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Hasan MR, Sharma P, Singh S, Narang J. Smartphone-Integrated Wireless Portable Potentiostat to Develop 5th-Generation Dengue Pocket Aptasensor toward Portronicx-Approach. ACS APPLIED BIO MATERIALS 2024; 7:2299-2308. [PMID: 38476032 DOI: 10.1021/acsabm.3c01299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
Smartphones' widespread availability and worldwide connection are advancing the idea of mobile-based healthcare and promise to transform the business of biosensors. Biosensors based on smartphones have been investigated in several ways, including employing a smartphone in place of a detector or as an instrumental interface. The current work demonstrates the first successful detection of dengue virus using a smartphone-based pocket sensor combined with a wireless potentiostat. The platform developed comprises a smartphone, a wireless portable potentiostat, an Android app, and a three-electrode setup. The combination of portable diagnostic with electronic application is referred to as "Portronicx", and this is the first time that the term "Portronicx" has been used in a dengue sensor, so the current study has the potential to be commercialized in the market with the tag line "Portronicx-commercialization" in the future. Miniaturization improves alternative setup options in terms of instrument size, affordability, mobility, touch-mobile display, and design versatility. The current work proved the excellent combination of a wireless potentiostat with an aptasensor to detect dengue antigen within 20 s with good LOD (0.1 μg/mL) and easy to carry in their pockets. The created platform also performed effectively in human serum. This study replaced all of the instruments with a lightweight touch smartphone, paving the way for the production of fifth-generation electrochemical aptasensors, with potential implications for healthcare applications on the verge of commercialization.
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Affiliation(s)
- Mohd Rahil Hasan
- Department of Biotechnology, Jamia Hamdard, New Delhi 110062, India
| | | | - Saumitra Singh
- Department of Biotechnology, Jamia Hamdard, New Delhi 110062, India
| | - Jagriti Narang
- Department of Biotechnology, Jamia Hamdard, New Delhi 110062, India
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2
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Design, Synthesis, and Characterization of Novel Bis-Uracil Chitosan Hydrogels Modified with Zinc Oxide Nanoparticles for Boosting Their Antimicrobial Activity. Polymers (Basel) 2023; 15:polym15040980. [PMID: 36850260 PMCID: PMC9964190 DOI: 10.3390/polym15040980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/04/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
A new series of hydrogels was successfully prepared by incorporating various substituted bisuracil (R-BU) linkages between chitosan Schiff's base chains (R-BU-CsSB) and between chitosan chains (R-BU-Cs). After protection of the amino groups of chitosan by benzaldehyde, yielding chitosan Schiff's base (CsSB), the reaction with epichlorohydrin was confined on the -OH on C6 to produce epoxy chitosan Schiff's base (ECsSB), which was reacted with R-BU to form R-BU-CsSB hydrogels, and finally, the bioactive amino groups of chitosan were restored to obtain R-BU-Cs hydrogels. Further, some R-BU-Cs-based ZnO nanoparticle (R-BU-Cs/ZnONPs) composites were also prepared. Appropriate techniques such as elemental analysis, FTIR, XRD, SEM, and EDX were used to verify their structures. Their inhibition potency against all the tested microbes were arranged as: ZnONPs bio-composites > R-BU-Cs hydrogels > R-BU-CsSB hydrogels > Cs. Their inhibition performance against Gram-positive bacteria was better than Gram-negative ones. Their minimum inhibitory concentration (MIC) values decreased as a function of the negative resonance effect of the substituents in the aryl ring of R-BU linkages in the hydrogels. Compared with Vancomycin, the ZnONPs bio-composites showed superior inhibitory effects against most of the tested Gram-negative bacteria, all inspected Gram-positive ones, and all investigated fungi.
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Al-Shuaeeb RAA, Abd El-Mageed HR, Ahmed SA, Mohamed HS, Hamza ZS, Rafi MO, Rahman MS. Identification of potent COVID-19 main protease inhibitors by loading of favipiravir on Mg 12O 12 and Zn 12O 12 nanoclusters: an in silico strategy for COVID-19 treatment. J Biomol Struct Dyn 2023; 41:11437-11449. [PMID: 36591698 DOI: 10.1080/07391102.2022.2162967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/18/2022] [Indexed: 01/03/2023]
Abstract
Pandemic new severe acute respiratory syndrome coronavirus (SARS-CoV-2) virus has increased throughout the world. There is no effective treatment against this virus until now. Since its appearance in Wuhan, China in December 2019, SARS-CoV-2 becomes the largest challenge the world is opposite today, including the discovery of an antiviral drug for this virus. Several viral proteins have been prioritized as SARS-CoV-2 antiviral drug targets, among them the papain-like protease (PLpro) and the main protease (Mpro). Inhibition of these proteases would target viral replication, viral maturation and suppression of host innate immune responses. Potential candidates have been identified to show inhibitory effects against Mpro, both in biochemical assays and viral replication in cells. There are different molecules such as lopinavir and favipiravir considerably inhibit the activity of Mpro in vitro. Different studies have shown that structurally improved favipiravir and other similar compounds can inhibit SARS-CoV-2 main protease. In this work, we study the interactions between favipiravir with Mg12O12 and Zn12O12 nanoclusters by density functional theory (DFT) and quantum mechanics atoms in molecules (QMAIM) methods to summarize the ability to load favipiravir onto Mg12O12 and Zn12O12 nanoclusters. Favipiravir-Mg12O12 and favipiravir-Zn12O12 lowest structures complexes were chosen to dock inside the SARS-CoV-2 main protease by molecular docking study. The molecular docking analysis revealed that the binding affinity of Mg12O12 and Zn12O12 nanoclusters inside the Mpro receptor is larger than that of favipiravir. Also, the loading of favipiravir on the surface of Mg12O12 and Zn12O12 nanoclusters increased the binding affinity against the Mpro receptor. Subsequently, 100 ns molecular dynamics simulation of the favipiravir-Mg12O12, and favipiravir-Zn12O12 docked inside the Mpro complexes established that favipiravir-Mg12O12, forms the most stable complex with the Mpro. Further molecular mechanics Poisson Boltzmann surface area (MMPBSA) analyses using the MD trajectories also demonstrated the higher binding affinity of favipiravir-Mg12O12 inside the Mpro. In summary, this study demonstrates a new way to characterize leads for novel anti-viral drugs against SARS-CoV-2, by improving the drug ability of favipiravir via loading it on Mg12O12 and Zn12O12 nanoclusters.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - H R Abd El-Mageed
- Micro-analysis and Environmental Research and Community Services Center, Faculty of Science, Beni-Suef University, Beni-Suef City, Egypt
| | - Shimaa A Ahmed
- Department of Chemistry, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Hussein S Mohamed
