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Abstract
There has been a recent surge of advances in biomolecular assays based on the measurement of discrete molecular targets as opposed to signals averaged across molecular ensembles. Many of these "digital" assay designs derive from now-mature technologies involving single-molecule imaging and microfluidics and provide an assortment of new modalities to quantify nucleic acids and proteins in biospecimens such as blood and tissue homogenates. A primary new benefit is the robust detection of trace analytes at attomolar to femtomolar concentrations for which many ensemble assays cannot distinguish signals above noise levels. In addition, multiple biomolecules can be differentiated within a mixture using optical barcodes, with much faster and simpler readouts compared with sequencing methods. In ideal digital assays, signals should, in theory, further represent absolute molecular counts, rather than relative levels, eliminating the need for calibration standards that are the mainstay of typical assays. Several digital assay platforms have now been commercialized but challenges hinder the adoption and diversification of these new formats, as there are broad needs to balance sensitivity and dynamic range of detection, increase analyte multiplexing, improve sample throughput, and reduce cost. Our lab and others have developed technologies to address these challenges by redesigning molecular probes and labels, improving molecular transport within detection focal volumes, and applying solution-based readout methods in flow.This Account describes the principles, formats, and design constraints of digital biomolecular assays that apply optical labels toward the goal of simple and routine target counting that may ultimately approach absolute readout standards. The primary challenges can be understood from fundamental concepts in thermodynamics and kinetics of association reactions, mass transport, and discrete statistics. Major advances include (1) new inorganic nanocrystal probes for more robust counting compared with dyes, (2) diverse molecular amplification tools that endow attachment of numerous labels to single targets, (3) specialized surfaces with patterned features for electromagnetic coupling to labels for signal amplification, (4) surface capture enhancement methods to concentrate targets through disruption of diffusion depletion zones, and (5) flow counting in which analytes are rapidly counted in solution without pull-down to a surface. Further progress and integration of these tools for biomolecular counting could improve the precision of laboratory measurements in life sciences research and benefit clinical diagnostic assays for low abundance biomarkers in limiting biospecimen volumes that are out of reach of traditional ensemble-level bioassays.
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Affiliation(s)
- Chia-Wei Kuo
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Andrew M Smith
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Materials Science & Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Carle Illinois College of Medicine, Urbana, Illinois 61801, United States
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Yan J, Zhao C, Ma Y, Yang W. Covalently Attaching Hollow Silica Nanoparticles on a COC Surface for the Fabrication of a Three-Dimensional Protein Microarray. Biomacromolecules 2022; 23:2614-2623. [PMID: 35603741 DOI: 10.1021/acs.biomac.2c00354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Compared to traditional two-dimensional (2D) biochips, three-dimensional (3D) biochips exhibit the advantages of higher probe density and detection sensitivity due to their designable surface microstructure as well as enlarged surface area. In the study, we proposed an approach to prepare a 3D protein chip by deposition of a monolayer of functionalized hollow silica nanoparticles (HSNs) on an activated cyclic olefin copolymer (COC) substrate. First, the COC substrate was chemically modified through the photografting technique to tether poly[3-(trimethoxysilyl) propyl methacrylate] (PTMSPMA) brushes on it. Then, a monolayer of HSNs was deposited on the modified COC and covalently attached via a condensation reaction between the hydrolyzed pendant siloxane groups of PTMSPMA and the Si-OH groups of HSNs. The roughness of the COC substrate significantly increased to 50.3 nm after depositing a monolayer of HSNs (ranging from 100 to 700 nm), while it only caused a negligible reduction in the light transmittance of COC. The HSN-modified COC was further functionalized with epoxide groups by a silane coupling agent for binding proteins. Immunoglobulin G could be effectively immobilized on this substrate with the highest immobilization efficiency of 75.2% and a maximum immobilization density of 1.236 μg/cm2, while the highest immobilization efficiency on a 2D epoxide group-modified glass slide was only 57.4%. Moreover, immunoassay results confirmed a competitive limit of detection (LOD) (1.06 ng/mL) and a linear detection range (1-100 ng/mL) of the 3D protein chip. This facile and effective approach for fabricating nanoparticle-based 3D protein microarrays has great potential in the field of biorelated detection.
