Chemistry / Kimya
Permanent URI for this collectionhttps://hdl.handle.net/11147/4072
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Article Citation - WoS: 5Citation - Scopus: 4Polarity Induced Vapochromism and Vapoluminescence of Polythiophene Derivatives for Volatile Organic Compounds Classification(Elsevier, 2023) Karabacak, Soner; Qun, David Lee Chao; Ammanath, Gopal; Yeasmin, Sanjida; Yağmurcukardeş, Mehmet; Palaniappan, Alagappan; Liedberg, Bo; Yıldız, Ümit HakanPolarity induced vapochromic and vapoluminescent properties of cationic poly-3-alkoxythiophene derivatives (PT) casted on polyvinylidene fluoride (PVDF) membranes are reported. PT with six different pendant groups are designed to differentially interact with volatile organic compounds (VOC) of varying polarities, thereby enabling their classification. PT exhibit a rapid vapochromic response with a concurrent modulation of vapoluminescence due to the non-covalent cation-? interactions between the pendant groups and the PT backbone. Adsorption of VOC on pendant groups alters the conformation of PT backbone, thus resulting in an increase in intensity and blue shifting of fluorescence emission within the visible spectrum. The vapoluminescent responses are found to be more sensitive with a limit of detection (LOD) of ?7 ppm and a wider dynamic range as compared to the vapochromic responses with a LOD of ?60 ppm for the detection of a model VOC: chloroform. Notably, all the PT illustrate an instantaneous recovery of colour and luminescence upon desorption of VOC. PT interaction with VOC of varying polarities was ascertained using density functional theory (DFT) and principal component analysis (PCA) methodologies. In summary, the polarity induced vapochromic and vapoluminescent properties of PT could yield a selective and sensitive vapochromic and fluorometric dual-mode VOC detection platform. © 2023Article Citation - WoS: 35Citation - Scopus: 44Current Trends and Challenges in Point-Of Urinalysis of Biomarkers in Trace Amounts(Elsevier, 2022) Yeasmin, Sanjida; Ammanath, Gopal; Önder, Ahmet; Yan, Evelias; Yıldız, Ümit Hakan; Palaniappan, Alagappan; Liedberg, BoUrinalysis enables non-invasive point-of-care (POC) testing of numerous biomarkers at their physiological and elevated levels, obviating the need for sophisticated equipment or trained personnel. POC urinalysis is used to identify biomarkers that are rich in urine (greater than 1 μM), such as lactate, uric acid, glucose, ions, and adenosine. Urine also contains biomarkers such as small molecules, nucleic acids, neurotransmitters, and drugs in trace amounts (less than 1 μM). These biomarkers are of significant importance for health care monitoring, diagnosis of various disorders (cancer, metabolic diseases, etc.) and illicit drug control (cocaine, steroids, etc.). While POC detection of urinary biomarkers at higher concentration (μM to mM) levels is feasible, direct assaying of biomarkers in nM to fM levels is challenging, as assay responses are typically masked by interferences from the urine sample matrix. This report is a consolidated review of emerging trends and challenges in the POC urinalysis for detecting biomarkers that are less abundant in urine. The sensing mechanisms, analytical device fabrication, discrete and integrated sample pre-treatment procedures for POC assaying of urinary markers in trace amounts are elaborated. Subsequently, the utilization of smart data analytics for facilitating personalized urinalysis is presented. A comprehensive outlook on associated challenges in POC urinalysis of biomarkers in trace amounts is further provided, which would facilitate the advancement of POC urinalysis for a wide range of healthcare applications.Article Citation - WoS: 11Citation - Scopus: 12Colorimetric and Fluorometric Profiling of Advanced Glycation End Products(American Chemical Society, 2022) Ammanath, Gopal; Delachi, Carla Giorgia; Karabacak, Soner; Ali, Yusuf; Boehm, Bernhard O.; Yıldız, Ümit Hakan; Alagappan, Palaniappan; Liedberg, BoProfiling 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.Article Citation - WoS: 7Citation - Scopus: 7A Perspective on Polythiophenes as Conformation Dependent Optical Reporters for Label-Free Bioanalytics(American Chemical Society, 2022) Sinsinbar, Gaurav; Palaniappan, Alagappan; Yıldız, Ümit