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Yu Y, Gu Z, Li M, Pu Y, Geballa Koukoula A, Peters J, Yang Y, Hong X. Cytosine-rich mismatched DNA aptamer combined with superparamagnetic photonic crystal sensing material for the specific visual detection of silver ions. Talanta 2024; 270:125551. [PMID: 38103284 DOI: 10.1016/j.talanta.2023.125551] [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: 07/27/2023] [Revised: 12/07/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
DNA aptamer superparamagnetic photonic crystals (DSPCs), enriched with a highly selective cytosine-rich mismatched single-stranded DNA aptamer (CRDA), were successfully employed in a novel visual detection strategy for the detection of silver ions (Ag+). The technologies of superparamagnetic colloidal nanospheres (SCNs), DNA aptamer, and photonic crystals were combined to fabricate DPSCs. The aptamer was immobilized via electrostatic adsorption with amino groups that were chemically introduced on the surface of the SCNs, forming D-NH-SCNs. The detection is achieved by forming an Ag+ complex (C-Ag+-C) between Ag+ and D-NH-SCN. The DSPCs assembled under a magnetic field by D-NH-SCNs effectively detected Ag+ in the range of 1 μg/L to 5 mg/L, corresponding to the critical concentration range for heavy metals in drinking water. During the detection, the DSPC exhibited a wavelength blueshift from 652.8 nm to 626.4 nm (26.4 nm), as well as changes in reflection intensity. Notably, when detecting Ag+, a change in DSPC color from orange to yellow was observed. In summary, the developed visual detection material facilitates direct Ag + sensing. In the future, different DNA aptamers will be modified further to detect various targets in the fields of medicine, environmental monitoring, and food safety.
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Affiliation(s)
- Ying Yu
- College of Vocational Education, Yunnan Normal University, Kunming, 650092, China
| | - Zhijia Gu
- Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Maokang Li
- College of Vocational Education, Yunnan Normal University, Kunming, 650092, China
| | - Yongfu Pu
- College of Vocational Education, Yunnan Normal University, Kunming, 650092, China
| | - Ariadni Geballa Koukoula
- Wageningen Food Safety Research (WFSR), Wageningen University & Research, Wageningen, 6708WB, Netherlands
| | - Jeroen Peters
- Wageningen Food Safety Research (WFSR), Wageningen University & Research, Wageningen, 6708WB, Netherlands
| | - Ying Yang
- College of Vocational Education, Yunnan Normal University, Kunming, 650092, China
| | - Xiaodi Hong
- Department of Cellular Biophysics, Max Planck Institute for Medical Research, Heidelberg, 69120, Germany; College of Vocational Education, Yunnan Normal University, Kunming, 650092, China.
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2
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Makiyan F, Rahimi F, Hajati M, Shafiekhani A, Rezayan AH, Ansari-Pour N. Label-free discrimination of single nucleotide changes in DNA by reflectometric interference Fourier transform spectroscopy. Colloids Surf B Biointerfaces 2019; 181:714-720. [PMID: 31228854 DOI: 10.1016/j.colsurfb.2019.05.066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 05/12/2019] [Accepted: 05/26/2019] [Indexed: 10/26/2022]
Abstract
Phenotypic variation - such as disease susceptibility and differential drug response - has a strong genetic component. Substantial effort has therefore been made to identify causal genomic variants explaining such variation among humans. Point mutations (PMs), which are single nucleotide changes in the genome, have been identified to be the most abundant form of causal genomic variants, making them useful, reliable diagnostic markers. Methods developed to genotype PMs have moved towards solid-phase assays, which not only show greater sensitivity and specificity, but also enable scalability and faster processing time. Most current assays are, however, based on fluorescent probes, which makes them relatively expensive. To develop a more cost-effective label-free genotyping method, we used a porous silicon (PSi) base as an efficient support for DNA biosensing and coupled it with reflectometric interference Fourier transform spectroscopy (RIFTS). To assess the versatility of this approach, we tested both a single nucleotide substitution in VKORC1 (-1639G > A; rs9923231) and a single nucleotide insertion in BRCA1 (5382insC; rs80357906). We demonstrate that the PSi-RIFTS method can efficiently detect both PM types with high sensitivity where hybridization of complementary DNA can be quantifiably differentiated from mismatch and non-complementary hybridization events. In addition, we show that the PSi base with immobilized DNA not only can be re-used to type further samples, but it also remains stable for 14 days, suggesting its potential for high-throughput applications.
