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Yucel M, Onbas R, Arslan Yildiz A, Yildiz UH. The Soft Nanodots as Fluorescent Probes for Cell Imaging: Analysis of Cell and Spheroid Penetration Behavior of Single Chain Polymer Dots. Macromol Biosci 2024; 24:e2300402. [PMID: 38102867 DOI: 10.1002/mabi.202300402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 11/22/2023] [Indexed: 12/17/2023]
Abstract
This study describes the formation, size control, and penetration behavior of polymer nanodots (Pdots) consisting of single or few chain polythiophene-based conjugated polyelectrolytes (CPEs) via nanophase separation between good solvent and poor solvent of CPE. Though the chain singularity may be associated with dilution nanophase separation suggests that molecules of a good solvent create a thermodynamically driven solvation layer surrounding the CPEs and thereby separating the single chains even in their poor solvents. This statement is therefore corroborated with emission intensity/lifetime, particle size, and scattering intensity of polyelectrolyte in good and poor solvents. Regarding the augmented features, Pdots are implemented into cell imaging studies to understand the nuclear penetration and to differentiate the invasive characteristics of breast cancer cells. The python based red, green, blue (RGB) color analysis depicts that Pdots have more nuclear penetration ability in triple negative breast cancer cells due to the different nuclear morphology in shape and composition and Pdots have penetrated cell membrane as well as extracellular matrix in spheroid models. The current Pdot protocol and its utilization in cancer cell imaging are holding great promise for gene/drug delivery to target cancer cells by explicitly achieving the very first priority of nuclear intake.
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Affiliation(s)
- Muge Yucel
- Department of Chemistry and Pharmacy, Friedrich-Alexander Universität Erlangen-Nürnberg, 91058, Erlangen, Germany
- Department of Bioengineering, Izmir Institute of Technology, İzmir, 35430, Turkey
| | - Rabia Onbas
- Department of Bioengineering, Izmir Institute of Technology, İzmir, 35430, Turkey
| | - Ahu Arslan Yildiz
- Department of Bioengineering, Izmir Institute of Technology, İzmir, 35430, Turkey
| | - Umit Hakan Yildiz
- Department of Chemistry, Izmir Institute of Technology, İzmir, 35430, Turkey
- Department of Polymer Science and Engineering, Izmir Institute of Technology, İzmir, 35430, Turkey
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2
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Nalıncı Barbak N, Kıbrıs E, Demirci FC, Elmacı Irmak N. Molecular dynamics simulation of ssDNA and cationic polythiophene. J Mol Graph Model 2023; 123:108501. [PMID: 37182506 DOI: 10.1016/j.jmgm.2023.108501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 05/16/2023]
Abstract
In this work, molecular dynamics simulations of complexes composed of single strand DNA (ssDNA) sequences and cationic oligothiophenes are performed to understand experimental findings and the sensing ability of polythiophene electrolytes toward ssDNA. The simulation results exhibit no significant structural effect for replacing the cationic amine moiety with imidazole derivative on the side group of the oligomer. Adding a homopurine strand elongates the oligomer backbone; on the contrary, mixing up the homopyrimidine strand causes compression. On the other hand, these ssDNAs do not notably affect the compactness of the oligomer backbones. The anion-cation interactions play an essential role in the structural and spectroscopic change of cationic polythiophenes (CPTs) upon complexation with ssDNAs. The red shift of CPTs in the UV-VIS spectra with the addition of homopurine strands might be explained by the strong anion-cation, weak π -cation interactions, and high binding affinities. Nonpolar interactions (vdW and SA) and complex solvation energies dominate binding free energies. Hydrogen interaction analyses show that oligomers most likely approach the ssDNAs from their backbone upon complexation except for the duplex containing homopyrimidine strand and oligothiophene possessing imidazole derivative side chain.
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Affiliation(s)
- Nehir Nalıncı Barbak
- Faculty of Science, Department of Chemistry, Izmir Institute of Technology, 35430, Urla, Izmir, Turkiye
| | - Erman Kıbrıs
- Faculty of Science, Department of Chemistry, Izmir Institute of Technology, 35430, Urla, Izmir, Turkiye
| | - Fethi Can Demirci
- Faculty of Science, Department of Chemistry, Izmir Institute of Technology, 35430, Urla, Izmir, Turkiye
| | - Nuran Elmacı Irmak
- Faculty of Science, Department of Chemistry, Izmir Institute of Technology, 35430, Urla, Izmir, Turkiye.