Hakan; Liedberg, BoPoly(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.Article Citation - WoS: 39Citation - Scopus: 37Flow-Through Colorimetric Assay for Detection of Nucleic Acids in Plasma(Elsevier, 2019) Ammanath, Gopal; Yeasmi, Sanjida; Srinivasulu, Yuvasri; Vats, Mukti; Cheema, Jamal Ahmed; Nabilah, Fairuz; Liedberg, Bo; Yıldız, Ümit HakanA flow-through colorimetric assay for detection of nucleic acids in plasma is reported. The proposed assay features an array of four polyvinylidene fluoride (PVDF) membranes impregnated with cationic poly (3-alkoxy-4-methylthiophene) (PT) as an optical reporter. The sensing strategy is based on monitoring the changes in optical properties of PT, upon complexation with target nucleic acids in the presence and in the absence of their corresponding complementary peptide nucleic acids (PNAs). As a proof of concept, the proposed methodology is validated using two biomarkers; lung cancer associated microRNA (mir21) and hepatitis B virus DNA (HBV-DNA). The flow-through colorimetric assay enabled detection of mir21 and HBV-DNA in plasma without requiring tedious sample pre-treatment and clean up protocols. Colorimetric responses for mir21 and HBV-DNA were obtained at nanomolar concentrations over five orders of magnitudes (from 1 nM to 10 mu M), with a limit of detection of -0.6 nM and -2 nM in DI water and plasma, respectively. A logic gate system was developed to utilize the colorimetric assay responses as inputs for discrimination of mir21 and HBV-DNA and subsequently to obtain a profile of nucleic acids in samples that exceed respective clinical threshold limits, thereby enabling rapid and point of care (POC) disease diagnosis. Furthermore, the proposed methodology can be utilized for detection of a large number of nucleic acids in plasma by extending the array of PT impregnated membranes incorporated with their corresponding complementary PNAs. (C) 2019 Elsevier B.V. All rights reserved.Article Citation - WoS: 18Citation - Scopus: 19Hand-Held Volatilome Analyzer Based on Elastically Deformable Nanofibers(American Chemical Society, 2018) Yücel, Müge; Akın, Osman; Çayören, Mehmet; Akduman, İbrahim; Palaniappan, Alagappan; Liedberg, Bo; Hızal, Gürkan; İnci, Fatih; Yıldız, Ümit HakanThis study reports on a hand-held volatilome analyzer for selective determination of clinically relevant biomarkers in exhaled breath. The sensing platform is based on electrospun polymer nanofiber-multiwalled carbon nanotube (MWCNT) sensing microchannels. Polymer nanofibers of poly(vinylidene fluoride) (PVDF), polystyrene (PS), and poly(methyl methacrylate) (PMMA) incorporated with MWCNT exhibits a stable response to interferences of humidity and CO2 and provides selective deformations upon exposure of exhaled breath target volatilomes acetone and toluene, exhibiting correlation to diabetes and lung cancer, respectively. The sensing microchannels "P1" (PVDF-MWCNT), "P2" (PS-MWCNT), and "P3" (PMMA-MWCNT) are integrated with a microfluidic cartridge (μ-card) that facilitates collection and concentration of exhaled breath. The volatilome analyzer consists of a conductivity monitoring unit, signal conditioning circuitries and a low energy display module. A combinatorial operation algorithm was developed for analyzing normalized resistivity changes of the sensing microchannels upon exposure to breath in the concentration ranges between 35 ppb and 3.0 ppm for acetone and 1 ppb and 10 ppm for toluene. Subsequently, responses of volatilomes from individuals in the different risk groups of diabetes were evaluated for validation of the proposed methodology. We foresee that proposed methodology provides an avenue for rapid detection of volatilomes thereby enabling point of care diagnosis in high-risk group individuals.Article Citation - WoS: 32Citation - Scopus: 32Luminescent Device for the Detection of Oxidative Stress Biomarkers in Artificial Urine(American Chemical Society, 2018) Ammanath, Gopal; Yıldız, Ümit Hakan; Palaniappan, Alagappan; Liedberg, BoA 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.Article Citation - WoS: 10Citation - Scopus: 12Tuning Pendant Groups of Polythiophene on Carbon Nanotubes for Vapour Classification(Elsevier Ltd., 2017) Tu, Meng-Che; Svm, Hari Krishna; Thilini, Alahakoon; Wallace, Lim Tse