- Chemistry of Medicinal and Aromatic Plants Department, Research institute of medicinal and aromatic plants (RIMAP), Beni-Suef University, Beni-Suef, Egypt
| | - Zeinab S Hamza
- Chemistry of Medicinal and Aromatic Plants Department, Research institute of medicinal and aromatic plants (RIMAP), Beni-Suef University, Beni-Suef, Egypt
| | - Md Oliullah Rafi
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jessore Sadar Upazila, Bangladesh
| | - Md Shahedur Rahman
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jessore Sadar Upazila, Bangladesh
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4
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Natmai S, Kuntip N, Japrung D, Pongprayoon P. The aggregation of multiple miR-29a cancer biomarkers induced by graphene quantum dots: Molecular dynamics simulations. J Mol Graph Model 2022; 116:108267. [PMID: 35849900 DOI: 10.1016/j.jmgm.2022.108267] [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: 03/21/2022] [Revised: 06/26/2022] [Accepted: 06/30/2022] [Indexed: 12/15/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that play a role in regulating gene expression. MiRNAs are focused on as potential cancer biomarkers due to their involvement in the cancer development. New effective techniques for extracting miRNA from a biological matrix is important. Recently, graphene quantum dots (GQDs) have been used to detect DNA/RNA in many sensor platforms, but the application in miRNA extraction remains limited. To extract miRNAs, the miRNA adsorption and desorption on GQD are the key. Thus, in this work, the adsorption mechanism of excess miRNA on GQD in solution is revealed using Molecular dynamics simulations. The miRNA assemblies on one and two GQDs were studied to explore the possibility of using GQD for miRNA extraction. The folded miR-29a molecule, one of key cancer biomarkers, is used as an miRNA model. Three systems with one (6miR) and two GQDs (with parallel (6miR_2GP) and sandwich (6miR_2GS) organisations) in six-miR-29a solution were set. The data show excess miR-29a can reduce the miR-29a-GQD binding efficiency. The opening of intrabase pairing of GQD-absorbed miR-29a facilitates the interbase coupling resulting in the self-aggregation of miR-29a. The GQD organisation also affects the miR-29a adsorption ability. The additional GQDs result in the tighter miR-29a adsorption which can retard the miR-29a desorption. The proper GQD concentration is thus important to successfully collect all miR-29a and accommodate the easy miR-29a dissociation. Our results can be useful for a design of DNA probe and choosing decent nanosized GRA concentration for experimental setups.
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Affiliation(s)
- Saowalak Natmai
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Nattapon Kuntip
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Deanpen Japrung
- National Nanotechnology Center, National Science and Technology Development Agency, Thailand Science Park, Pathumthani, 12120, Thailand
| | - Prapasiri Pongprayoon
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand; Center for Advanced Studied in Nanotechnology for Chemical, Food, and Agricultural Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok, 10900, Thailand.
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5
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Fu X, Cheng X, Liao W, Guo J, Li L. A metallic CP3 monolayer with very high absorption coefficients for visible light and as the CO2 absorbent. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.140041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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6
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Kurban M, Muz İ. Size-dependent adsorption performance of ZnO nanoclusters for drug delivery applications. Struct Chem 2022; 34:1061-1071. [PMID: 36196262 PMCID: PMC9523195 DOI: 10.1007/s11224-022-02063-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/18/2022] [Indexed: 11/25/2022]
Affiliation(s)
- Mustafa Kurban
- Department of Electrical and Electronics Engineering, Kırşehir Ahi Evran University, 40100 Kırşehir, Turkey
| | - İskender Muz
- Department of Mathematics and Science Education, Nevşehir Hacı Bektaş Veli University, 50300 Nevşehir, Turkey
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7
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Phenol/Chloroform-Free TiO2-Based miRNA Extraction from Cell Lysate. Int J Mol Sci 2022; 23:ijms23168848. [PMID: 36012112 PMCID: PMC9407779 DOI: 10.3390/ijms23168848] [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: 07/16/2022] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 11/17/2022] Open
Abstract
While microRNAs are considered as excellent biomarkers of various diseases, there are still several remaining challenges regarding their isolation. In this study, we aimed to design a novel RNA isolation method that would help to overcome those challenges. Therefore, we present a novel phenol/chloroform-free, low-cost method for miRNA extraction. Within this method, RNA is extracted from cell lysate with an isopropanol/water/NaCl system, followed by solid-phase extraction using TiO2 microspheres to effectively separate short RNAs from long RNA molecules. We also demonstrated the pH-dependent selectivity of TiO2 microspheres towards different sizes of RNA. We were able to regulate the size range of extracted RNAs with simple adjustments in binding conditions used during the solid-phase extraction.
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8
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Kuntip N, Japrung D, Pongprayoon P. What Happens When a Complementary DNA Meets miR-29a Cancer Biomarker in Complex with a Graphene Quantum Dot. ACS APPLIED BIO MATERIALS 2021; 4:8368-8376. [PMID: 35005926 DOI: 10.1021/acsabm.1c00943] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
MicroRNAs (miRNAs), short single-stranded noncoding RNA molecules, serve as potential cancer biomarkers due to their involvement in cancer development. One of the strategies to extract miRNAs is to perform the miRNA adsorption on nanomaterials and dissociation by a complementary DNA strand (DNA probe). Recently, graphene quantum dots (GQDs) were found to show a good ability to absorb miRNAs. Thus, in this work, the mechanism of the GQD-adhered miRNA capture by its complementary DNA is revealed using molecular dynamics simulations. miR-29a, a potential cancer biomarker, is used as a miRNA model. Three systems containing one and four chains of miR-29a in addition to one and four complementary DNA probes (1R1D, 1R4D, and 4R4D) were studied. GQDs are the prime targets of a DNA attack. The full coverage of GQDs is required to protect the adsorption of DNA probes on the GQD face. The nucleobase-backbone interactions are the main contributors to miR-DNA interactions in this work. The interbase paring becomes small because most nucleobases of miR-29a and their probe are stacked to maintain their secondary structures, and some are absorbed on the GQD surface. Apparently, weakening of the nucleobase-GQD π-π stacking and the intrabase-pairing strength is needed for extracting miR-29a by a probe. Although no GQD-absorbed miR-29a desorption is found here, the basic principles obtained can be useful for further utilization of GQDs and their derivatives for miRNA extraction and detection.