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Affiliation(s)
- Farideh Makiyan
- Division of Nanobiotechnology, Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Fereshteh Rahimi
- Division of Nanobiotechnology, Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran.
| | - Marziyeh Hajati
- Division of Nanobiotechnology, Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Azizollah Shafiekhani
- Physics Department, Alzahra University, Tehran, Iran; School of Physics, Institute for Research in Fundamental Sciences, Tehran, Iran
| | - Ali Hossein Rezayan
- Division of Nanobiotechnology, Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Naser Ansari-Pour
- Division of Biotechnology, Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran; Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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3
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Hu F, Zhou M, Yan P, Li D, Lai W, Bian K, Dai R. Identification of mine water inrush using laser-induced fluorescence spectroscopy combined with one-dimensional convolutional neural network. RSC Adv 2019; 9:7673-7679. [PMID: 35521194 PMCID: PMC9061159 DOI: 10.1039/c9ra00805e] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 02/19/2019] [Indexed: 11/21/2022] Open
Abstract
The application of laser-induced fluorescence (LIF) combined with machine learning methods can make up for the shortcomings of traditional hydrochemical methods in the accurate and rapid identification of mine water inrush in coal mines. However, almost all of these methods require preprocessing such as principal component analysis (PCA) or drawing the spectral map as an essential step. Here, we provide our solution for the classification of mine water inrush, in which a one-dimensional convolutional neural network (1D CNN) is trained to automatically identify mine water inrush according to the LIF spectroscopy without the need for preprocessing. First, the architecture and parameters of the model were optimized and the 1D CNN model containing two convolutional blocks was determined to be the best model for the identification of mine water inrush. Then, we evaluated the performance of the 1D CNN model using the LIF spectral dataset of mine water inrush containing 540 training samples and 135 test samples, and we found that all 675 samples could be accurately identified. Finally, superior classification performance was demonstrated by comparing with a traditional machine learning algorithm (genetic algorithm-support vector machine) and a deep learning algorithm (two-dimensional convolutional neural network). The results show that LIF spectroscopy combined with 1D CNN can be used for the fast and accurate identification of mine water inrush without the need for complex pretreatments.
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Affiliation(s)
- Feng Hu
- School of Electrical and Information Engineering, Anhui University of Science and Technology No. 168 Taifeng Road Huainan 232001 PR China +86-13955443311
| | - Mengran Zhou
- School of Electrical and Information Engineering, Anhui University of Science and Technology No. 168 Taifeng Road Huainan 232001 PR China +86-13955443311
| | - Pengcheng Yan
- School of Electrical and Information Engineering, Anhui University of Science and Technology No. 168 Taifeng Road Huainan 232001 PR China +86-13955443311
| | - Datong Li
- School of Electrical and Information Engineering, Anhui University of Science and Technology No. 168 Taifeng Road Huainan 232001 PR China +86-13955443311
| | - Wenhao Lai
- School of Electrical and Information Engineering, Anhui University of Science and Technology No. 168 Taifeng Road Huainan 232001 PR China +86-13955443311
| | - Kai Bian
- School of Electrical and Information Engineering, Anhui University of Science and Technology No. 168 Taifeng Road Huainan 232001 PR China +86-13955443311
| | - Rongying Dai
- School of Electrical and Information Engineering, Anhui University of Science and Technology No. 168 Taifeng Road Huainan 232001 PR China +86-13955443311
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4
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Piya R, Zhu Y, Soeriyadi AH, Silva SM, Reece PJ, Gooding JJ. Micropatterning of porous silicon Bragg reflectors with poly(ethylene glycol) to fabricate cell microarrays: Towards single cell sensing. Biosens Bioelectron 2019; 127:229-235. [DOI: 10.1016/j.bios.2018.12.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 11/21/2018] [Accepted: 12/02/2018] [Indexed: 12/23/2022]
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Tieu T, Alba M, Elnathan R, Cifuentes‐Rius A, Voelcker NH. Advances in Porous Silicon–Based Nanomaterials for Diagnostic and Therapeutic Applications. ADVANCED THERAPEUTICS 2018. [DOI: 10.1002/adtp.201800095] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Terence Tieu
- Monash Institute of Pharmaceutical Sciences Monash University Parkville Campus, 381 Royal Parade Parkville Victoria 3052 Australia
- T. Tieu, Dr. M. Alba, Prof. N. H. Voelcker CSIRO Manufacturing Bayview Avenue Clayton Victoria 3168 Australia
| | - Maria Alba