Loong; Moochhala, Shabbir; Yıldız, Ümit Hakan; Palaniappan, Al.; Liedberg, BoPoly(3-alkoxythiophene) (PT) with varying ratios of triethylamine and 1-methyl imidazole pendant groups and horizontally aligned single walled carbon nanotubes (SWCNT) are utilized in this study for volatile organic compounds (VOCs) classification. PTs with five different ratios of pendant groups are incorporated with SWCNT and are evaluated as chemiresistor arrays for analysis of VOCs such as ethanol, acetone, toluene, chloroform, isoprene and ethylene. Varying PT pendant groups yielded differential SWCNT current responses attributed to their chemical affinities for the VOCs tested. Principal component analysis (PCA) for vapour classification illustrated that the vapour responses are separable, thus, highlighting vapour discrimination ability of SWCNT with controlled ratios of PT pendant groups. The proposed methodology is a facile VOC classification approach for two main reasons; (i) PT could easily modified with various pendants groups containing appropriate chemical moieties for preferential interaction with various VOCs and (ii) increasing the number PTs with appropriate pendant group modifications would provide additional inputs to PCA thereby enabling capturing and assaying of a wide range of VOCs.Article Citation - WoS: 41Citation - Scopus: 44Vapor Phase Solvatochromic Responses of Polydiacetylene Embedded Matrix Polymers(Royal Society of Chemistry, 2017) Tu, Meng-Che; Cheema, Jamal Ahmed; Yıldız, Ümit Hakan; Palaniappan, Alagappan; Liedberg, BoThe solvatochromic response of polydiacetylene (PDA) in the vapor phase is enabled upon incorporation with matrix polymers such as polyvinylpyrrolidone (PVP), polyethylene glycol (PEG), polyacrylic acid (PAA), and poly-4-vinylpyridine (P4VP). The matrix polymers provide a soft/gel-like framework for accommodating photopolymerized PDA, while facilitating its conformational alternations upon interaction with preconcentrated volatile organic compounds (VOCs). The matrix polymers enabled the differentiation of VOCs owing to their varying morphology, chemical affinity and solubility in VOCs. The ratios between PDA and the matrix polymers are optimized according to the obtained solvatochromic responses evaluated in varying temperature, humidity and storage conditions. As a proof of concept, a finger-print array for differentiation of 7 VOCs is demonstrated using matrix polymer-embedded PDA. The obtained results indicate that the response time and sensitivity of the proposed methodology supersedes previous reports on solvatochromic VOC assays. Furthermore, the proposed methodology would enable differentiation of a wide range of VOCs upon incorporation of additional matrix polymers with varying sorption properties.Article Citation - WoS: 24Citation - Scopus: 23Tailoring Conformation-Induced Chromism of Polythiophene Copolymers for Nucleic Acid Assay at Resource Limited Settings(American Chemical Society, 2016) Rajwar, Deepa; Ammanath, Gopal; Cheema, Jamal Ahmed; Palaniappan, Alagappan; Yıldız, Ümit Hakan; Liedberg, BoHere we report on the design and synthesis of cationic water-soluble thiophene copolymers as reporters for colorimetric detection of microRNA (miRNA) in human plasma. Poly(3-alkoxythiophene) (PT) polyelectrolytes with controlled ratios of pendant groups such as triethylamine/1-methyl imidazole were synthesized for optimizing interaction with target miRNA sequence (Tseq). Incorporation of specific peptide nucleic acid (PNA) sequences with the cationic polythiophenes yielded distinguishable responses upon formation of fluorescent PT-PNA-Tseq triplex and weakly fluorescent PT-Tseq duplex, thereby enabling selective detection of target miRNA. Unlike homopolymers of PT (hPT), experimental results indicate the possibility of utilizing copolymers of PT (cPT) with appropriate ratios of pendant groups for miRNA assay in complex matrices such as plasma. As an illustration, colorimetric responses were obtained for lung cancer associated miRNA sequence (mir21) in human plasma, with a detection limit of 10 nM, illustrating the feasibility of proposed methodology for clinical applications without involving sophisticated instrumentation. The described methodology therefore possesses high potential for low-cost nucleic acid assays in resource-limited settings.