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Diggines B, Whittle S, Yadav I, Holmes EP, Rollins DE, Catley TE, Doyle PS, Pyne ALB. Multiscale topological analysis of kinetoplast DNA via high-resolution AFM. Phys Chem Chem Phys 2024; 26:25798-25807. [PMID: 39354753 DOI: 10.1039/d4cp01795a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2024]
Abstract
Kinetoplast DNA is a complex nanoscale network, naturally assembled from thousands of interconnected DNA circles within the mitochondrion of certain parasites. Despite the relevance of this molecule to parasitology and the recent discovery of tuneable mechanics, its topology remains highly contested. Here we present a multiscale analysis into the structure of kDNA using a combination of high-resolution atomic force microscopy and custom-designed image analysis protocols. By capturing a notably large set of high-resolution images, we are able to look beyond individual kDNA variations and quantify population properties throughout several length scales. Within the sample, geometric fluctuations of area and mean curvature are observed, corresponding with previous in vitro measurements. These translate to localised variations in density, with a sample-wide decrease in DNA density from the outer rim of the molecule to the centre and an increase in pore size. Nodes were investigated in a single molecule study, and their estimated connectivity significantly exceeded mean valence, with a high dependence on their position in the network. While node separation was approximately half the minicircle circumference, it followed a strong bimodal distribution, suggesting more complex underlying behaviour. Finally, upon selective digestion of the network, breakdown of the fibril-cap heterogeneity was observed, with molecules expanding less upon immobilisation on the mica surface. Additionally, preferential digestion was seen in localised areas of the network, increasing pore size disproportionately. Overall, the combination of high-resolution AFM and single molecule image analysis provides a promising method to the continued investigation of complex nanoscale structures. These findings support the ongoing characterisation of kDNA topology to aid understanding of its biological and mechanical phenomena.
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Affiliation(s)
- Bradley Diggines
- Department of Materials Science and Engineering, University of Sheffield, Sheffield, UK.
| | - Sylvia Whittle
- Department of Materials Science and Engineering, University of Sheffield, Sheffield, UK.
| | - Indresh Yadav
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar, Odisha 752050, India
| | - Elizabeth P Holmes
- Department of Materials Science and Engineering, University of Sheffield, Sheffield, UK.
| | - Daniel E Rollins
- Department of Materials Science and Engineering, University of Sheffield, Sheffield, UK.
| | - Thomas E Catley
- Department of Materials Science and Engineering, University of Sheffield, Sheffield, UK.
| | - Patrick S Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| | - Alice L B Pyne
- Department of Materials Science and Engineering, University of Sheffield, Sheffield, UK.
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Cui R, Wang Z, Li L, Liu L, Li Z, Liu X, Chen T, Rauf A, Kang X, Guo Y. Bionic nanopore recognition receptors for single-molecule enantioselectivity studies of chiral drugs. Anal Chim Acta 2024; 1318:342960. [PMID: 39067929 DOI: 10.1016/j.aca.2024.342960] [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: 01/25/2024] [Revised: 06/09/2024] [Accepted: 07/08/2024] [Indexed: 07/30/2024]
Abstract
BACKGROUND Enantiodiscrimination of chiral drugs is critical for understanding physiological phenomena and ensuring medical safety. Although enantiomers of these drugs share identical physicochemical properties, they exhibit significant differences in pharmacodynamic, pharmacokinetic, and toxicological properties due to the differences in their three-dimensional shapes. Therefore, the development of effective methods for chiral recognition is of great significance and has been a hot topic in chemo/biological studies. RESULTS In this study, we designed a recognition receptor comprising a α-hemolysin (α-HL) nanopore and sulfobutyl ether-β-cyclodextrin (SBEβCD) for identifying the enantiomers of the antidepressant duloxetine at the single-molecule level. Chiral molecules were discriminated based on the different current blockages within the recognition receptor. The results indicated a strong interaction between R-duloxetine and the recognition receptor. By combining the experimental data and molecular docking results, we explored the recognition mechanism of the designed nanopore recognition receptor for chiral drug molecules. It was found that hydrophobic and electrostatic interactions play key roles in chiral recognition. Additionally, by comparing the binding kinetics of enantiomers to cyclodextrins in confined nanospace and bulk solution, we found that enantiomeric identification was better facilitated in the confined nanospace. Finally, the enantiomeric excess (ee) of the enantiomeric duloxetine mixture was measured using this recognized receptor. SIGNIFICANCE This strategy has the advantages of low cost, high sensitivity, and no need for additional derivative modifications, providing a new perspective on the development of chiral recognition sensors with excellent enantioselectivity in drug design, pharmaceuticals, and biological applications.
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Affiliation(s)
- Rikun Cui
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Zhenzhao Wang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Linna Li
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Lili Liu
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Zhen Li
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Xingtong Liu
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Tingting Chen
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Ayesha Rauf
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Xiaofeng Kang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Yanli Guo
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, PR China.