- Monash Institute of Pharmaceutical Sciences Monash University Parkville Campus, 381 Royal Parade Parkville Victoria 3052 Australia
- T. Tieu, Dr. M. Alba, Prof. N. H. Voelcker CSIRO Manufacturing Bayview Avenue Clayton Victoria 3168 Australia
| | - Roey Elnathan
- Monash Institute of Pharmaceutical Sciences Monash University Parkville Campus, 381 Royal Parade Parkville Victoria 3052 Australia
| | - Anna Cifuentes‐Rius
- Monash Institute of Pharmaceutical Sciences Monash University Parkville Campus, 381 Royal Parade Parkville Victoria 3052 Australia
| | - Nicolas H. Voelcker
- Monash Institute of Pharmaceutical Sciences Monash University Parkville Campus, 381 Royal Parade Parkville Victoria 3052 Australia
- Prof. N. H. Voelcker Melbourne Centre for Nanofabrication Victorian Node of the Australian National Fabrication Facility 151 Wellington Road Clayton Victoria 3168 Australia
- T. Tieu, Dr. M. Alba, Prof. N. H. Voelcker CSIRO Manufacturing Bayview Avenue Clayton Victoria 3168 Australia
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Inan H, Poyraz M, Inci F, Lifson MA, Baday M, Cunningham BT, Demirci U. Photonic crystals: emerging biosensors and their promise for point-of-care applications. Chem Soc Rev 2017; 46:366-388. [PMID: 27841420 PMCID: PMC5529146 DOI: 10.1039/c6cs00206d] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Biosensors are extensively employed for diagnosing a broad array of diseases and disorders in clinical settings worldwide. The implementation of biosensors at the point-of-care (POC), such as at primary clinics or the bedside, faces impediments because they may require highly trained personnel, have long assay times, large sizes, and high instrumental cost. Thus, there exists a need to develop inexpensive, reliable, user-friendly, and compact biosensing systems at the POC. Biosensors incorporated with photonic crystal (PC) structures hold promise to address many of the aforementioned challenges facing the development of new POC diagnostics. Currently, PC-based biosensors have been employed for detecting a variety of biotargets, such as cells, pathogens, proteins, antibodies, and nucleic acids, with high efficiency and selectivity. In this review, we provide a broad overview of PCs by explaining their structures, fabrication techniques, and sensing principles. Furthermore, we discuss recent applications of PC-based biosensors incorporated with emerging technologies, including telemedicine, flexible and wearable sensing, smart materials and metamaterials. Finally, we discuss current challenges associated with existing biosensors, and provide an outlook for PC-based biosensors and their promise at the POC.
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Affiliation(s)
- Hakan Inan
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Stanford University School of Medicine, Department of Radiology, Canary Center at Stanford for Cancer Early Detection, 3155 Porter Drive, Palo Alto, CA 94304, USA.
| | - Muhammet Poyraz
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Stanford University School of Medicine, Department of Radiology, Canary Center at Stanford for Cancer Early Detection, 3155 Porter Drive, Palo Alto, CA 94304, USA. and Department of Electrical Engineering, Stanford University, Stanford, CA, USA
| | - Fatih Inci
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Stanford University School of Medicine, Department of Radiology, Canary Center at Stanford for Cancer Early Detection, 3155 Porter Drive, Palo Alto, CA 94304, USA.
| | - Mark A Lifson
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Stanford University School of Medicine, Department of Radiology, Canary Center at Stanford for Cancer Early Detection, 3155 Porter Drive, Palo Alto, CA 94304, USA.
| | - Murat Baday
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Stanford University School of Medicine, Department of Radiology, Canary Center at Stanford for Cancer Early Detection, 3155 Porter Drive, Palo Alto, CA 94304, USA.
| | - Brian T Cunningham
- Department of Electrical and Computer Engineering, Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Utkan Demirci
- Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Stanford University School of Medicine, Department of Radiology, Canary Center at Stanford for Cancer Early Detection, 3155 Porter Drive, Palo Alto, CA 94304, USA. and Department of Electrical Engineering (by courtesy), Stanford University, Stanford, CA, USA
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7
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Qin G, Yam CM, Kumar A, Lopez-Romero JM, Li S, Huynh T, Li Y, Yang B, Contreras-Caceres R, Cai C. Preparation, characterization, and protein-resistance of films derived from a series of α-oligo(ethylene glycol)-ω-alkenes on H–Si(111) surfaces. RSC Adv 2017. [DOI: 10.1039/c6ra28497c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Films on Si(111) were prepared by photo-activated grafting of CH2CH(CH2)m(OCH2CH2)nOCH3 (m = 8, 9; n = 3–7) by using different vacuum conditions. High vacuum produced a higher thickness (40 Å) and <0.8% fibrinogen adsorption (C10EG7). Films were stable even after 28 days.