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Zhou E, Song N, Xiao Q, Farooq Z, Jia Z, Wen J, Dai C, Ma C, Tu J, Shen J, Fu T, Yi B. Construction of transgenic detection system of Brassica napus L. based on single nucleotide polymorphism chip. 3 Biotech 2022; 12:11. [PMID: 34966634 PMCID: PMC8655060 DOI: 10.1007/s13205-021-03062-6] [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: 04/10/2021] [Accepted: 11/09/2021] [Indexed: 01/03/2023] Open
Abstract
Brassica napus L. is a vital oil crop in China. As auxiliary tools for rapeseed breeding, transgenic technologies play a considerable role in heterosis, variety improvement, and pest resistance. Research on transgenic detection technologies is of great significance for the introduction, supervision, and development of transgenic rapeseed in China. However, the transgenic detection methods currently in use are complex and time-consuming, with low output. A single nucleotide polymorphism (SNP) chip can effectively overcome such limitations. In the present study, we collected 40 transgenic elements and designed 291 probes. The probe sequences were submitted to Illumina Company, and the Infinium chip technology was used to prepare SNP chips. In the present Brassica napus transgenic detection experiment, 84 high-quality probes of 17 transgenic elements were preliminarily screened, and genotyping effect was optimised for the probe signal value. Ultimately, a transgenic detection system for B. napus was developed. The developed system has the advantages of simple operation, minimal technical errors, and stable detection outcomes. A transgenic detection sensitivity test revealed that the probe designed could accurately detect 1% of transgenic samples and had high detection sensitivity. In addition, in repeatability tests, the CaMV35S promoter coefficient of variation was approximately 3.58%. Therefore, the SNP chip had suitable repeatability in transgene detection. The SNP chip developed could be used to construct transgenic detection systems for B. napus. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-03062-6.
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Affiliation(s)
- Enqiang Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Nuan Song
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Qing Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Zunaira Farooq
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Zhibo Jia
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Cheng Dai
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430000 China
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Sun C, Vinayak MV, Cheng S, Hu W. Facile Functionalization Strategy for Ultrasensitive Organic Protein Biochips in Multi-Biomarker Determination. Anal Chem 2021; 93:11305-11311. [PMID: 34323475 DOI: 10.1021/acs.analchem.1c02601] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In recent years, organic field-effect transistors (OFETs) have shown great potential for advanced protein biochips due to their inherent biocompatibility and high-throughput detectability. However, the development of OFET-based protein biochips is still at an early stage. On the one hand, single-biomarker determination is not sufficient for the diagnosis of cancer; thus, simultaneous monitoring of electrical signals toward multi-biomarkers is widely concerned and explored. On the other hand, an optimized functionalization strategy for efficient protein immobilization is another key to make OFET-based protein biochips accessible with improved detection performance. Herein, a facile functionalization strategy is developed for excellent charge-transport thin films by suppressing the gelation of diketopyrrolopyrrole (DPP)-based polymer semiconductors with the addition of the glutaraldehyde cross-linking agent. Besides, functional groups are introduced on the device surface for efficient attachment of antibodies as receptors via a condensation reaction, enabling simultaneous determination of α-fetoprotein biomarker and carcinoembryonic antigen biomarker with improved sensitivity and reliability. Therefore, the proposed high-throughput OFET-based protein biochip has the potential to be widely utilized in early liver cancer diagnosis.