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3
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Sinsinbar G, Gudlur S, Liedberg B. Rapid Detection of Escherichia coli: Optimized Peptide-Polythiophene Interactions Help Reduce Assay Time and Improve Naked-Eye Detection. ACS APPLIED MATERIALS & INTERFACES 2022; 14:31541-31550. [PMID: 35797225 DOI: 10.1021/acsami.2c03294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Recent improvements in methods for rapid detection of microbial contamination in food and water samples have aided in the development of on-site and point-of-care testing. Early detection, made possible via on-site testing, can help limit the spread of food and waterborne illnesses. Recently, we reported a novel fluorescence-based Omptin-Polythiophene assay (the assay) to detect Escherichia coli in contaminated water samples. The assay targets OmpT─an E. coli outer membrane protease─and exploits the protease's ability to cleave at dibasic sites within a peptide. By combining a peptide substrate optimized for OmpT with a conjugated polythiophene reporter molecule whose optical properties vary upon interaction with the intact or cleaved peptide, we demonstrated the detection of 1-10 CFU/mL and 105 CFU/mL E. coli in 5.5 and 1 h, respectively. In comparison, most microbial detection methods that rely on culturing and plating techniques take anywhere between 8 and 24 h to report their results. Herein we report significant improvements in the assay which include reducing the assay time from an already short 1 h to a mere 10 min for detecting E. coli in highly contaminated samples and augmenting the assay with colorimetric sensing capability for naked eye discernment under normal visible light or under UV-A light. These improvements were made possible by characterizing the optical changes resulting from the interaction of the peptide with five carboxylate-functionalized polythiophene variants carrying different 3- side chain carboxylic acids and by identifying preferential peptide substrates via the screening of ten peptide sequence variants for OmpT activity.
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Affiliation(s)
- Gaurav Sinsinbar
- Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Drive, Singapore 637553, Singapore
| | - Sushanth Gudlur
- Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Drive, Singapore 637553, Singapore
| | - Bo Liedberg
- Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Drive, Singapore 637553, Singapore
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4
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Sinsinbar G, Palaniappan A, Yildiz UH, Liedberg B. A Perspective on Polythiophenes as Conformation Dependent Optical Reporters for Label-Free Bioanalytics. ACS Sens 2022; 7:686-703. [PMID: 35226461 DOI: 10.1021/acssensors.1c02476] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Poly(3-alkylthiophene) (PT)-based conjugated polyelectrolytes (CPEs) constitute an important class of responsive polymers with excellent optical properties. The electrostatic interactions between PTs and target analytes trigger complexation and concomitant conformational changes of the PT backbones that produce distinct optical responses. These conformation-induced optical responses of the PTs enable them to be utilized as reporters for detection of various analytes by employing simple UV-vis spectrophotometry or the naked eye. Numerous PTs with unique pendant groups have been synthesized to tailor their interactions with analytes such as nucleotides, ions, surfactants, proteins, and bacterial and viral pathogens. In this perspective, we discuss PT-target analyte complexation for bioanalytical applications and highlight recent advancements in point-of-care and field deployable assays. Subsequently, we highlight a few areas of critical importance for future applications of PTs as reporters, including (i) design and synthesis of specific PTs to advance the understanding of the mechanisms of interaction with target analytes, (ii) using arrays of PTs and linear discriminant analysis for selective and specific detection of target analytes, (iii) translation of conventional homogeneous solution-based assays into heterogeneous membrane-based assay formats, and finally (iv) the potential of using PT as an alternative to conjugated polymer nanoparticles and dots in bioimaging.
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Affiliation(s)
- Gaurav Sinsinbar
- Centre for Biomimetic Sensor Science, School of Materials Science Engineering, Nanyang Technological University, 50 Nanyang Drive, Singapore, 637553
| | - Alagappan Palaniappan
- Centre for Biomimetic Sensor Science, School of Materials Science Engineering, Nanyang Technological University, 50 Nanyang Drive, Singapore, 637553
| | - Umit Hakan Yildiz
- Department of Chemistry, Izmir Institute of Technology, İzmir 35430, Turkey
- Department of Photonic Science and Engineering, Izmir Institute of Technology, İzmir 35430, Turkey
- Department of Polymer Science and Engineering, Izmir Institute of Technology, İzmir 35430, Turkey
| | - Bo Liedberg
- Centre for Biomimetic Sensor Science, School of Materials Science Engineering, Nanyang Technological University, 50 Nanyang Drive, Singapore, 637553
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Ammanath G, Delachi CG, Karabacak S, Ali Y, Boehm BO, Yildiz UH, Alagappan P, Liedberg B. Colorimetric and Fluorometric Profiling of Advanced Glycation End Products. ACS APPLIED MATERIALS & INTERFACES 2022; 14:94-103. [PMID: 34964349 DOI: 10.1021/acsami.1c16261] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Profiling of advanced glycation end products (AGEs) is an emerging area of clinical significance for disease diagnosis and prognosis. Typically, concentrations of AGEs are estimated in laboratories by trained personnel using sophisticated equipment. Herein, a facile approach for colorimetric and fluorometric profiling of AGEs is reported for rapid and on-site analysis. The concentrations of AGE levels in plasma are estimated via changes in optical properties of polythiophenes (PTs) upon interaction with aptamers (Apts) in the presence and in the absence of AGEs. To validate the proposed approach, glyceraldehyde-derived AGEs (AGE class 1 [AGE1]), the biomarker associated with cardiovascular diseases and diabetes, are used as a model system. Colorimetric analysis yielded linear responses for AGE1 for clinically relevant concentration ranges between 1.5 and 300 μg/mL with a limit of detection (LOD) of ∼1.3 μg/mL. Subsequently, an approach utilizing PTs with four different pendant groups in conjunction with four different Apts is demonstrated for qualitative colorimetric profiling and for quantitative fluorometric profiling of up to four AGEs in clinical matrices. Principal component analysis (PCA) of fluorometric responses of AGE-spiked samples yielded distinct responses for the different AGEs tested. Thus, the proposed approach ascertains rapid profiling of spiked AGEs in plasma samples without the requirement of preanalytical processing and advanced instrumentation, thereby facilitating on-site diagnosis.