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Affiliation(s)
- Guoting Qin
- College of Optometry
- University of Houston
- Houston
- USA
| | - Chi Ming Yam
- Department of Chemistry & Center for Materials Chemistry
- University of Houston
- Houston
- USA
| | - Amit Kumar
- Department of Chemistry & Center for Materials Chemistry
- University of Houston
- Houston
- USA
| | - J. Manuel Lopez-Romero
- Departamento de Química Orgánica
- Facultad de Ciencias
- Universidad de Málaga
- 29071 Málaga
- Spain
| | - Sha Li
- Department of Chemistry & Center for Materials Chemistry
- University of Houston
- Houston
- USA
| | - Toan Huynh
- Department of Chemistry & Center for Materials Chemistry
- University of Houston
- Houston
- USA
| | - Yan Li
- Department of Chemistry & Center for Materials Chemistry
- University of Houston
- Houston
- USA
| | - Bin Yang
- Department of Chemistry & Center for Materials Chemistry
- University of Houston
- Houston
- USA
| | | | - Chengzhi Cai
- Department of Chemistry & Center for Materials Chemistry
- University of Houston
- Houston
- USA
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8
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Tenenbaum E, Segal E. Optical biosensors for bacteria detection by a peptidomimetic antimicrobial compound. Analyst 2016; 140:7726-33. [PMID: 26456237 DOI: 10.1039/c5an01717c] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
In this work we present a label-free optical biosensor for rapid bacteria detection using a novel peptide-mimetic compound, as the recognition element. The biosensor design is based on an oxidized porous silicon (PSiO2) nanostructure used as the optical transducer, functionalized with the sequence K-[C12K]7 (referred to as K-7α12), which is a synthetic antimicrobial peptide. This compound is a member of a family of oligomers of acylated lysines (OAKs), mimicking the hydrophobicity and charge of natural antimicrobial peptides. The OAK is tethered to the PSiO2 film and the changes in the reflectivity spectrum are monitored upon exposure to Escherichia coli (E. coli) bacterial suspensions and their lysates. We show that capture of bacterial cell fragments induces predictable changes in the reflectivity spectrum, proportional to E. coli concentrations, thereby enabling rapid, sensitive and reproducible detection of E. coli at concentrations as low as 10(3) cells per mL. While for intact bacterial cells, the K-7α12-tethered PSiO2 shows a poor capturing ability, resulting in an insignificant optical response. The biosensor performance is also studied upon exposure to model Gram positive and negative bacterial lysates, suggesting preferential capture of E. coli cell fragments in the presented scheme. These OAK-based biosensors offer significant advantages in comparison with conventional antibody-based assays, in terms of their simple and cost-effective production, while providing numerous possible sequence combinations for designing new detection schemes.
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Affiliation(s)
- Elena Tenenbaum
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, Israel.
| | - Ester Segal
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, Israel. and Russell Berrie Nanotechnology Institute, Technion - Israel Institute of Technology, Haifa, Israel
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9
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Krismastuti FSH, Cavallaro A, Prieto-Simon B, Voelcker NH. Toward Multiplexing Detection of Wound Healing Biomarkers on Porous Silicon Resonant Microcavities. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2016; 3:1500383. [PMID: 27812471 PMCID: PMC5067563 DOI: 10.1002/advs.201500383] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 12/17/2015] [Indexed: 06/06/2023]
Abstract
Bacterial wound infections can cause septicemia and lead to limb amputation or death. Therefore, early detection of bacteria is important in chronic wound management. Here, an optical biosensor based on porous silicon resonant microcavity (pSiRM) structure modified with fluorogenic peptide substrate is demonstrated to detect the presence of Sortase A (SrtA), a bacterial enzyme found in the cell membrane protein of Staphylococcus aureus. The combination of fluorescence enhancement effects of the pSiRM architecture with the incorporation of SrtA fluorogenic peptide substrate within the pSi matrix enables the sensing of SrtA with an outstanding limit of detection of 8 × 10-14 m. Modification of the pSiRM structure with microscale spots of two fluorogenic peptide substrates, one specific for SrtA and the other for matrix metalloproteinases, effectively demonstrates the feasibility to perform multiplexed biomarker analysis. The results in this study highlight the potential of the pSiRM sensing platform as a point-of-care diagnostic tool for biomarkers of bacterial wound infection.
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Affiliation(s)
- Fransiska Sri Herwahyu Krismastuti
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology Future Industries Institute University of South Australia Mawson Lakes, Adelaide South Australia 5095 Australia
| | - Alex Cavallaro
- Future Industries Institute University of South Australia Mawson Lakes South Australia 5095 Australia
| | - Beatriz Prieto-Simon
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology Future Industries Institute University of South Australia Mawson Lakes, Adelaide South Australia 5095 Australia
| | - Nicolas H Voelcker
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology Future Industries Institute University of South Australia Mawson Lakes, Adelaide South Australia 5095 Australia
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10
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Mohammadi Ziarani G, Hassanzadeh Z, Gholamzadeh P, Asadi S, Badiei A. Advances in click chemistry for silica-based material construction. RSC Adv 2016. [DOI: 10.1039/c5ra26034e] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Click chemistry is undoubtedly the most powerful 1,3-dipolar cycloaddition reaction in organic synthesis.
