric assay.
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Affiliation(s)
- Xiaodi Su
- Institute of Materials Research and Engineering, 3 Research Link, Singapore 117602.
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41
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Ginya H, Asahina J, Yoshida M, Segawa O, Asano T, Ikeda H, Hatano YM, Shishido M, Johansson BM, Zhou Q, Hallberg M, Takahashi M, Nyberg F, Tajima H, Yohda M. Development of the Handy Bio-Strand and its application to genotyping of OPRM1 (A118G). Anal Biochem 2007; 367:79-86. [PMID: 17570330 DOI: 10.1016/j.ab.2007.04.052] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2007] [Revised: 04/28/2007] [Accepted: 04/30/2007] [Indexed: 11/23/2022]
Abstract
We previously developed a three-dimensional microarray system, the Bio-Strand, which exhibits advantages in automated DNA analysis in combination with our Magtration Technology. In the current study, we have developed a compact system for the Bio-Strand, the Handy Bio-Strand, which consists of several tools for the preparation of Bio-Strand Tip, hybridization, and detection. Using the Handy Bio-Strand, we performed single nucleotide polymorphism (SNP) genotyping of OPRM1 (A118G) by allele-specific oligonucleotide competitive hybridization (ASOCH). DNA fragments containing SNP sites were amplified from genomic DNA by PCR and then were fixed on a microporous nylon thread. Thus, prepared Bio-Strand Tip was hybridized with allele-specific Cy5 probes (<15mer), on which the SNP site was designed to be located in the center. By optimizing the amount of competitors, the selectivity of Cy5 probes increased without a drastic signal decrease. OPRM1 (A118G) genotypes of 23 human genomes prepared from whole blood samples were determined by ASOCH using the Handy Bio-Strand. The results were perfectly consistent with those determined by PCR direct sequencing. ASOCH using the Handy Bio-Strand would be a very simple and reliable method for SNP genotyping for small laboratories and hospitals.
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Affiliation(s)
- Harumi Ginya
- Precision System Science, Kamihongou, Matsudo, Chiba 271-0064, Japan.
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42
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Pallister J, Gould A, Harrison D, Hyatt A, Jancovich J, Heine H. Development of real-time PCR assays for the detection and differentiation of Australian and European ranaviruses. JOURNAL OF FISH DISEASES 2007; 30:427-38. [PMID: 17584440 DOI: 10.1111/j.1365-2761.2007.00828.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Serious systemic disease in fish and amphibians is associated with the ranaviruses, epizootic haematopoietic necrosis virus (EHNV) and Bohle iridovirus (BIV) in Australia, and European sheatfish virus (ESV) and European catfish virus (ECV) in Europe. EHNV, ESV and ECV are recognized causative agents of the OIE (Office International des Epizooties) notifiable systemic necrotizing iridovirus syndrome and are currently identified by protein-based assays, none of which are able to rapidly identify the specific agents. The aim of this study was to develop TaqMan real-time PCR assays that differentiated these viruses using nucleotide sequence variation in two ranavirus genes. A conserved probe representing 100% sequence homology was used as a reference for virus-specific probes. The virus-specific probes produced a similar signal level to the conserved probe while those probes binding to non-target viral DNA produced an altered fluorescent curve. The pattern of probe binding was characteristic for each virus. Sensitivity, specificity and dynamic range of the assay were assessed. The test is currently useful as a research and initial screening tool, with the potential to become a sensitive and specific method for detection and differentiation of ranaviruses with further development.
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Affiliation(s)
- J Pallister
- CSIRO Livestock Industries, Australian Animal Health Laboratory, Geelong, Victoria, Australia.
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Thomas SW, Joly GD, Swager TM. Chemical Sensors Based on Amplifying Fluorescent Conjugated Polymers. Chem Rev 2007; 107:1339-86. [PMID: 17385926 DOI: 10.1021/cr0501339] [Citation(s) in RCA: 2932] [Impact Index Per Article: 172.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Samuel W Thomas
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Najari A, Ho HA, Gravel JF, Nobert P, Boudreau D, Leclerc M. Reagentless Ultrasensitive Specific DNA Array Detection Based on Responsive Polymeric Biochips. Anal Chem 2006; 78:7896-9. [PMID: 17105186 DOI: 10.1021/ac061650+] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Self-assembled molecular structures immobilized on solid substrates and composed of fluorophore-tagged oligonucleotide probes and an optical polymeric transducer were investigated for the trace level detection of DNA target molecules. Rapid and efficient energy transfer between the polymeric transducer and fluorophores within the molecular aggregates leads to a massive intrinsic amplification of the fluorescence signal and to the label-free detection of as little as 300 DNA molecules, with the specificity required for the detection of single-nucleotide mismatches. This capacity for attomolar detection levels while the sensing structures are attached onto solid supports could lead to the development of biochip platforms for fast and simple PCR-free multitarget DNA detection.
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Affiliation(s)
- Ahmed Najari
- Department of Chemistry and Centre de Recherches sur la Science et L'ingénierie des Macromolécules (CERSIM), Université Laval, Québec, Canada G1K 7P4
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