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Affiliation(s)
- Nattapon Kuntip
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Deanpen Japrung
- National Nanotechnology Center, National Science and Technology Development Agency, Thailand Science Park, Pathumthani 12120, Thailand
| | - Prapasiri Pongprayoon
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand.,Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand
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9
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Goswami B, Khan BA. Understanding the photovoltaic performances of ZnSe quantum dot-fullerene nanocomposites: A computational study. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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10
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Adsorption behavior of uracil on external surface of MgO nanotubes: A new class of hybrid nano-bio materials. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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Kuntip N, Japrung D, Pongprayoon P. Modeling the Adsorption of the miR-29a Cancer Biomarker on a Graphene Quantum Dot. ACS OMEGA 2021; 6:21764-21772. [PMID: 34471778 PMCID: PMC8388069 DOI: 10.1021/acsomega.1c03404] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/30/2021] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are small noncoding RNA molecules associated with the regulation of gene expression in organisms. MiRNAs are focused on as potential cancer biomarkers due to their involvement in cancer development. New potential techniques for miRNA detection are rapidly developed, while there is a lack of effective extraction approaches, especially for miRNAs. Recently, graphene quantum dots (GQDs) have been involved in many disease biosensor platforms including miRNA detection, but no application in miRNA extraction is studied. To extract miRNAs, miRNA adsorption and desorption on GQDs are the key. Thus, in this work, the adsorption mechanism of miRNA on GQDs in solution is revealed using molecular dynamics simulations. The aim is to explore the possibility of using GQDs for miRNA extraction. The folded miR-29a molecule, one of the key cancer biomarkers, is used as a miRNA model. Two systems with one (1miR) and four (4miR) chains of miR-29a were set. MiR-29a molecules in all systems are simultaneously adsorbed on the GQD surface. Our finding highlights the ability of the GQD in collecting miRNAs in solution. In 1miR, the whole miR-29a chain sits on the GQD face, whereas all miR-29a molecules in 4miR show the "clamping" conformation. No "lying flat" orientation of miR-29a is observed due to the existence of the preserved hairpin region. Interestingly, the 5' end shows tighter binding than the 3' terminus. A design of complementary DNA with the recognition segment involving the sequences close to the 3' end can promote effective miR-29a desorption.
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Affiliation(s)
- Nattapon Kuntip
- Department
of Chemistry, Faculty of Science, Kasetsart
University, Chatuchak, Bangkok 10900, Thailand
| | - Deanpen Japrung
- National
Nanotechnology Center, National Science
and Technology Development Agency, Thailand Science Park, Pathumthani 12120, Thailand
- . Phone:+66-2564-6665. Fax:+66-25647000
| | - Prapasiri Pongprayoon
- Department
of Chemistry, Faculty of Science, Kasetsart
University, Chatuchak, Bangkok 10900, Thailand
- Center
for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural
Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand
- . Phone: +66-2562-5555. Fax:+66-2579-3955
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12
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Kalia A, Kaur J, Tondey M, Manchanda P, Bindra P, Alghuthaymi MA, Shami A, Abd-Elsalam KA. Differential Antimycotic and Antioxidant Potentials of Chemically Synthesized Zinc-Based Nanoparticles Derived from Different Reducing/Complexing Agents against Pathogenic Fungi of Maize Crop. J Fungi (Basel) 2021; 7:223. [PMID: 33803825 PMCID: PMC8003151 DOI: 10.3390/jof7030223] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 03/17/2021] [Indexed: 12/12/2022] Open
Abstract
The present study aimed for the synthesis, characterization, and comparative evaluation of anti-oxidant and anti-fungal potentials of zinc-based nanoparticles (ZnNPs) by using different reducing or organic complexing-capping agents. The synthesized ZnNPs exhibited quasi-spherical to hexagonal shapes with average particle sizes ranging from 8 to 210 nm. The UV-Vis spectroscopy of the prepared ZnNPs showed variation in the appearance of characteristic absorption peak(s) for the various reducing/complexing agents i.e., 210 (NaOH and NaBH4), 220 (albumin, and thiourea), 260 and 330 (starch), and 351 nm (cellulose) for wavelengths spanning over 190-800 nm. The FT-IR spectroscopy of the synthesized ZnNPs depicted the functional chemical group diversity. On comparing the antioxidant potential of these ZnNPs, NaOH as reducing agent, (NaOH (RA)) derived ZnNPs presented significantly higher DPPH radical scavenging potential compared to other ZnNPs. The anti-mycotic potential of the ZnNPs as performed through an agar well diffusion assay exhibited variability in the extent of inhibition of the fungal mycelia with maximum inhibition at the highest concentration (40 mg L-1). The NaOH (RA)-derived ZnNPs showcased maximum mycelial inhibition compared to other ZnNPs. Further, incubation of the total genomic DNA with the most effective NaOH (RA)-derived ZnNPs led to intercalation or disintegration of the DNA of all the three fungal pathogens of maize with maximum DNA degrading effect on Macrophomina phaseolina genomic DNA. This study thus identified that differences in size and surface functionalization with the protein (albumin)/polysaccharides (starch, cellulose) diminishes the anti-oxidant and anti-mycotic potential of the generated ZnNPs. However, the NaOH emerged as the best reducing agent for the generation of uniform nano-scale ZnNPs which possessed comparably greater anti-oxidant and antimycotic activities against the three test maize pathogenic fungal cultures.
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Affiliation(s)
- Anu Kalia
- Electron Microscopy and Nanoscience Laboratory, Department of Soil Science, College of Agriculture, Punjab Agricultural University, Ludhiana 141004, Punjab, India
| | - Jashanpreet Kaur
- Department of Microbiology, College of Basic Sciences and Humanities, Punjab Agricultural University, Ludhiana 141004, Punjab, India; (J.K.); (M.T.)
| | - Manisha Tondey
- Department of Microbiology, College of Basic Sciences and Humanities, Punjab Agricultural University, Ludhiana 141004, Punjab, India; (J.K.); (M.T.)
| | - Pooja Manchanda
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana 141004, Punjab, India;
| | - Pulkit Bindra
- Institute of Nanoscience and Technology, Habitat Centre, Phase-10, Sector-64, Mohali 160062, Punjab, India;
| | - Mousa A. Alghuthaymi
- Biology Department, Science and Humanities College, Shaqra University, Alquwayiyah 11726, Saudi Arabia
| | - Ashwag Shami
- Biology Department, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh 11617, Saudi Arabia
| | - Kamel A. Abd-Elsalam
- Plant Pathology Research Institute, Agricultural Research Center (ARC), Giza 12619, Egypt;
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Abd El-Mageed H. Zinc oxide nanoclusters and nanoparticles as a drug carrier for cisplatin and nedaplatin anti-cancer drugs, insights from DFT methods and MC simulation. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1842533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- H.R. Abd El-Mageed
- Micro-analysis and Environmental Research and Community Services Center, Faculty of Science, Beni-Suef University, Beni-Suef City, Egypt
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14
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Xiao F, Chen Z, Wei Z, Tian L. Hydrophobic Interaction: A Promising Driving Force for the Biomedical Applications of Nucleic Acids. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001048. [PMID: 32832360 PMCID: PMC7435255 DOI: 10.1002/advs.202001048] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/28/2020] [Indexed: 05/13/2023]
Abstract
The comprehensive understanding and proper use of supramolecular interactions have become critical for the development of functional materials, and so is the biomedical application of nucleic acids (NAs). Relatively rare attention has been paid to hydrophobic interaction compared with hydrogen bonding and electrostatic interaction of NAs. However, hydrophobic interaction shows some unique properties, such as high tunability for application interest, minimal effect on NA functionality, and sensitivity to external stimuli. Therefore, the widespread use of hydrophobic interaction has promoted the evolution of NA-based biomaterials in higher-order self-assembly, drug/gene-delivery systems, and stimuli-responsive systems. Herein, the recent progress of NA-based biomaterials whose fabrications or properties are highly determined by hydrophobic interactions is summarized. 1) The hydrophobic interaction of NA itself comes from the accumulation of base-stacking forces, by which the NAs with certain base compositions and chain lengths show properties similar to thermal-responsive polymers. 2) In conjugation with hydrophobic molecules, NA amphiphiles show interesting self-assembly structures with unique properties in many new biosensing and therapeutic strategies. 3) The working-mechanisms of some NA-based complex materials are also dependent on hydrophobic interactions. Moreover, in recent attempts, NA amphiphiles have been applied in organizing macroscopic self-assembly of DNA origami and controlling the cell-cell interactions.