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Affiliation(s)
| | | | | | - Shima Asadi
- Department of Chemistry
- Alzahra University
- Tehran
- Iran
| | - Alireza Badiei
- School of Chemistry
- College of Science
- University of Tehran
- Tehran
- Iran
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11
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Gupta B, Mai K, Lowe SB, Wakefield D, Di Girolamo N, Gaus K, Reece PJ, Gooding JJ. Ultrasensitive and Specific Measurement of Protease Activity Using Functionalized Photonic Crystals. Anal Chem 2015; 87:9946-53. [DOI: 10.1021/acs.analchem.5b02529] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Bakul Gupta
- School
of Chemistry, The Australian Centre for NanoMedicine and ARC Centre
of Excellence in Convergent Bio-Nano Science and Technology, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - Kelly Mai
- School
of Medical Sciences, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - Stuart B. Lowe
- School
of Chemistry, The Australian Centre for NanoMedicine and ARC Centre
of Excellence in Convergent Bio-Nano Science and Technology, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - Denis Wakefield
- School
of Medical Sciences, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - Nick Di Girolamo
- School
of Medical Sciences, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - Katharina Gaus
- EMBL
Australia Node in Single Molecule Science, School of Medical Sciences
and ARC Centre of Excellence in Advanced Molecular Imaging, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - Peter J. Reece
- School
of Physics, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - J. Justin Gooding
- School
of Chemistry, The Australian Centre for NanoMedicine and ARC Centre
of Excellence in Convergent Bio-Nano Science and Technology, UNSW Australia, Sydney, New South Wales 2052, Australia
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12
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Huber P. Soft matter in hard confinement: phase transition thermodynamics, structure, texture, diffusion and flow in nanoporous media. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:103102. [PMID: 25679044 DOI: 10.1088/0953-8984/27/10/103102] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Spatial confinement in nanoporous media affects the structure, thermodynamics and mobility of molecular soft matter often markedly. This article reviews thermodynamic equilibrium phenomena, such as physisorption, capillary condensation, crystallisation, self-diffusion, and structural phase transitions as well as selected aspects of the emerging field of spatially confined, non-equilibrium physics, i.e. the rheology of liquids, capillarity-driven flow phenomena, and imbibition front broadening in nanoporous materials. The observations in the nanoscale systems are related to the corresponding bulk phenomenologies. The complexity of the confined molecular species is varied from simple building blocks, like noble gas atoms, normal alkanes and alcohols to liquid crystals, polymers, ionic liquids, proteins and water. Mostly, experiments with mesoporous solids of alumina, gold, carbon, silica, and silicon with pore diameters ranging from a few up to 50 nm are presented. The observed peculiarities of nanopore-confined condensed matter are also discussed with regard to applications. A particular emphasis is put on texture formation upon crystallisation in nanoporous media, a topic both of high fundamental interest and of increasing nanotechnological importance, e.g. for the synthesis of organic/inorganic hybrid materials by melt infiltration, the usage of nanoporous solids in crystal nucleation or in template-assisted electrochemical deposition of nano structures.
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Affiliation(s)
- Patrick Huber
- Hamburg University of Technology (TUHH), Institute of Materials Physics and Technology, Eißendorfer Str. 42, D-21073 Hamburg-Harburg (Germany
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13
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Guan B, Magenau A, Ciampi S, Gaus K, Reece PJ, Gooding JJ. Antibody Modified Porous Silicon Microparticles for the Selective Capture of Cells. Bioconjug Chem 2014; 25:1282-9. [DOI: 10.1021/bc500144u] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Bin Guan
- School of Chemistry, ‡The Australian Centre for NanoMedicine, §ARC Centre of Excellence
in Convergent Bio-Nano Science and Technology, ∥Centre for Vascular Research, and ⊥School of Physics, The University of New South Wales, Sydney, Australia 2052
| | - Astrid Magenau
- School of Chemistry, ‡The Australian Centre for NanoMedicine, §ARC Centre of Excellence
in Convergent Bio-Nano Science and Technology, ∥Centre for Vascular Research, and ⊥School of Physics, The University of New South Wales, Sydney, Australia 2052
| | - Simone Ciampi
- School of Chemistry, ‡The Australian Centre for NanoMedicine, §ARC Centre of Excellence
in Convergent Bio-Nano Science and Technology, ∥Centre for Vascular Research, and ⊥School of Physics, The University of New South Wales, Sydney, Australia 2052
| | - Katharina Gaus
- School of Chemistry, ‡The Australian Centre for NanoMedicine, §ARC Centre of Excellence
in Convergent Bio-Nano Science and Technology, ∥Centre for Vascular Research, and ⊥School of Physics, The University of New South Wales, Sydney, Australia 2052
| | - Peter J. Reece
- School of Chemistry, ‡The Australian Centre for NanoMedicine, §ARC Centre of Excellence
in Convergent Bio-Nano Science and Technology, ∥Centre for Vascular Research, and ⊥School of Physics, The University of New South Wales, Sydney, Australia 2052
| | - J. Justin Gooding
- School of Chemistry, ‡The Australian Centre for NanoMedicine, §ARC Centre of Excellence
in Convergent Bio-Nano Science and Technology, ∥Centre for Vascular Research, and ⊥School of Physics, The University of New South Wales, Sydney, Australia 2052
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14
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Fenzl C, Hirsch T, Wolfbeis OS. Photonische Kristalle für die Chemo- und Biosensorik. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201307828] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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15
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Fenzl C, Hirsch T, Wolfbeis OS. Photonic crystals for chemical sensing and biosensing. Angew Chem Int Ed Engl 2014; 53:3318-35. [PMID: 24473976 DOI: 10.1002/anie.201307828] [Citation(s) in RCA: 367] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Indexed: 01/03/2023]
Abstract
This Review covers photonic crystals (PhCs) and their use for sensing mainly chemical and biochemical parameters, with a particular focus on the materials applied. Specific sections are devoted to a) a lead-in into natural and synthetic photonic nanoarchitectures, b) the various kinds of structures of PhCs, c) reflection and diffraction in PhCs, d) aspects of sensing based on mechanical, thermal, optical, electrical, magnetic, and purely chemical stimuli, e) aspects of biosensing based on biomolecules incorporated into PhCs, and f) current trends and limitations of such sensors.