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Affiliation(s)
- Gopal Ammanath
- Centre for Biomimetic Sensor Science, Nanyang Technological University, 637553 Singapore, Singapore
- School of Materials Science and Engineering, Nanyang Technological University, 639798 Singapore, Singapore
| | - Carla Giorgia Delachi
- Centre for Biomimetic Sensor Science, Nanyang Technological University, 637553 Singapore, Singapore
- School of Materials Science and Engineering, Nanyang Technological University, 639798 Singapore, Singapore
| | - Soner Karabacak
- Department of Chemistry, Izmir Institute of Technology, Urla, 35430 Izmir, Turkey
| | - Yusuf Ali
- Lee Kong Chian School of Medicine, Nanyang Technological University, 308232 Singapore, Singapore
| | - Bernhard O Boehm
- Lee Kong Chian School of Medicine, Nanyang Technological University, 308232 Singapore, Singapore
| | - Umit Hakan Yildiz
- Department of Chemistry, Izmir Institute of Technology, Urla, 35430 Izmir, Turkey
| | - Palaniappan Alagappan
- Centre for Biomimetic Sensor Science, Nanyang Technological University, 637553 Singapore, Singapore
- School of Materials Science and Engineering, Nanyang Technological University, 639798 Singapore, Singapore
| | - Bo Liedberg
- Centre for Biomimetic Sensor Science, Nanyang Technological University, 637553 Singapore, Singapore
- School of Materials Science and Engineering, Nanyang Technological University, 639798 Singapore, Singapore
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6
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Hu Q, Luo Y, Cao X, Chen Z, Huang Y, Niu L. Bioinspired Electro-RAFT Polymerization for Electrochemical Sensing of Nucleic Acids. ACS APPLIED MATERIALS & INTERFACES 2021; 13:54794-54800. [PMID: 34751560 DOI: 10.1021/acsami.1c17564] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Sensing of ultralow-abundance nucleic acids (NAs) is integral to medical diagnostics and pathogen screening. We present herein an electrochemical method for the highly selective and amplified sensing of NAs, using a peptide nucleic acid (PNA) recognition probe and a bioinspired electro-RAFT polymerization (BERP)-based amplification strategy. The presented method is based on the recognition of target NAs by end-tethered PNA probes, the labeling of thiocarbonylthio reversible addition-fragmentation chain transfer (RAFT) agents, and the BERP-assisted growth of ferrocenyl polymers. The dynamic growth of polymers is electrochemically regulated by the reduction of 1-methylnicotinamide (MNA) organic cations, the redox center of nicotinamide adenine dinucleotide (NAD+, coenzyme I). Specifically, electroreduction of the MNA cations causes the fragmentation of thiocarbonylthio RAFT agents into radical species, triggering the polymerization of ferrocenyl monomers, thereby recruiting plenty of ferrocene electroactive tags for amplified sensing. It is obvious that the BERP-based strategy is inexpensive and simple in operation. Benefiting from the high specificity of the PNA recognition probe and the amplified signal by the BERP-based strategy, this method is highly selective and the detection limit is as low as 0.58 fM (S/N = 3). Besides, it is applicable to the sensing of NAs in serum samples, thus showing great promise in the selective and amplified sensing of NAs.
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Affiliation(s)
- Qiong Hu
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Yilin Luo
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Xiaojing Cao
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Zhuohua Chen
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Yanyu Huang
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Li Niu
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
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7
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Yucel M, Koc A, Ulgenalp A, Akkoc GD, Ceyhan M, Yildiz UH. PCR-Free Methodology for Detection of Single-Nucleotide Polymorphism with a Cationic Polythiophene Reporter. ACS Sens 2021; 6:950-957. [PMID: 33621051 DOI: 10.1021/acssensors.0c02130] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This study presents a nonamplification-based nucleic acid assay for the detection of single-nucleotide polymorphism (SNP) associated with familial Mediterranean fever (FMF) besides polymerase chain reaction (PCR)-based methodologies. The major objective is to show the potential of the proposed assay for rapid screening of FMF in a Mediterranean region of 400 million population. The assay relies on binding difference of specially designed wild and mutant primers to the target genomic DNA, followed by determination of unbound primers by quick titration of a cationic polythiophene reporter. The fluorescent reporter exhibits signal transition from 525 to 580 nm in the presence of unbound primers, and it correlates the binding affinity of label-free primers to the homozygous wild and mutant genomes. As a proof of concept, 26 real samples are studied relying on the ON and OFF fluorescence signals of the cationic polythiophene reporter. The results are analyzed by principal component analysis (PCA), which provides clear separation of healthy and patient individuals. The further analysis by support vector machine (SVM) classification has revealed that our assay converges to 96% overall accuracy. These results support that the PCR-free nucleic acid assay has a significant potential for rapid and cost-effective screening of familial Mediterranean fever.