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Affiliation(s)
- Fan Xiao
- Department of Materials Science and EngineeringSouthern University of Science and Technology1088 Xueyuan Blvd.Nanshan DistrictShenzhenGuangdong518055P. R. China
- School of Materials Science and EngineeringHarbin Institute of TechnologyNangang DistrictHarbin150001P. R. China
| | - Zhe Chen
- Department of Materials Science and EngineeringSouthern University of Science and Technology1088 Xueyuan Blvd.Nanshan DistrictShenzhenGuangdong518055P. R. China
- Cancer Centre and Centre of ReproductionDevelopment and AgingFaculty of Health SciencesUniversity of MacauTaipaMacau999078P. R. China
| | - Zixiang Wei
- Department of Materials Science and EngineeringSouthern University of Science and Technology1088 Xueyuan Blvd.Nanshan DistrictShenzhenGuangdong518055P. R. China
- Cancer Centre and Centre of ReproductionDevelopment and AgingFaculty of Health SciencesUniversity of MacauTaipaMacau999078P. R. China
| | - Leilei Tian
- Department of Materials Science and EngineeringSouthern University of Science and Technology1088 Xueyuan Blvd.Nanshan DistrictShenzhenGuangdong518055P. R. China
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15
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Youssef MS, Elamawi RM. Evaluation of phytotoxicity, cytotoxicity, and genotoxicity of ZnO nanoparticles in Vicia faba. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:18972-18984. [PMID: 30238264 DOI: 10.1007/s11356-018-3250-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 09/14/2018] [Indexed: 05/25/2023]
Abstract
Due to the accelerating use of manufactured nanomaterials, more research is needed to define their impact on plants. The present investigation aimed at evaluating the effect of different levels (0.0, 10, 25, 50, and 100 mg/L) of ZnO nanoparticles (NPs) on Vicia faba during seed germination and seedling establishment. Additionally, V. faba root meristems were used as a model to monitor the cytotoxic and genotoxic effects resulting from exposure to ZnO NPs. The influence of ZnO NPs on three isoenzyme systems, peroxidase, α, and β esterase, was also evaluated using native-PAGE. Our results showed that lower concentrations of ZnO NPs (especially 10 and 25 mg/L) enhanced seed germination and improved seedling growth, while higher concentrations (100 and 200 mg/L) resulted in phytotoxicity. Cytological investigations of ZnO NPs-treated V. faba root cells denoted the clastogenic and aneugenic nature of ZnO NPs. Differential increase in mitotic index and significant alterations in cell cycle were observed upon exposure to ZnO NPs. High concentrations of ZnO NPs markedly induced chromosomal aberration, micronuclei, and vacuolated nuclei formation. Chromosomal breakage, chromosomal bridges, ring chromosomes, laggard chromosomes, and stickiness were also observed at a higher rate. The PAGE analysis showed that ZnO NPs treatments altered the expression patterns of all studied enzyme systems. Collectively, results from this work will help to further understand the phytotoxic effects of nanomaterials.
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Affiliation(s)
- Mohamed S Youssef
- Botany Department, Faculty of Science, Kafrelsheikh University, Kafrelsheikh, 33516, Egypt.
| | - Rabab M Elamawi
- Rice Pathology Department, Plant Pathology Research Institute, Agricultural Research Center, Sakha, Kafrelsheikh, 33717, Egypt
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16
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Wiesmann N, Tremel W, Brieger J. Zinc oxide nanoparticles for therapeutic purposes in cancer medicine. J Mater Chem B 2020; 8:4973-4989. [DOI: 10.1039/d0tb00739k] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Zinc oxide nanoparticles are characterized by a good biocompatibility while providing a versatile potential as innovative therapeutic agents in cancer medicine.
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Affiliation(s)
- Nadine Wiesmann
- Department of Otorhinolaryngology, Head and Neck Surgery
- University Medical Centre of the Johannes Gutenberg-University
- Laboratory for Molecular Tumor Biology
- 55131 Mainz
- Germany
| | - Wolfgang Tremel
- Department of Chemistry
- Johannes Gutenberg-University
- 55128 Mainz
- Germany
| | - Juergen Brieger
- Department of Otorhinolaryngology, Head and Neck Surgery
- University Medical Centre of the Johannes Gutenberg-University
- Laboratory for Molecular Tumor Biology
- 55131 Mainz
- Germany
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17
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Zhang C, Sun G, Senapati S, Chang HC. A bifurcated continuous field-flow fractionation (BCFFF) chip for high-yield and high-throughput nucleic acid extraction and purification. LAB ON A CHIP 2019; 19:3853-3861. [PMID: 31621762 PMCID: PMC6982425 DOI: 10.1039/c9lc00818g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
We report a bifurcated continuous field-flow fractionation (BCFFF) chip for high-yield and high-throughput (20 min) extraction of nucleic acids from physiological samples. The design uses a membrane ionic transistor to sustain low-ionic strength in a localized region at a junction, such that the resulting high field can selectively isolate high-charge density nucleic acids from the main flow channel and insert them into a standardized buffer in a side channel that bifurcates from the junction. The high local electric field and the bifurcated field-flow design facilitate concentration reduction of both divalent cation (Ca2+) and molecular PCR inhibitors by more than two orders of magnitude, even with high-throughput continuous loading. The unique design with a large (>20 mM mm-1) on-chip ionic-strength gradient allows miniaturization into a high-throughput field-flow fractionation chip that can be integrated with upstream lysing and downstream PCR/sensor modules for various nucleic acid detection/quantification applications. A concentration-independent 85% yield for extraction and an overall post-PCR yield exceeding 60% are demonstrated for a 111 bp dsDNA in 10 μL of human plasma, compared to no amplification with the raw sample. A net yield four times larger than a commercial extraction kit is demonstrated for miR-39 in human plasma.