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Affiliation(s)
- Christoph Fenzl
- Institut für Analytische Chemie, Chemo- und Biosensorik, Universität Regensburg, 93040 Regensburg (Germany) http://www.wolfbeis.de
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Krismastuti FSH, Brooks WLA, Sweetman MJ, Sumerlin BS, Voelcker NH. A photonic glucose biosensor for chronic wound prognostics. J Mater Chem B 2014; 2:3972-3983. [DOI: 10.1039/c4tb00231h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
An optical biosensor based on the switching of poly(4-vinylphenylboronic acid) (PVPBA) grafted to the pores of porous silicon (pSi) films in response to pH and glucose.
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Affiliation(s)
| | - William L. A. Brooks
- George & Josephine Butler Polymer Research Laboratory
- Center for Macromolecular Science & Engineering
- Department of Chemistry
- University of Florida
- Gainesville, USA
| | | | - Brent S. Sumerlin
- George & Josephine Butler Polymer Research Laboratory
- Center for Macromolecular Science & Engineering
- Department of Chemistry
- University of Florida
- Gainesville, USA
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17
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Soeriyadi AH, Gupta B, Reece PJ, Gooding JJ. Optimising the enzyme response of a porous silicon photonic crystal via the modular design of enzyme sensitive polymers. Polym Chem 2014. [DOI: 10.1039/c3py01638b] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The incorporation of a versatile and tuneable polymer–peptide network into the pores of porous silicon photonic crystals improves the selectivity of porous silicon optical biosensors to detect certain types of matrix metalloproteinase enzymes.
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Affiliation(s)
- Alexander H. Soeriyadi
- School of Chemistry
- University of New South Wales
- Sydney, Australia
- Australian Centre of NanoMedicine
- University of New South Wales
| | - Bakul Gupta
- School of Chemistry
- University of New South Wales
- Sydney, Australia
- Australian Centre of NanoMedicine
- University of New South Wales
| | - Peter J. Reece
- School of Physics
- University of New South Wales
- Sydney, Australia
| | - J. Justin Gooding
- School of Chemistry
- University of New South Wales
- Sydney, Australia
- Australian Centre of NanoMedicine
- University of New South Wales
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18
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Zhu Y, Gupta B, Guan B, Ciampi S, Reece PJ, Gooding JJ. Photolithographic strategy for patterning preformed, chemically modified, porous silicon photonic crystal using click chemistry. ACS APPLIED MATERIALS & INTERFACES 2013; 5:6514-6521. [PMID: 23781770 DOI: 10.1021/am4006012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Porous silicon (PSi) is an ideal platform for label-free biosensing, and the development of porous silicon patterning will open a pathway to the development of highly parallel PSi biochips for detecting multiple analytes. The optical response of PSi photonic crystal is determined by the changes in the effective bulk refractive index resulting from reactions/events occurring within the internal pore space. Therefore, introducing precise chemical functionalities in the pores of PSi is essential to ensure device selectivity. Here we describe the fabrication of PSi patterns that possess discrete chemical functionalities that are restricted to precise locations. The key difference to previous patterning protocols for PSi is that the entire porous material is first modified with a self-assembled monolayer of a α,ω-diyne adsorbate prior to patterning using a microfabricated titanium mask. The distal alkyne moieties in the monolayer are then amenable to further selective modification by the archetypal "click" reaction, the copper catalyzed alkyne-azide cycloaddition (CuAAC), using the titanium mask as a resist. This type of patterning is suitable for further immobilization of biological recognition elements, and presents a new platform for highly parallel PSi biosensor for multiple detections.