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Affiliation(s)
- Muge Yucel
- Department of Bioengineering and Biotechnology, Izmir Institute of Technology, Izmir 35430, Turkey
| | - Altug Koc
- Department of Medical Genetics, Faculty of Medicine, Dokuz Eylul University, Izmir 35330, Turkey
| | - Ayfer Ulgenalp
- Department of Medical Genetics, Faculty of Medicine, Dokuz Eylul University, Izmir 35330, Turkey
| | - Gun Deniz Akkoc
- Department of Chemistry, Izmir Institute of Technology, İzmir 35430, Turkey
| | - Metin Ceyhan
- Department of Basic Oncology, Institute of Oncology, Dokuz Eylul University, Izmir 35330, Turkey
| | - Umit Hakan Yildiz
- Department of Chemistry, Izmir Institute of Technology, İzmir 35430, Turkey
- Department of Photonic Science and Engineering, Izmir Institute of Technology, Izmir 35430, Turkey
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8
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Kıbrıs E, Barbak NN, Irmak NE. CHARMM force field generation for a cationic thiophene oligomer with ffTK. J Mol Model 2021; 27:34. [PMID: 33420831 DOI: 10.1007/s00894-020-04610-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 11/16/2020] [Indexed: 10/22/2022]
Abstract
In the present work, CHARMM force field parameters are generated for a cationic oligomer of N, N, N-trimethyl-3-(4-methylthiophen-3-yl) oxy) propan-1-aminium) which has the potential for sensing biological molecules such as nucleic acids, nucleobases. We have used ffTK (force field tool kit) to obtain potential parameters. MD simulations are performed for 20-mer and its complexes with AMP and ATP. The simulation results are analyzed to see the number of phosphates in adenosine nucleotides effects on the structure of the backbone of oligomer. The UV-VIS calculations for the conformers which possess the most probable radius of gyration are carried out and compared to the experimental ones to validate the generated force field. Graphical Abstract Recent studies have shown that, biologically important anions (ATP, AMP, vb.) change the spectroscopic properties of cationic polythiophenes (CPT) in the solutions. This work aims to generate CHARMM compatible force field parameters for a CPT to explain experimental studies. The type of interactions will be investigated deeply to lead new biosensor studies by examining the formation and the structure of complexes that consist of a oligothiophene and biological molecules, ATP, AMP by molecular dynamic simulations.
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Affiliation(s)
- Erman Kıbrıs
- Faculty of Science, Department of Chemistry, İzmir Institute of Technology, 35430, Urla, Izmir, Turkey
| | - Nehir Nalıncı Barbak
- Faculty of Science, Department of Chemistry, İzmir Institute of Technology, 35430, Urla, Izmir, Turkey
| | - Nuran Elmacı Irmak
- Faculty of Science, Department of Chemistry, İzmir Institute of Technology, 35430, Urla, Izmir, Turkey.
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9
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Tan J, Peng B, Tang L, Zeng G, Lu Y, Wang J, Ouyang X, Zhu X, Chen Y, Feng H. CuS QDs/Co 3O 4 Polyhedra-Driven Multiple Signal Amplifications Activated h-BN Photoeletrochemical Biosensing Platform. Anal Chem 2020; 92:13073-13083. [PMID: 32872771 DOI: 10.1021/acs.analchem.0c02002] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Herein, we developed an unmodified hexagonal boron nitride (h-BN) photoelectrochemical (PEC) biosensing platform with a low background signal and high sensitivity based on CuS quantum dots (QDs)/Co3O4 polyhedra-driven multiple signal amplifications. The prepared porous h-BN nanosheets with large specific surface areas, as the photoelectric substrate material, can provide extensive active reaction sites. Meanwhile, the CuS QDs/Co3O4 polyhedra were synthesized by the zeolitic imidazolate framework (ZIF-67) and utilized as a multiple signal amplifier, which can not only drive the p-n semiconductor quenching effect to compete with the h-BN photoelectrode for the consumption of electron donors and exciting light but also trigger a mimetic enzymatic catalytic precipitation effect to inhibit electron transfer. The quenching ability and peroxidase-like activity of CuS QDs/Co3O4 polyhedra were evaluated to prove its superiority, and the possible mechanisms of electron transfer and enzymatic catalytic were further analyzed in detail. The developed PEC biosensing platform for the chlorpyrifos assay presented outstanding performance with a wide linear range from 1 × 10-1 to 1 × 107 ng mL-1 and a low detection limit of 0.34 pg mL-1 and exhibited excellent selectivity, reproducibility, and stability. In addition, the CuS QDs/Co3O4 polyhedra-activated h-BN PEC biosensing platform may exhibit universality for various analytes via replacing the corresponding target aptamer sequence. This work provides a remarkable inspiration and valuable reference for the development of the PEC biosensor, and the signal amplifier-enabled unmodified PEC biosensing platform strategy has a bright application in early safety warning, bioanalysis and clinical diagnosis.