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Affiliation(s)
- Chenguang Zhang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA. and Center for Microfluidics and Medical Diagnostics, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Gongchen Sun
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Satyajyoti Senapati
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA. and Center for Microfluidics and Medical Diagnostics, University of Notre Dame, Notre Dame, IN 46556, USA and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Hsueh-Chia Chang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA. and Center for Microfluidics and Medical Diagnostics, University of Notre Dame, Notre Dame, IN 46556, USA and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA and Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
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18
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Wang YM, Trinh MP, Zheng Y, Guo K, Jimenez LA, Zhong W. Analysis of circulating non-coding RNAs in a non-invasive and cost-effective manner. Trends Analyt Chem 2019; 117:242-262. [PMID: 32292220 PMCID: PMC7156030 DOI: 10.1016/j.trac.2019.07.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Non-coding RNAs (ncRNAs) participate in regulation of gene expression, and are highly relevant to pathological development. They are found to be stably present in diverse body fluids, including those in the circulatory system, which can be sampled non-invasively for clinical tests. Thus, circulating ncRNAs have great potential to be disease biomarkers. However, tremendous efforts are desired to discover and utilize ncRNAs as biomarkers in clinical diagnosis, calling for technological advancement in analysis of circulating ncRNAs in biospecimens. Hence, this review summarizes the recent developments in this area, highlighting the works devoted to cancer diagnosis and prognosis. Three main directions are focused: 1) Extraction and purification of ncRNAs from body fluids; 2) Quantification of the purified circulating ncRNAs; and 3) Microfluidic platforms for integration of both steps to enable point-of-care diagnostics. These technologies have laid a solid foundation to move forward the applications of circulating ncRNAs in disease diagnosis and cure.
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Affiliation(s)
- Yu-Min Wang
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
- Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, School of Chemistry and Environment, South China Normal University, Guangzhou, Guangdong 510006, P. R. China
| | - Michael Patrick Trinh
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
| | - Yongzan Zheng
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
| | - Kaizhu Guo
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
| | - Luis A. Jimenez
- Program in Biomedical Sciences, University of California at Riverside, Riverside, California 92521, United States
| | - Wenwan Zhong
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
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19
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Jayaraman J, Pavadai N, Venugopal T, Ramaiyan R. Interfacial charge-transfer in Cu-TiO2-HBDPPIN-Ag film and AIEE-active chemosensor. J Photochem Photobiol A Chem 2019. [DOI: 10.1016/j.jphotochem.2019.03.046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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20
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Yazhiniprabha M, Vaseeharan B, Sonawane A, Behera A. In vitro and In vivo toxicity assessment of phytofabricated ZnO nanoparticles showing bacteriostatic effect and larvicidal efficacy against Culex quinquefasciatus. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2019; 192:158-169. [DOI: 10.1016/j.jphotobiol.2019.01.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 01/05/2019] [Accepted: 01/29/2019] [Indexed: 11/16/2022]
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21
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Ghasemi A, Taghartapeh MR, Soltani A, Mahon PJ. Adsorption behavior of metformin drug on boron nitride fullerenes: Thermodynamics and DFT studies. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.11.124] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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22
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Kumari I, Kaur N, Gupta S, Goel N. Nucleotide conjugated (ZnO) 3 cluster: Interaction and optical characteristics using TDDFT. J Mol Graph Model 2018; 87:211-219. [PMID: 30554067 DOI: 10.1016/j.jmgm.2018.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 11/06/2018] [Accepted: 12/03/2018] [Indexed: 11/18/2022]
Abstract
Binding of four DNA nucleotide units with (ZnO)3 cluster in an aqueous phase has been investigated using density functional theory (DFT) and time dependent-density functional theory (TDDFT) method and the stability order for (ZnO)3-nucleobases/sugar/phosphate systems is predicted as phosphate > C > A > S > T ∼ G. The order of binding energy for (ZnO)3-nucleotide hybrid systems is observed to be (ZnO)3 + nuc-C ˃ (ZnO)3 + nuc-A ˃ (ZnO)3 + nuc-G ˃ (ZnO)3 + nuc-T. The binding of nucleotide units with the cluster has been explained on the basis of molecular electrostatic potential (MEP) plots, hydrogen bonding, glycosidic torsion angles, density of state (DOS) plots. The photophysical properties of (ZnO)3-nucleotide complexes have been studied using TDDFT approach. Among all (ZnO)3-nucleotide complexes, the absorption spectra of (ZnO)3 + nuc-A and (ZnO)3 + nuc-C complexes are seen to undergo red shift with respect to their bare nucleotide units that would be useful in the optical sensing of the respective nucleotides of DNA. It is interesting to note that binding of the nucleotide unit with the cluster makes it fluorescent, the study reports the fluorescence activity of (ZnO)3 + nuc-T complex.
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Affiliation(s)
- Indu Kumari
- Theoretical & Computational Chemistry Group, Department of Chemistry, Centre of Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India
| | - Navjot Kaur
- Theoretical & Computational Chemistry Group, Department of Chemistry, Centre of Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India
| | - Shuchi Gupta
- Department of Applied Sciences, University Institute of Engineering and Technology, Panjab University, Chandigarh, 160014, India
| | - Neetu Goel
- Theoretical & Computational Chemistry Group, Department of Chemistry, Centre of Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India.
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23
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Das S, Mukhopadhyay S, Chatterjee S, Devi PS, Suresh Kumar G. Fluorescent ZnO-Au Nanocomposite as a Probe for Elucidating Specificity in DNA Interaction. ACS OMEGA 2018; 3:7494-7507. [PMID: 30087915 PMCID: PMC6068853 DOI: 10.1021/acsomega.7b02096] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 05/08/2018] [Indexed: 05/10/2023]
Abstract
In this work, we report the interaction of a fluorescent ZnO-Au nanocomposite with deoxyribonucleic acid (DNA), leading to AT-specific DNA interaction, which is hitherto not known. For this study, three natural double-stranded (ds) DNAs having different AT:GC compositions were chosen and a ZnO-Au nanocomposite has been synthesized by anchoring a glutathione-protected gold nanocluster on the surface of egg-shell-membrane (ESM)-based ZnO nanoparticles. The ESM-based bare ZnO nanoparticles did not show any selective interaction toward DNA, whereas intrinsic fluorescence of the ZnO-Au nanocomposite shows an appreciable blue shift (Δλmax = 18 nm) in the luminescence wavelength of 520 nm in the presence of ds calf thymus (CT) DNA over other studied DNAs. In addition, the interaction of the nanocomposite through fluorescence studies with single-stranded (ss) CT DNA, synthetic polynucleotides, and nucleobases/nucleotides (adenine, thymine, deoxythymidine monophosphate, deoxyadenosine monophosphate) was also undertaken to delineate the specificity in interaction. A minor blue shift (Δλmax = 5 nm) in the emission wavelength at 520 nm was observed for single-stranded CT DNA, suggesting the proficiency of the nanocomposite for discriminating ss and ds CT DNA. More importantly, fluorescence signals from the nano-bio-interaction could be measured directly without any modification of the target, which is the foremost advantage emanated from this study compared with other previous reports. The AT base-pair-induced enhancement was also found to be highest for the melting temperature of CT DNA (ΔTmCT = 6.7 °C). Furthermore, spectropolarimetric experiments followed by calorimetric analysis provided evidence for specificity in AT-rich DNA interaction. This study would lead to establish the fluorescent ZnO-Au nanocomposite as a probe for nanomaterial-based DNA-binding study, featuring its specific interaction toward AT-rich DNA.