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Ko HS, Kang M, Lee JT, Bae JY. Synthesis of Mesoporous Silica Sol with Low Refractive Properties for Increasing Transmittance. MICROMACHINES 2024; 15:892. [PMID: 39064403 PMCID: PMC11278989 DOI: 10.3390/mi15070892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 06/25/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024]
Abstract
Currently, coating with anti-reflective materials is an attractive approach to improve the quality of screen-based displays. In this study, mesoporous silica particles were systematically synthesized as a function of surfactant (i.e., CTAC-cetyltrimethylammonium chloride) concentration to serve as main coating fillers possessing low refractive indices. Precisely changing the amount of the CTAC surfactant, silica sol with an average diameter of 50 nm exhibits distinctively different specific surface areas, pore size, and pore volume. Prior to the preparation of final coating solutions containing these silica particle fillers, the percentage of solid content was optimized on a glass slide. The use of 50 wt% solid content exhibited the highest transmittance of light. Among various content levels of silica sol, the use of 3.5 wt% of silica particles in the solid content displayed the highest transmittance (i.e., best anti-reflectiveness). Under the almost identical coating layers prepared with the fixed amount of silica particles possessing different surface areas, pore size, and pore volume, it appears that the largest pore volume played the most important role in improving the anti-reflective properties. Experimentally understanding the key feature of low-refractive filler materials under the optimized conditions could provide a clear view to develop highly effective anti-reflective materials for various display applications.
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Affiliation(s)
| | | | | | - Jae Young Bae
- Department of Chemistry, Keimyung University, Daegu 42601, Republic of Korea; (H.-S.K.); (M.K.); (J.-t.L.)
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Bistervels MH, Hoogendoorn NT, Kamp M, Schoenmaker H, Brouwer AM, Noorduin WL. Light-controlled morphological development of self-organizing bioinspired nanocomposites. NANOSCALE 2024; 16:2310-2317. [PMID: 38230748 PMCID: PMC10832358 DOI: 10.1039/d3nr05828j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 01/09/2024] [Indexed: 01/18/2024]
Abstract
Nature's intricate biominerals inspire fundamental questions on self-organization and guide innovations towards functional materials. While advances in synthetic self-organization have enabled many levels of control, generating complex shapes remains difficult. Specifically, controlling morphologies during formation at the single micro/nanostructure level is the key challenge. Here, we steer the self-organization of barium carbonate nanocrystals and amorphous silica into complex nanocomposite morphologies by photogeneration of carbon dioxide (CO2) under ultraviolet (UV) light. Using modulations in the UV light intensity, we select the growth mode of the self-organization process inwards or outwards to form helical and coral-like morphologies respectively. The spatiotemporal control over CO2 photogeneration allows formation of different morphologies on pre-assigned locations, switching between different growth modes-to form for instance a coral on top of a helix or vice versa, and subtle sculpting and patterning of the nanocomposites during formation. These findings advance the understanding of these versatile self-organization processes and offer new prospects for tailored designs of functional materials using photochemically driven self-organization.
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Affiliation(s)
| | | | - Marko Kamp
- AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands.
| | | | - Albert M Brouwer
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam 1090 GD, The Netherlands
| | - Willem L Noorduin
- AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands.
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam 1090 GD, The Netherlands
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Fernandes RDV, Pranovich A, Valyukh S, Zille A, Hallberg T, Järrendahl K. Iridescence Mimicking in Fabrics: A Ultraviolet/Visible Spectroscopy Study. Biomimetics (Basel) 2024; 9:71. [PMID: 38392117 PMCID: PMC10887316 DOI: 10.3390/biomimetics9020071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/24/2024] Open
Abstract
Poly(styrene-methyl methacrylate-acrylic acid) photonic crystals (PCs), with five different sizes (170, 190, 210, 230 and 250 nm), were applied onto three plain fabrics, namely polyamide, polyester and cotton. The PC-coated fabrics were analyzed using scanning electronic microscopy and two UV/Vis reflectance spectrophotometric techniques (integrating sphere and scatterometry) to evaluate the PCs' self-assembly along with the obtained spectral and colors characteristics. Results showed that surface roughness of the fabrics had a major influence on the color produced by PCs. Polyamide-coated fabrics were the only samples having an iridescent effect, producing more vivid and brilliant colors than polyester and cotton samples. It was observed that as the angle of incident light increases, a hypsochromic shift in the reflection peak occurs along with the formation of new reflection peaks. Furthermore, color behavior simulations were performed with an illuminant A light source on polyamide samples. The illuminant A simulation showed greener and yellower structural colors than those illuminated with D50. The polyester and cotton samples were analyzed using scatterometry to check for iridescence, which was unseen upon ocular inspection and then proven to be present in these samples. This work allowed a better comprehension of how structural colors and their iridescence are affected by the textile substrate morphology and fiber type.