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Affiliation(s)
- Jisui Tan
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China.,Ministry of Education, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Changsha, Hunan 410082, China
| | - Bo Peng
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China.,Ministry of Education, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Changsha, Hunan 410082, China
| | - Lin Tang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China.,Ministry of Education, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Changsha, Hunan 410082, China
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China.,Ministry of Education, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Changsha, Hunan 410082, China
| | - Yue Lu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China.,Ministry of Education, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Changsha, Hunan 410082, China
| | - Jiajia Wang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China.,Ministry of Education, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Changsha, Hunan 410082, China
| | - Xilian Ouyang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China.,Ministry of Education, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Changsha, Hunan 410082, China
| | - Xu Zhu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China.,Ministry of Education, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Changsha, Hunan 410082, China
| | - Yu Chen
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China.,Ministry of Education, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Changsha, Hunan 410082, China
| | - Haopeng Feng
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China.,Ministry of Education, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Changsha, Hunan 410082, China
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10
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Yeasmin S, Ammanath G, Ali Y, Boehm BO, Yildiz UH, Palaniappan A, Liedberg B. Colorimetric Urinalysis for On-Site Detection of Metabolic Biomarkers. ACS APPLIED MATERIALS & INTERFACES 2020; 12:31270-31281. [PMID: 32551533 DOI: 10.1021/acsami.0c09179] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Over the past few decades, colorimetric assays have been developed for cost-effective and rapid on-site urinalysis. Most of these assays were employed for detection of biomarkers such as glucose, uric acid, ions, and albumin that are abundant in urine at micromolar to millimolar levels. In contrast, direct assaying of urinary biomarkers such as glycated proteins, low-molecular-weight reactive oxygen species, and nucleic acids that are present at significantly lower levels (nanomolar to picomolar) remain challenging due to the interferences from the urine sample matrix. State-of-the-art assays for detection of trace amounts of urinary biomarkers typically utilize time-consuming and equipment-dependent sample pretreatment or clean-up protocols prior to assaying, which limits their applicability for on-site analysis. Herein, we report a colorimetric assay for on-site detection of trace amount of generic biomarkers in urine without involving tedious sample pretreatment protocols. The detection strategy is based on monitoring the changes in optical properties of poly(3-(4-methyl-3'-thienyloxy)propyltriethylammonium bromide) upon interacting with an aptamer or a peptide nucleic acid in the presence and absence of target biomarkers of relevance for the diagnosis of metabolic complications and diabetes. As a proof of concept, this study demonstrates facile assaying of advanced glycation end products, 8-hydroxy-2'-deoxyguanosine and hepatitis B virus DNA in urine samples at clinically relevant concentrations, with limits of detection of ∼850 pM, ∼650 pM, and ∼ 1 nM, respectively. These analytes represent three distinct classes of biomarkers: (i) glycated proteins, (ii) low-molecular-weight reactive oxygen species, and (iii) nucleic acids. Hence, the proposed methodology is applicable for rapid detection of generic biomarkers in urine, without involving sophisticated equipment and skilled personnel, thereby enabling on-site urinalysis. At the end of the contribution, we discuss the opportunity to translate the homogeneous assay into a paper-based format.
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Affiliation(s)
- Sanjida Yeasmin
- Centre for Biomimetic Sensor Science, Nanyang Technological University, 637553 Singapore
- School of Materials Science and Engineering, Nanyang Technological University, 639798 Singapore
| | - Gopal Ammanath
- Centre for Biomimetic Sensor Science, Nanyang Technological University, 637553 Singapore
- School of Materials Science and Engineering, Nanyang Technological University, 639798 Singapore
| | - Yusuf Ali
- Lee Kong Chian School of Medicine, Nanyang Technological University, 308232 Singapore
| | - Bernhard O Boehm
- Lee Kong Chian School of Medicine, Nanyang Technological University, 308232 Singapore
| | - Umit Hakan Yildiz
- Department of Chemistry, Izmir Institute of Technology, Urla, Izmir 35430, Turkey
| | - Alagappan Palaniappan
- Centre for Biomimetic Sensor Science, Nanyang Technological University, 637553 Singapore
- School of Materials Science and Engineering, Nanyang Technological University, 639798 Singapore
| | - Bo Liedberg
- Centre for Biomimetic Sensor Science, Nanyang Technological University, 637553 Singapore
- School of Materials Science and Engineering, Nanyang Technological University, 639798 Singapore
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11
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PNA-Based MicroRNA Detection Methodologies. Molecules 2020; 25:molecules25061296. [PMID: 32178411 PMCID: PMC7144472 DOI: 10.3390/molecules25061296] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 03/06/2020] [Accepted: 03/09/2020] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs or miRs) are small noncoding RNAs involved in the fine regulation of post-transcriptional processes in the cell. The physiological levels of these short (20-22-mer) oligonucleotides are important for the homeostasis of the organism, and therefore dysregulation can lead to the onset of cancer and other pathologies. Their importance as biomarkers is constantly growing and, in this context, detection methods based on the hybridization to peptide nucleic acids (PNAs) are gaining their place in the spotlight. After a brief overview of their biogenesis, this review will discuss the significance of targeting miR, providing a wide range of PNA-based approaches to detect them at biologically significant concentrations, based on electrochemical, fluorescence and colorimetric assays.