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Affiliation(s)
- Sumita Das
- Sensor
and Actuator Division, CSIR-Central Glass
and Ceramic Research Institute, Kolkata 700032, India
| | - Soumita Mukhopadhyay
- Sensor
and Actuator Division, CSIR-Central Glass
and Ceramic Research Institute, Kolkata 700032, India
| | - Sabyasachi Chatterjee
- Biophysical
Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Parukuttyamma Sujatha Devi
- Sensor
and Actuator Division, CSIR-Central Glass
and Ceramic Research Institute, Kolkata 700032, India
- E-mail: , . Phone: +91-33-2483
8082. Fax: 91-33-2473 0957
| | - Gopinatha Suresh Kumar
- Biophysical
Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
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24
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Ganguly BN, Maity B, Maity TK, Manna J, Roy M, Mukherjee M, Debnath S, Saha P, Shilpa N, Rana RK. l-Cysteine-Conjugated Ruthenium Hydrous Oxide Nanomaterials with Anticancer Active Application. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:1447-1456. [PMID: 29281292 DOI: 10.1021/acs.langmuir.7b01408] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bioactive nanomaterials, namely: ruthenium hydrous oxide (or ruthenium oxy-hydroxide), RuOx(OH)y and also a surface-conjugated novel material of the same within the template of an amino acid molecule, l-cysteine, have been studied. These compounds have been prepared through a simple wet chemical route, under physiological conditions, such that they could be suitably used in anticancer applications. Several physical methods were used for the nanomaterial characterization, e.g.: thermal analysis of the as prepared ruthenium hydrous oxide by differential scanning calorimetry (DSC) followed by thermal gravimetric analysis (TGA). This confirms that the material is a precursor for anhydrous nanocrystalline ruthenium oxide (RuO2), as is affirmed by powder X-ray diffraction pattern. Also, optical spectroscopic absorption (UV-vis and FT-IR) study of these nanoparticles (NPs) to ascertain their surface conjugation with l-cysteine have been performed. Besides these, surface morphology of the NPs were studied by field emission scanning electron microscopy (FE-SEM) along with their elemental purity check through energy dispersive X-ray analysis (EDX). Their surface chemical microenvironments were examined by X-ray photo electron spectroscopy (XPS). The hydrodynamic size of the prepared NPs were measured through dynamic light scattering (DLS) studies. Further, biological consequences of these NPs on cancerous HeLa cells and their cytotoxicity effects have been reported with MTT assay, such an application has not been reported so far.
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Affiliation(s)
| | - Buddhadeb Maity
- Department of Chemistry, Mahishadal Raj College , Mahishadal, East Midnapur, West Bengal-721628, India
| | - Tapan Kumar Maity
- Department of Chemistry, Mahishadal Raj College , Mahishadal, East Midnapur, West Bengal-721628, India
| | - Joydeb Manna
- Department of Chemistry, Mahishadal Raj College , Mahishadal, East Midnapur, West Bengal-721628, India
| | - Modhusudan Roy
- Saha Institute of Nuclear Physics , Kolkata-700064, India
| | | | | | - Partha Saha
- Saha Institute of Nuclear Physics , Kolkata-700064, India
- Homi Bhaba National Institute , Mumbai-700094, India
| | - Nagaraju Shilpa
- Nanomaterials Laboratory, I & PC Division, CSIR-Indian Institute of Chemical Technology , Hyderabad-500007, India
| | - Rohit Kumar Rana
- Nanomaterials Laboratory, I & PC Division, CSIR-Indian Institute of Chemical Technology , Hyderabad-500007, India
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25
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Das S, Chatterjee S, Pramanik S, Devi PS, Kumar GS. A new insight into the interaction of ZnO with calf thymus DNA through surface defects. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2018; 178:339-347. [DOI: 10.1016/j.jphotobiol.2017.10.039] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 10/17/2017] [Accepted: 10/30/2017] [Indexed: 01/14/2023]
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26
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Jimenez LA, Gionet-Gonzales MA, Sedano S, Carballo JG, Mendez Y, Zhong W. Extraction of microRNAs from biological matrices with titanium dioxide nanofibers. Anal Bioanal Chem 2017; 410:1053-1060. [PMID: 29030663 DOI: 10.1007/s00216-017-0649-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 09/13/2017] [Accepted: 09/16/2017] [Indexed: 12/21/2022]
Abstract
MicroRNAs (miRNAs) are small RNAs that bind to mRNA targets and regulate their translation. A functional study of miRNAs and exploration of their utility as disease markers require miRNA extraction from biological samples, which contain large amounts of interfering compounds for downstream RNA identification and quantification. The most common extraction methods employ silica columns or the TRIzol reagent but give out low recovery for small RNAs probably due to their short strand lengths. Herein, we fabricated the titanium dioxide nanofibers using electrospinning to facilitate miRNA extraction and developed the optimal buffer conditions to improve miRNA recovery from biological matrices of cell lysate and serum. We found that our TiO2 fibers could obtain a recovery of 18.0 ± 3.6% for miRNA fibers while carrying out the extraction in the more complex medium of cell lysate, much higher than the 0.02 ± 0.0001% recovery from the commercial kit. The much improved extraction of miRNAs from our fibers could be originated from the strong coordination between TiO2 and RNA's phosphate backbone. In addition, the binding, washing, and elution buffers judiciously developed in the present study can achieve selective extraction of small RNA shorter than 500 nucleotides in length. Our results demonstrate that TiO2 nanofibers can work as a valuable tool for extraction of miRNAs from biological samples with high recovery. Graphical abstract Schematic for extraction of small RNAs using TiO2 nanofibers.
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Affiliation(s)
- Luis A Jimenez
- Program in Biomedical Sciences, University of California, 900 University Ave., Riverside, CA, 92521, USA
| | | | - Sabrina Sedano
- Department of Chemistry, University of California, 900 University Ave., Riverside, CA, 92521, USA
| | - Jocelyn G Carballo
- Department of Chemistry, University of California, 900 University Ave., Riverside, CA, 92521, USA
| | - Yomara Mendez
- Department of Chemistry, University of California, 900 University Ave., Riverside, CA, 92521, USA
| | - Wenwan Zhong
- Department of Chemistry, University of California, 900 University Ave., Riverside, CA, 92521, USA.