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Affiliation(s)
- Rui D V Fernandes
- Centre for Textile Science and Technology (2C2T), University of Minho, 4800-058 Guimarães, Portugal
| | - Alina Pranovich
- Department of Science and Technology (ITN), Linköping University, SE-601 74 Norrköping, Sweden
- Media and Information Technology (MIT), Linköping University, SE-601 74 Norrköping, Sweden
| | - Sergiy Valyukh
- Department of Physics, Chemistry and Biology (IFM), Linköping University, SE-581 83 Linköping, Sweden
| | - Andrea Zille
- Centre for Textile Science and Technology (2C2T), University of Minho, 4800-058 Guimarães, Portugal
| | - Tomas Hallberg
- Division of Electromagnetic Warfare, Swedish Defense Research Agency (FOI), SE-583 30 Linköping, Sweden
| | - Kenneth Järrendahl
- Department of Physics, Chemistry and Biology (IFM), Linköping University, SE-581 83 Linköping, Sweden
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Harun-Ur-Rashid M, Jahan I, Foyez T, Imran AB. Bio-Inspired Nanomaterials for Micro/Nanodevices: A New Era in Biomedical Applications. MICROMACHINES 2023; 14:1786. [PMID: 37763949 PMCID: PMC10536921 DOI: 10.3390/mi14091786] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/14/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023]
Abstract
Exploring bio-inspired nanomaterials (BINMs) and incorporating them into micro/nanodevices represent a significant development in biomedical applications. Nanomaterials, engineered to imitate biological structures and processes, exhibit distinctive attributes such as exceptional biocompatibility, multifunctionality, and unparalleled versatility. The utilization of BINMs demonstrates significant potential in diverse domains of biomedical micro/nanodevices, encompassing biosensors, targeted drug delivery systems, and advanced tissue engineering constructs. This article thoroughly examines the development and distinctive attributes of various BINMs, including those originating from proteins, DNA, and biomimetic polymers. Significant attention is directed toward incorporating these entities into micro/nanodevices and the subsequent biomedical ramifications that arise. This review explores biomimicry's structure-function correlations. Synthesis mosaics include bioprocesses, biomolecules, and natural structures. These nanomaterials' interfaces use biomimetic functionalization and geometric adaptations, transforming drug delivery, nanobiosensing, bio-inspired organ-on-chip systems, cancer-on-chip models, wound healing dressing mats, and antimicrobial surfaces. It provides an in-depth analysis of the existing challenges and proposes prospective strategies to improve the efficiency, performance, and reliability of these devices. Furthermore, this study offers a forward-thinking viewpoint highlighting potential avenues for future exploration and advancement. The objective is to effectively utilize and maximize the application of BINMs in the progression of biomedical micro/nanodevices, thereby propelling this rapidly developing field toward its promising future.
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Affiliation(s)
- Mohammad Harun-Ur-Rashid
- Department of Chemistry, International University of Business Agriculture and Technology, Dhaka 1230, Bangladesh;
| | - Israt Jahan
- Department of Cell Physiology, Graduate School of Medicine, Nagoya University, Nagoya 466-8550, Japan;
| | - Tahmina Foyez
- Department of Pharmacy, United International University, Dhaka 1212, Bangladesh;
| | - Abu Bin Imran
- Department of Chemistry, Bangladesh University of Engineering and Technology, Dhaka 1000, Bangladesh
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Bae H. Biomimicry Industry and Patent Trends. Biomimetics (Basel) 2023; 8:288. [PMID: 37504176 PMCID: PMC10807642 DOI: 10.3390/biomimetics8030288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/21/2023] [Accepted: 06/29/2023] [Indexed: 07/29/2023] Open
Abstract
This study examines the current technological level and industrial/technical trends in the field of biomimicry technology, as well as recent technological and research and development trends. Patent analysis was conducted, focusing on technology that uses design elements and biological/ecological characteristics to provide solutions to technological problems. The technological scope of the analysis included the field of technologies and materials that apply to the conditions found in ecology, as well as robot machines and devices designed to mimic certain animals and ecological elements. The search for patents was conducted in Korea, the United States, Japan, and Europe from 1975 to 2021, resulting in a total of 8278 raw data cases, from which 940 valid patents were selected. The percentage of patent document and the status of both domestic and foreign applicants varied among the countries of Korea, the United States, Japan, and Europe. Based on the results of the patent analysis, it was found that biomimicry technology is in a growth phase that is expected to continue in the future and that Korea and the United States are leading the development of this technology.
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Affiliation(s)
- Haejin Bae
- Ecological Technology Research Team, Division of Ecological Application Research, National Institute of Ecology, Seocheon-gun 33657, Republic of Korea
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