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Affiliation(s)
- Ying Zhu
- School of Chemistry and the Australian Centre for NanoMedicine, University of New South Wales, Sydney 2052, Australia
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19
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Krismastuti FSH, Pace S, Melville E, Cowin A, Dargaville TR, Voelcker NH. Matrix Metalloproteinase Biosensor Based on a Porous Silicon Reflector. Aust J Chem 2013. [DOI: 10.1071/ch13352] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Matrix metalloproteinases (MMP) are proteolytic enzymes important to wound healing. In non-healing wounds, it has been suggested that MMP levels become dysfunctional, hence it is of great interest to develop sensors to detect MMP biomarkers. This study presents the development of a label-free optical MMP biosensor based on a functionalised porous silicon (pSi) thin film. The biosensor is fabricated by immobilising a peptidomimetic MMP inhibitor in the porous layer using hydrosilylation followed by amide coupling. The binding of MMP to the immobilised inhibitor translates into a change of effective optical thickness over time. We investigated the effect of surface functionalisation on the stability of the pSi surface and evaluated sensing performance. We successfully demonstrated MMP detection in buffer solution and human wound fluid at physiologically relevant concentrations. This biosensor may find application as a point-of-care device that is prognostic of the healing trajectory of chronic wounds.
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20
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Gupta B, Zhu Y, Guan B, Reece PJ, Gooding JJ. Functionalised porous silicon as a biosensor: emphasis on monitoring cells in vivo and in vitro. Analyst 2013; 138:3593-615. [DOI: 10.1039/c3an00081h] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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Ciampi S, James M, Choudhury MH, Darwish NA, Gooding JJ. The detailed characterization of electrochemically switchable molecular assemblies on silicon electrodes. Phys Chem Chem Phys 2013; 15:9879-90. [DOI: 10.1039/c3cp50355k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Pal S, Fauchet PM, Miller BL. 1-D and 2-D photonic crystals as optical methods for amplifying biomolecular recognition. Anal Chem 2012; 84:8900-8. [PMID: 22947038 PMCID: PMC3491098 DOI: 10.1021/ac3012945] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Label-free sensing strategies are an intensely studied and increasingly used alternative to signal amplification via fluorescent labels and enzymatic methods. This article discusses one class of optical sensors, termed "photonic crystals", that effectively amplify binding events (such as analyte capture) via strong light-matter interactions.
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Affiliation(s)
- Sudeshna Pal
- Department of Electrical and Computer Engineering, University of Rochester, Rochester, New York 14642
- Department of Mechanical, Materials, and Aerospace Engineering University of Central Florida, Orlando, Florida 32816
| | - Philippe M. Fauchet
- Department of Electrical and Computer Engineering, University of Rochester, Rochester, New York 14642
- Department of Electrical Engineering and Computer Science Vanderbilt University, Nashville, Tennessee 37235
| | - Benjamin L. Miller
- Department of Dermatology, University of Rochester, Rochester, New York 14642
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23
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Kumeria T, Losic D. Controlling interferometric properties of nanoporous anodic aluminium oxide. NANOSCALE RESEARCH LETTERS 2012; 7:88. [PMID: 22280884 PMCID: PMC3287969 DOI: 10.1186/1556-276x-7-88] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 01/26/2012] [Indexed: 05/24/2023]
Abstract
A study of reflective interference spectroscopy [RIfS] properties of nanoporous anodic aluminium oxide [AAO] with the aim to develop a reliable substrate for label-free optical biosensing is presented. The influence of structural parameters of AAO including pore diameters, inter-pore distance, pore length, and surface modification by deposition of Au, Ag, Cr, Pt, Ni, and TiO2 on the RIfS signal (Fabry-Perot fringe) was explored. AAO with controlled pore dimensions was prepared by electrochemical anodization of aluminium using 0.3 M oxalic acid at different voltages (30 to 70 V) and anodization times (10 to 60 min). Results show the strong influence of pore structures and surface modifications on the interference signal and indicate the importance of optimisation of AAO pore structures for RIfS sensing. The pore length/pore diameter aspect ratio of AAO was identified as a suitable parameter to tune interferometric properties of AAO. Finally, the application of AAO with optimised pore structures for sensing of a surface binding reaction of alkanethiols (mercaptoundecanoic acid) on gold surface is demonstrated.