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Aydın HB, Cheema JA, Ammanath G, Toklucu C, Yucel M, Özenler S, Palaniappan A, Liedberg B, Yildiz UH. Pixelated colorimetric nucleic acid assay. Talanta 2020; 209:120581. [PMID: 31892020 PMCID: PMC7111824 DOI: 10.1016/j.talanta.2019.120581] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 11/17/2019] [Accepted: 11/19/2019] [Indexed: 12/12/2022]
Abstract
Conjugated polyelectrolytes (CPEs) have been widely used as reporters in colorimetric assays targeting nucleic acids. CPEs provide naked eye detection possibility by their superior optical properties however, as concentration of target analytes decrease, trace amounts of nucleic acid typically yield colorimetric responses that are not readily perceivable by naked eye. Herein, we report a pixelated analysis approach for correlating colorimetric responses of CPE with nucleic acid concentrations down to 1 nM, in plasma samples, utilizing a smart phone with an algorithm that can perform analytical testing and data processing. The detection strategy employed relies on conformational transitions between single stranded nucleic acid-cationic CPE duplexes and double stranded nucleic acid-CPE triplexes that yield distinct colorimetric responses for enabling naked eye detection of nucleic acids. Cationic poly[N,N,N-triethyl-3-((4-methylthiophen-3-yl)oxy)propan-1-aminium bromide] is utilized as the CPE reporter deposited on a polyvinylidene fluoride (PVDF) membrane for nucleic acid assay. A smart phone application is developed to capture and digitize the colorimetric response of the individual pixels of the digital images of CPE on the PVDF membrane, followed by an analysis using the algorithm. The proposed pixelated approach enables precise quantification of nucleic acid assay concentrations, thereby eliminating the margin of error involved in conventional methodologies adopted for interpretation of colorimetric responses, for instance, RGB analysis. The obtained results illustrate that a ubiquitous smart phone could be utilized for point of care colorimetric nucleic acids assays in complex matrices without requiring sophisticated software or instrumentation.
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Affiliation(s)
- Hakan Berk Aydın
- Department of Chemistry, Izmir Institute of Technology, Urla, 35430, Izmir, Turkey
| | - Jamal Ahmed Cheema
- Center for Biomimetic Sensor Science, Nanyang Technological University, 637553, Singapore; School of Materials Science and Engineering, Nanyang Technological University, 639798, Singapore
| | - Gopal Ammanath
- Center for Biomimetic Sensor Science, Nanyang Technological University, 637553, Singapore; Nanyang Institute of Technology in Health and Medicine, Interdisciplinary Graduate School, Nanyang Technological University, 637553, Singapore; School of Materials Science and Engineering, Nanyang Technological University, 639798, Singapore
| | - Cihan Toklucu
- Department of Computer Engineering, Izmir Institute of Technology, Urla, 35430, Izmir, Turkey
| | - Muge Yucel
- Department of Bioengineering, Izmir Institute of Technology, Urla, 35430, Izmir, Turkey
| | - Sezer Özenler
- Department of Chemistry, Izmir Institute of Technology, Urla, 35430, Izmir, Turkey
| | - Alagappan Palaniappan
- Center for Biomimetic Sensor Science, Nanyang Technological University, 637553, Singapore; School of Materials Science and Engineering, Nanyang Technological University, 639798, Singapore
| | - Bo Liedberg
- Center for Biomimetic Sensor Science, Nanyang Technological University, 637553, Singapore; School of Materials Science and Engineering, Nanyang Technological University, 639798, Singapore.
| | - Umit Hakan Yildiz
- Department of Chemistry, Izmir Institute of Technology, Urla, 35430, Izmir, Turkey.