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27
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Thanikachalam V, Sarojpurani E, Jayabharathi J. Interfacial charge-transfer process in nanosemiconductor- N -benzylpiperidine phenanthroimidazole (BDPI)-metal heterostructure: A combined experimental and theoretical studies of BDPI-(FeO) n composites. J Photochem Photobiol A Chem 2017. [DOI: 10.1016/j.jphotochem.2017.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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28
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Ramani M, Mudge MC, Morris RT, Zhang Y, Warcholek SA, Hurst MN, Riviere JE, DeLong RK. Zinc Oxide Nanoparticle-Poly I:C RNA Complexes: Implication as Therapeutics against Experimental Melanoma. Mol Pharm 2017; 14:614-625. [PMID: 28135100 DOI: 10.1021/acs.molpharmaceut.6b00795] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
There is current interest in harnessing the combined anticancer and immunological effect of nanoparticles (NPs) and RNA. Here, we evaluate the bioactivity of poly I:C (pIC) RNA, bound to anticancer zinc oxide NP (ZnO-NP) against melanoma. Direct RNA association to unfunctionalized ZnO-NP is shown by observing change in size, zeta potential, and absorption/fluorescence spectra upon complexation. RNA corona was visualized by transmission electron microscopy (TEM) for the first time. Binding constant (Kb = 1.6-2.8 g-1 L) was determined by modified Stern-Volmer, absorption, and biological surface activity index analysis. The pIC-ZnO-NP complex increased cell death for both human (A375) and mouse (B16F10) cell lines and suppressed tumor cell growth in BALB/C-B16F10 mouse melanoma model. Ex vivo tumor analysis indicated significant molecular activity such as changes in the level of phosphoproteins JNK, Akt, and inflammation markers IL-6 and IFN-γ. High throughput proteomics analysis revealed zinc oxide and poly I:C-specific and combinational patterns that suggested possible utility as an anticancer and immunotherapeutic strategy against melanoma.
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Affiliation(s)
| | - Miranda C Mudge
- Department of Biomedical Science, Missouri State University , Springfield, Missouri 65897, United States
| | - R Tyler Morris
- Department of Biomedical Science, Missouri State University , Springfield, Missouri 65897, United States
| | | | | | - Miranda N Hurst
- Department of Biomedical Science, Missouri State University , Springfield, Missouri 65897, United States
| | | | - Robert K DeLong
- Department of Biomedical Science, Missouri State University , Springfield, Missouri 65897, United States
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29
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Jayabharathi J, Prabhakaran A, Karunakaran C, Thanikachalam V, Sundharesan M. Study of interfacial charge transfer in nanosemiconductor-molecule composites. J PHYS ORG CHEM 2017. [DOI: 10.1002/poc.3600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | - Annadurai Prabhakaran
- Department of Chemistry; Annamalai University; Annamalainagar 608 002 Tamilnadu India
| | | | | | - Munusamy Sundharesan
- Department of Chemistry; Annamalai University; Annamalainagar 608 002 Tamilnadu India
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30
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Das S, Pramanik S, Chatterjee S, Das PP, Devi PS, Suresh Kumar G. Selective Binding of Genomic Escherichia coli DNA with ZnO Leads to White Light Emission: A New Aspect of Nano-Bio Interaction and Interface. ACS APPLIED MATERIALS & INTERFACES 2017; 9:644-657. [PMID: 28029245 DOI: 10.1021/acsami.6b11109] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Here, we report for the first time, a novel and intriguing application of deoxyribonucleic acid (DNA) in the area of optics by demonstrating white light emission by tuning the emission of a nanomaterial, ZnO rods, exhibiting surface defects, in the presence of genomic Escherichia coli DNA with a comparatively high quantum efficiency. In order to understand the DNA specificity, we have also studied the interaction of ZnO with CT, and ML DNA, ss EC DNA, synthetic polynucleotides and different mononucleosides and bases. Further, in order to understand the effect of particle shape and defects present in ZnO, we have also extended our study with ZnO rods prepared at higher temperature exhibiting red emission and ZnO particles exhibiting yellow emission. Interestingly, none of the above studies resulted in white light emission from ZnO-DNA complex. Our studies unequivocally confirmed that the concentration and the nature of DNA and ZnO together plays a crucial role in obtaining CIE coordinates (0.33, 0.33) close to white light. The much enhanced melting temperature (Tm) of EC DNA and the energetics factors confirm enhanced hydrogen bonding of ZnO with EC DNA leading to a new emission band. Our experimental observations not only confirm the selective binding of ZnO to EC DNA but also open a new perspective for developing energy saving light emitting materials through nano-bio interactions.
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Affiliation(s)
- Sumita Das
- Sensor and Actuator Division, CSIR-Central Glass and Ceramic Research Institute , Kolkata-700032, India
| | - Srikrishna Pramanik
- Sensor and Actuator Division, CSIR-Central Glass and Ceramic Research Institute , Kolkata-700032, India
| | - Sabyasachi Chatterjee
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology , Kolkata-700032, India
| | - Partha Pratim Das
- Sensor and Actuator Division, CSIR-Central Glass and Ceramic Research Institute , Kolkata-700032, India
| | | | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology , Kolkata-700032, India
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31
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Ahmed F, Arshi N, Dwivedi S, Koo BH, Azam A, Alsharaeh E. Low temperature growth of ZnO nanotubes for fluorescence quenching detection of DNA. JOURNAL OF MATERIALS SCIENCE. MATERIALS IN MEDICINE 2016; 27:189. [PMID: 27844304 DOI: 10.1007/s10856-016-5805-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 10/28/2016] [Indexed: 06/06/2023]
Abstract
In this work, large-scale and single-crystalline ZnO nanotubes were fabricated by a simple technique from an aqueous solution at a low temperature of 65 °C. According to detailed morphology, structural and compositional analyses showed that the ZnO nanotubes [diameter ~200 nm (wall thickness ~50 nm); length ~1 µm] have single-crystallite with wurtzite structure. As-prepared ZnO nanotubes showed an effective fluorescence quenching for the detection of calf thymus DNA. In particular, increasing DNA concentrations (5-50 µM) into the fixed concentration of ZnO nanotubes (50 µM) progressively quenched the intrinsic fluorescence of nanotubes, which showed that the nanotubes fluorescence was efficiently quenched upon binding to DNA. At the highest ZnO-DNA molar ratios of 1:1.8, around 50.1 % of fluorescence quenching of DNA was observed. Significance of this study provides simple, cost-effective, and low temperature synthesis of ZnO nanotubes revealed better fluorescence property toward a platform of DNA sensor. ZnO nanotubes with diameter of ~200 nm (wall thickness ~50 nm) and length of about 1 µm prepared at low temperature (65 °C) showed fluorescence was efficiently quenched upon binding to DNA. In particular, around 50.1 % of DNA fluorescence quenching at the highest ZnO-DNA molar ratios of 1:1.8 was observed.
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Affiliation(s)
- Faheem Ahmed
- College of Science & General Studies, Alfaisal University, Riyadh, Saudi Arabia.
| | - Nishat Arshi
- College of Science & General Studies, Alfaisal University, Riyadh, Saudi Arabia
| | - Saurabh Dwivedi
- Department of Applied Physics, Aligarh Muslim University, Aligarh, India
| | - Bon Heun Koo
- School of Materials Science & Engineering, Changwon National University, Changwon, South Korea
| | - Ameer Azam
- Department of Applied Physics, Aligarh Muslim University, Aligarh, India
| | - Edreese Alsharaeh
- College of Science & General Studies, Alfaisal University, Riyadh, Saudi Arabia.