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Affiliation(s)
- Tushar Kumeria
- Ian Wark Research Institute, University of South Australia, Mawson Lakes, Adelaide, South Australia, 5095, Australia
| | - Dusan Losic
- Ian Wark Research Institute, University of South Australia, Mawson Lakes, Adelaide, South Australia, 5095, Australia
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24
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Ciampi S, Guan B, Darwish NA, Zhu Y, Reece PJ, Justin Gooding J. A multimodal optical and electrochemical device for monitoring surface reactions: redox active surfaces in porous silicon Rugate filters. Phys Chem Chem Phys 2012; 14:16433-9. [DOI: 10.1039/c2cp43461j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Ciampi S, James M, Le Saux G, Gaus K, Justin Gooding J. Electrochemical “Switching” of Si(100) Modular Assemblies. J Am Chem Soc 2011; 134:844-7. [DOI: 10.1021/ja210048x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Simone Ciampi
- School of Chemistry, The University of New South Wales, Sydney, NSW 2052,
Australia
| | - Michael James
- School of Chemistry, The University of New South Wales, Sydney, NSW 2052,
Australia
- Bragg Institute, Australian Nuclear Science and Technology Organisation (ANSTO), Locked Bag 2001, Kirrawee DC, NSW 2232, Australia
| | - Guillaume Le Saux
- School of Chemistry, The University of New South Wales, Sydney, NSW 2052,
Australia
| | - Katharina Gaus
- Centre for Vascular Research, The University of New South Wales, Sydney, NSW 2052,
Australia
| | - J. Justin Gooding
- School of Chemistry, The University of New South Wales, Sydney, NSW 2052,
Australia
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26
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Ciampi S, James M, Michaels P, Gooding JJ. Tandem "click" reactions at acetylene-terminated Si(100) monolayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:6940-6949. [PMID: 21557551 DOI: 10.1021/la2013733] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We demonstrate a simple method for coupling alkynes to alkynes. The method involves tandem azide-alkyne cycloaddition reactions ("click" chemistry) for the immobilization of 1-alkyne species onto an alkyne modified surface in a one-pot procedure. In the case presented, these reactions take place on a nonoxidized Si(100) surface although the approach is general for linking alkynes to alkynes. The applicability of the method in the preparation of electrically well-behaved functionalized surfaces is demonstrated by coupling an alkyne-tagged ferrocene species onto alkyne-terminated Si(100) surfaces. The utility of the approach in biotechnology is shown by constructing a DNA sensing interface by derivatization of the acetylenyl surface with commercially available alkyne-tagged oligonucleotides. Cyclic voltametry, electrochemical impedance spectroscopy, X-ray photoelectron spectroscopy, and X-ray reflectometry are used to characterize the coupling reactions and performance of the final modified surfaces. These data show that this synthetic protocol gives chemically well-defined, electronically well-behaved, and robust (bio)functionalized monolayers on silicon semiconducting surfaces.
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Affiliation(s)
- Simone Ciampi
- School of Chemistry, The University of New South Wales, Sydney NSW 2052, Australia
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27
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Ciampi S, James M, Darwish N, Luais E, Guan B, Harper JB, Gooding JJ. Oxidative acetylenic coupling reactions as a surface chemistry tool. Phys Chem Chem Phys 2011; 13:15624-32. [DOI: 10.1039/c1cp21450k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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29
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Gooding JJ, Ciampi S. The molecular level modification of surfaces: from self-assembled monolayers to complex molecular assemblies. Chem Soc Rev 2011; 40:2704-18. [DOI: 10.1039/c0cs00139b] [Citation(s) in RCA: 390] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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30
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Fomina N, McFearin CL, Sermsakdi M, Morachis JM, Almutairi A. Low power, biologically benign NIR light triggers polymer disassembly. Macromolecules 2011; 44:8590-8597. [PMID: 22096258 PMCID: PMC3215095 DOI: 10.1021/ma201850q] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Near infrared (NIR) irradiation can penetrate up to 10 cm deep into tissues and be remotely applied with high spatial and temporal precision. Despite its potential for various medical and biological applications, there is a dearth of biomaterials that are responsive at this wavelength region. Herein we report a polymeric material that is able to disassemble in response to biologically benign levels of NIR irradiation upon two-photon absorption. The design relies on the photolysis of the multiple pendant 4-bromo7-hydroxycoumarin protecting groups to trigger a cascade of cyclization and rearrangement reactions leading to the degradation of the polymer backbone. The new material undergoes a 50% Mw loss after 25 sec of ultraviolet (UV) irradiation by single photon absorption and 21 min of NIR irradiation via two-photon absorption. Most importantly, even NIR irradiation at biologically benign laser power is sufficient to cause significant polymer disassembly. Furthermore, this material is well tolerated by cells both before and after degradation. These results demonstrate for the first time a NIR sensitive material with potential to be used for in vivo applications.
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Affiliation(s)
- Nadezda Fomina
- Skaggs School Pharmacy and Pharmaceutical Sciences, Department of NanoEngineering, Materials Science and Engineering and Biomedical Sciences Programs, University of California at San Diego, La Jolla, California 92093
| | - Cathryn L. McFearin
- Skaggs School Pharmacy and Pharmaceutical Sciences, Department of NanoEngineering, Materials Science and Engineering and Biomedical Sciences Programs, University of California at San Diego, La Jolla, California 92093
| | - Marleen Sermsakdi
- Skaggs School Pharmacy and Pharmaceutical Sciences, Department of NanoEngineering, Materials Science and Engineering and Biomedical Sciences Programs, University of California at San Diego, La Jolla, California 92093
| | - José M. Morachis
- Skaggs School Pharmacy and Pharmaceutical Sciences, Department of NanoEngineering, Materials Science and Engineering and Biomedical Sciences Programs, University of California at San Diego, La Jolla, California 92093
| | - Adah Almutairi
- Skaggs School Pharmacy and Pharmaceutical Sciences, Department of NanoEngineering, Materials Science and Engineering and Biomedical Sciences Programs, University of California at San Diego, La Jolla, California 92093
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