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Ammanath G, Yeasmin S, Srinivasulu Y, Vats M, Cheema JA, Nabilah F, Srivastava R, Yildiz UH, Alagappan P, Liedberg B. Flow-through colorimetric assay for detection of nucleic acids in plasma. Anal Chim Acta 2019; 1066:102-111. [DOI: 10.1016/j.aca.2019.03.036] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/13/2019] [Accepted: 03/17/2019] [Indexed: 01/04/2023]
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Xu Z, Zhang T, Gu Y, Liu F, Liu H, Lu N, Xu H, Yan X, Zhang Z, Lu P. New Strategy for Ultrasensitive Aptasensor Fabrication: D-A-D Constitution as a Charge Transfer Platform and Recognition Element. ACS APPLIED MATERIALS & INTERFACES 2019; 11:17894-17901. [PMID: 31009203 DOI: 10.1021/acsami.9b05689] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Over the past decade, various sensing systems based on aptamers have attracted a great deal of studies directed at designing highly selective biosensors. In this paper, we described a new-style electrochemical aptamer sensor (aptasensor) via a donor-acceptor link substrate, which was characterized by electrochemical methods and other helpful characterization instruments. Molecules with D-A-D configuration always undergo an intrinsic signal amplification due to the elongation of the π-electron conjugation. Triphenylamine, a peripheral electron donor, has excellent hole-transport property and is able to assemble on the surface of glassy carbon electrode by π-π stacking interaction. To further improve the performance of the adenosine triphosphate (ATP) sensor, we chose diphenylfumaronitrile-containing electron-withdrawing group as the central core to promote charge transfer, which can also efficiently combine with aptamers by multihydrogen bond function. Surprisingly, the sensing platform showed a wide liner range from 0.1 pM to 100 nM, with a detection limit of 0.018 pM. We examined the ATP in human serum sample, indicating that the novel aptasensor based on D-A-D conjugated polymer holds great possibility for practical detection of ATP. Moreover, it is foreseeable that the conjugated polymers of the D-A structure will have promising application in the preparation of biosensors.
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Fossépré M, Trévisan ME, Cyriaque V, Wattiez R, Beljonne D, Richeter S, Clément S, Surin M. Detection of the Enzymatic Cleavage of DNA through Supramolecular Chiral Induction to a Cationic Polythiophene. ACS APPLIED BIO MATERIALS 2019; 2:2125-2136. [DOI: 10.1021/acsabm.9b00123] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Mathieu Fossépré
- Laboratory for Chemistry of Novel Materials, Centre of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons (UMONS), 20 Place du Parc, Mons B-7000, Belgium
| | - Marie E. Trévisan
- Laboratory for Chemistry of Novel Materials, Centre of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons (UMONS), 20 Place du Parc, Mons B-7000, Belgium
| | - Valentine Cyriaque
- Proteomics and Microbiology Lab, Research Institute for Biosciences, University of Mons (UMONS), Avenue du Champs de Mars 6, Mons 7000, Belgium
| | - Ruddy Wattiez
- Proteomics and Microbiology Lab, Research Institute for Biosciences, University of Mons (UMONS), Avenue du Champs de Mars 6, Mons 7000, Belgium
| | - David Beljonne
- Laboratory for Chemistry of Novel Materials, Centre of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons (UMONS), 20 Place du Parc, Mons B-7000, Belgium
| | - Sébastien Richeter
- Institut Charles Gerhardt ICGM, UMR 5253 CNRS-ENSCM-UM, Université de Montpellier, CC1701 Place Eugène Bataillon, Montpellier Cedex 05F-34095, France
| | - Sébastien Clément
- Institut Charles Gerhardt ICGM, UMR 5253 CNRS-ENSCM-UM, Université de Montpellier, CC1701 Place Eugène Bataillon, Montpellier Cedex 05F-34095, France
| | - Mathieu Surin
- Laboratory for Chemistry of Novel Materials, Centre of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons (UMONS), 20 Place du Parc, Mons B-7000, Belgium
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Ammanath G, Yildiz UH, Palaniappan A, Liedberg B. Luminescent Device for the Detection of Oxidative Stress Biomarkers in Artificial Urine. ACS APPLIED MATERIALS & INTERFACES 2018; 10:7730-7736. [PMID: 29430928 DOI: 10.1021/acsami.7b17252] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A luminescent paper-based device for the visual detection of oxidative stress biomarkers is reported. The device consists of a polyvinylidene fluoride membrane impregnated with poly(3-alkoxy-4-methylthiophene) (PT) for colorimetric detection. 8-hydroxy-2'-deoxyguanosine (8-OHdG), a biomarker associated with oxidative stress, is used as a model system for validating the proposed methodology. The detection strategy is based on monitoring the changes in optical properties of PT associated with its conformational changes upon interaction with an aptamer in the presence and in the absence of 8-OHdG. Fluorometric and colorimetric monitoring revealed linear responses for 8-OHdG concentrations between 50 pM and 500 nM (∼14 pg/mL to 140 ng/mL), with limits of detection of ∼300 pM and ∼350 pM, respectively for ( n = 3). Colorimetric responses in artificial urine ascertained rapid, sensitive, and selective detection of 8-OHdG at clinically relevant (pM to nM) concentration levels. Furthermore, the proposed methodology enables point-of-care diagnostics for oxidative stress without requiring sophisticated instrumentation.