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32
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Ma L, Liu B, Huang PJJ, Zhang X, Liu J. DNA Adsorption by ZnO Nanoparticles near Its Solubility Limit: Implications for DNA Fluorescence Quenching and DNAzyme Activity Assays. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:5672-80. [PMID: 27166701 DOI: 10.1021/acs.langmuir.6b00906] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Zinc oxide (ZnO) is a highly important material, and Zn(2+) is a key metal ion in biology. ZnO and Zn(2+) interconvert via dissolution and hydrolysis/condensation. In this work, we explore their interactions with DNA, which is important for biointerface, analytical, and bioinorganic chemistry. Fluorescently labeled DNA oligonucleotides were adsorbed by a low concentration (around 5 μg/mL) of ZnO nanoparticles, near the solubility limit. Right after mixing, fluorescence quenching occurred, indicating DNA adsorption. Then, fluorescence recovered, attributable to ZnO dissolution. The dissolution rate followed A5 > T5 > C5. Dissolution was slower with longer DNA. The adsorption affinity was also measured by a displacement assay to be G5 > C5 > T5 > A5, suggesting that tightly adsorbed DNA can retard ZnO dissolution. Electrostatic interactions are important for DNA adsorption because ZnO is positively charged at neutral pH, and a high salt concentration inhibits DNA adsorption. Next, in situ formation of ZnO from Zn(2+) was studied. First, titrating Zn(2+) into a fluorescently labeled oligonucleotide at pH 7.5 resulted in an abrupt fluorescence quenching beyond 0.2 mM Zn(2+). At pH 6, quenching occurred linearly with the Zn(2+) concentration, suggesting the effect of Zn(2+) precipitation at pH 7.5. Second, a Zn(2+)-dependent DNA-cleaving DNAzyme was studied. This DNAzyme was inhibited at higher than 2 mM Zn(2+), attributable to Zn(2+) precipitation and adsorption of the DNAzyme. This paper has established the interplay between DNA, Zn(2+), and ZnO. This understanding can avoid misinterpretation of DNA assay results and adds knowledge to DNA immobilization.
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Affiliation(s)
- Lingzi Ma
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Biwu Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Xu Zhang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
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33
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Site specific interaction of aromatic amino acids with ZnO nanotubes: A density functional approach. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.04.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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34
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Jayabharathi J, Prabhakaran A, Karunakaran C, Thanikachalam V, Sundharesan M. Structural, optical and photoconductivity characteristics of pristine FeO·Fe2O3 and NTPI–FeO·Fe2O3 nanocomposite: aggregation induced emission enhancement of fluorescent organic nanoprobe of thiophene appended phenanthrimidazole derivative. RSC Adv 2016. [DOI: 10.1039/c5ra25545g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In this manuscript we report the successful synthesis of pristine FeO·Fe2O3, 1-(naphthalen-1-yl)-2-(thiophen-2-yl)-1H-phenanthro[9,10-d]imidazole (NTPI), fluorescent organic nanoparticles (FONs) of NTPI and NTPI–FeO·Fe2O3 nanocomposite.
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35
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Sharma SK, Kaur N, Singh J, Sankar S, Gaur SS, Lee S, Kim DY, Singh N, Singh H. Electrochemical Sensitive Determination of Nanomolar Guanine from ZnO Nanorods Coated on Platinum Electrode. ELECTROANAL 2015. [DOI: 10.1002/elan.201500242] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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36
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Preedia Babu E, Subastri A, Suyavaran A, Lokeshwara Rao P, Suresh Kumar M, Jeevaratnam K, Thirunavukkarasu C. Extracellularly synthesized ZnO nanoparticles interact with DNA and augment gamma radiation induced DNA damage through reactive oxygen species. RSC Adv 2015. [DOI: 10.1039/c5ra09935h] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
ZnONPs were synthesized using ferulic acid as the reductant and the intricate twofold role as DNA binders and radio sensitizers was revealed, which can pave the way for anticancer therapy.
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Affiliation(s)
- E. Preedia Babu
- Department of Biochemistry and Molecular Biology
- Pondicherry University
- India
| | - A. Subastri
- Department of Biochemistry and Molecular Biology
- Pondicherry University
- India
| | - A. Suyavaran
- Department of Biochemistry and Molecular Biology
- Pondicherry University
- India
| | - P. Lokeshwara Rao
- Department of Biochemistry and Molecular Biology
- Pondicherry University
- India
| | | | - K. Jeevaratnam
- Department of Biochemistry and Molecular Biology
- Pondicherry University
- India
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Jayabharathi J, Ramanathan P, Thanikachalam V, Karunakaran C. Optical and theoretical studies on Fe3O4–imidazole nanocomposite and clusters. NEW J CHEM 2015. [DOI: 10.1039/c4nj02068e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The larger surface curvature of nanocrystals reduces steric hindrance between surface binding molecules and provides a larger number of unsaturated dangling bonds on the nanocrystal surface.
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Jayabharathi J, Sundharesan M, Prabhakaran A, Karunakaran C. Understanding the binding interaction of imidazole with ZnO nanomaterials and clusters. RSC Adv 2015. [DOI: 10.1039/c4ra15957h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The order of binding energy values for imidazole adsorbed ZnO clusters through the preferred azomethine nitrogen site is imidazole–Zn4O4 (R) > imidazole–Zn3O3 > imidazole–Zn4O4 (W) > imidazole–Zn2O2.
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39
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Jayabharathi J, Karunakaran C, Kalaiarasi V. Thermodynamically feasible photoelectron transfer from bioactive π-expanded imidazole luminophores to ZnO nanocrystals. NEW J CHEM 2015. [DOI: 10.1039/c4nj02003k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The chemical affinity between the nitrogen atom of the imidazole and the zinc ion on the surface of the nano oxide may be a reason for strong interaction of the ligand on nanoparticles causing the enhancement.
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40
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Chandraboss VL, Karthikeyan B, Senthilvelan S. Experimental and first-principles study of guanine adsorption on ZnO clusters. Phys Chem Chem Phys 2014; 16:23461-75. [DOI: 10.1039/c4cp03274h] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electronic structure for interaction of guanine with Zn2O2 cluster and the most preferred N1-site to form a stable G–Zn2O2 model.
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Affiliation(s)
- V. L. Chandraboss
- Department of Chemistry
- Annamalai University
- Annamalai Nagar 608 002, India
| | - B. Karthikeyan
- Department of Chemistry
- Annamalai University
- Annamalai Nagar 608 002, India
| | - S. Senthilvelan
- Department of Chemistry
- Annamalai University
- Annamalai Nagar 608 002, India
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