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Affiliation(s)
- Gopal Ammanath
- Centre for Biomimetic Sensor Science , Nanyang Technological University , Singapore 637553
- Nanyang Institute of Technology in Health and Medicine, Interdisciplinary Graduate School , Nanyang Technological University , Singapore 637553
- School of Materials Science and Engineering , Nanyang Technological University , Singapore 639798
| | - Umit Hakan Yildiz
- Department of Chemistry , Izmir Institute of Technology , Urla, 35430 Izmir , Turkey
| | - Alagappan Palaniappan
- Centre for Biomimetic Sensor Science , Nanyang Technological University , Singapore 637553
- Nanyang Institute of Technology in Health and Medicine, Interdisciplinary Graduate School , Nanyang Technological University , Singapore 637553
| | - Bo Liedberg
- Centre for Biomimetic Sensor Science , Nanyang Technological University , Singapore 637553
- Nanyang Institute of Technology in Health and Medicine, Interdisciplinary Graduate School , Nanyang Technological University , Singapore 637553
- School of Materials Science and Engineering , Nanyang Technological University , Singapore 639798
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Ghosh R, Chatterjee DP, Das S, Mukhopadhyay TK, Datta A, Nandi AK. Influence of Hofmeister I - on Tuning Optoelectronic Properties of Ampholytic Polythiophene by Varying pH and Conjugating with RNA. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:12739-12749. [PMID: 29028346 DOI: 10.1021/acs.langmuir.7b03147] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A significant tuning of optoelectronic properties of polythiophene (PT) chains due to Hofmeister iodide (I-) ion is demonstrated in ampholytic polythiophene [polythiophene-g-poly{(N,N,N-trimethylamino iodide)ethyl methacrylate-co-methacrylic acid}, APT] at different pHs. In acidic medium, the absorption and emission signals of PT chromophore exhibit appreciable blue shift in the presence of I- as counteranion only. The cooperative effect of undissociated -COOH and quaternary ammonium groups immobilize I- near the apolar PT chain causing threading of grafted chains and hence twisting of the backbone attributing to the blue shift. As medium pH is increased, dethreading of the PT backbone occurs due to ionization of -COOH group, releasing quencher iodide ions from the vicinity of the PT chains resulting in a red shift in absorption and a sharp hike in fluorescence intensity (390 times) for an increase of excitons lifetime. With an increase of pH, morphology changes from a multivesicular aggregate with vacuoles to smaller size vesicles and finally to nanofibrillar network structure. Dethreading is also found when APT interacts with RNA showing a significant hike of fluorescence (22 times) for displacing iodide ions forming a nanofibrillar network morphology. Threading and dethreading also affect the resistance, capacitance, and Warburg impedance values of APT. Molecular dynamics simulation of a model APT chain in a water box supports the threading at lower pH where the iodide ions pose nearer to the PT chain than that at higher pH causing dethreading. So the influence of Hofmeister I- ion is established for tuning the optoelectronic properties of a novel PT based polyampholyte by changing pH or by conjugating with RNA.
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Affiliation(s)
- Radhakanta Ghosh
- Polymer Science Unit, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032, India
| | - Dhruba P Chatterjee
- Polymer Science Unit, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032, India
| | - Sujoy Das
- Polymer Science Unit, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032, India
| | - Titas K Mukhopadhyay
- Polymer Science Unit, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032, India
| | - Ayan Datta
- Polymer Science Unit, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032, India
| | - Arun K Nandi
- Polymer Science Unit, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032, India
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Ghosh R, Das S, Chatterjee DP, Nandi AK. Surfactant-Triggered Fluorescence Turn "on/off" Behavior of a Polythiophene-graft-Polyampholyte. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:8413-8423. [PMID: 27465928 DOI: 10.1021/acs.langmuir.6b01928] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Polythiophene-graft-polyampholyte (PTP) is synthesized using N,N-dimethylaminoethyl methacrylate and tert-butyl methacrylate monomers by grafting from polythiophene backbone, followed by hydrolysis. The resulting polymer exhibits aqueous solubility via formation of small-sized miceller aggregates with hydrophobic polythiophene at the center and radiating polyionic side chains (cationic or anionic depending on the pH of the medium) at the outer periphery. The critical micelle concentration of PTP in acidic solution (0.025 mg/mL, pH = 2.7) is determined from fluorescence spectroscopy. PTP exhibits reversible fluorescence on and off response in both acidic and basic medium with the sequential addition of differently charged ionic surfactants, repeatedly. The fluorescence intensity of PTP at pH 2.7 increases with the addition of an anionic surfactant, sodium dodecyl benzenesulfonate (SDBS), due to the self-aggregation forming compound micelles. The fluorescence intensity of these solutions again decreases on addition of a cationic surfactant, cetyltrimethylammonium bromide (CTAB), because of assembling of SDBS with CTAB, thus deassembling the PTP-SDBS aggregates. At pH 9.2, these turn on and turn off responses are also shown by PTP with the sequential addition of cationic surfactant (CTAB) and anionic surfactant (SDBS), respectively. This result shows that PTP has potential for surfactant-induced reversible fluorescence turn on and off using ionic surfactant (SDBS and CTAB) through self-assembling and deassembling of the ionic aggregates. The reversible aggregation and disaggregation process of PTP with the surfactants at both acidic and basic pH is supported from dynamic light scattering and Fourier transform infrared spectroscopy. The morphology of the above systems studied by transmission and scanning electron microscopy also supports the above aggregation and disaggregation process.
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Affiliation(s)
- Radhakanta Ghosh
- Polymer Science Unit, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032, India
| | - Sandip Das
- Polymer Science Unit, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032, India
| | | | - Arun K Nandi
- Polymer Science Unit, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032, India
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