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Affiliation(s)
- Chenfang Sun
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Department of Chemistry, School of Science, Tianjin University, Tianjin 300072, China
| | - Manikkedath V Vinayak
- Department of Chemistry, Government College Kariavattom, Thiruvananthapuram 695581, Kerala, India
| | - Shanshan Cheng
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Department of Chemistry, School of Science, Tianjin University, Tianjin 300072, China
| | - Wenping Hu
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Department of Chemistry, School of Science, Tianjin University, Tianjin 300072, China.,Beijing National Laboratory for Molecular Science, Key Laboratory of Organic Solids, Institution of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Binhai New City, Fuzhou 350207, China
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Humenik M, Winkler A, Scheibel T. Patterning of protein-based materials. Biopolymers 2020; 112:e23412. [PMID: 33283876 DOI: 10.1002/bip.23412] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 01/03/2023]
Abstract
Micro- and nanopatterning of proteins on surfaces allows to develop for example high-throughput biosensors in biomedical diagnostics and in general advances the understanding of cell-material interactions in tissue engineering. Today, many techniques are available to generate protein pattern, ranging from technically simple ones, such as micro-contact printing, to highly tunable optical lithography or even technically sophisticated scanning probe lithography. Here, one focus is on the progress made in the development of protein-based materials as positive or negative photoresists allowing micro- to nanostructured scaffolds for biocompatible photonic, electronic and tissue engineering applications. The second one is on approaches, which allow a controlled spatiotemporal positioning of a single protein on surfaces, enabled by the recent developments in immobilization techniques coherent with the sensitive nature of proteins, defined protein orientation and maintenance of the protein activity at interfaces. The third one is on progress in photolithography-based methods, which allow to control the formation of protein-repellant/adhesive polymer brushes.
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Affiliation(s)
- Martin Humenik
- Department of Biomaterials, Faculty of Engineering Science, Universität Bayreuth, Bayreuth, Germany
| | - Anika Winkler
- Department of Biomaterials, Faculty of Engineering Science, Universität Bayreuth, Bayreuth, Germany
| | - Thomas Scheibel
- Department of Biomaterials, Faculty of Engineering Science, Universität Bayreuth, Bayreuth, Germany.,Bayreuth Center for Colloids and Interfaces (BZKG), Universität Bayreuth, Bayreuth, Germany.,Bayreuth Center for Molecular Biosciences (BZMB), Universität Bayreuth, Bayreuth, Germany.,Bayreuth Center for Material Science (BayMAT), Universität Bayreuth, Bayreuth, Germany.,Bavarian Polymer Institute (BPI), Universität Bayreuth, Bayreuth, Germany
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Qi Y, Wang Y, Chen C, Zhao C, Ma Y, Yang W. Facile Surface Functionalization of Cyclic Olefin Copolymer Film with Anhydride Groups for Protein Microarray Fabrication. ACS APPLIED BIO MATERIALS 2020; 3:3203-3209. [PMID: 35025362 DOI: 10.1021/acsabm.0c00200] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Immobilization of protein at high efficiency is a challenge for fabricating polymer-based protein chips. Here, a simple but effective approach was developed to fabricate a cyclic olefin copolymer (COC)-based protein microarray with a high immobilization density. In this strategy, poly(maleic anhydride-co-vinyl acetate) (poly(MAH-co-VAc)) brushes were facilely attached on the COC surface via UV-induced graft copolymerization. The introduction of poly(MAH-co-VAc) brushes resulted in an obvious increase in the surface roughness of COC. The functionalized COC showed little reduction in transparency compared with pristine COC, indicating that the photografting treatment did not alter its optical property. The graft density of the anhydride groups on the modified COC could be tuned from 0.46 to 3.2 μmol/cm2. The immobilization efficiency of immunoglobulin G (IgG) on functionalized COC reached 88% due to the high reactivity between anhydride groups and amine groups of IgGs. An immunoassay experiment demonstrated that the microarray showed high sensitivity to the target analyte.
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Yoon J, Shin M, Lim J, Kim DY, Lee T, Choi J. Nanobiohybrid Material‐Based Bioelectronic Devices. Biotechnol J 2020; 15:e1900347. [DOI: 10.1002/biot.201900347] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/19/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Jinho Yoon
- Department of Chemical and Biomolecular EngineeringSogang University 35 Baekbeom‐Ro Mapo‐Gu Seoul 04107 Republic of Korea
| | - Minkyu Shin
- Department of Chemical and Biomolecular EngineeringSogang University 35 Baekbeom‐Ro Mapo‐Gu Seoul 04107 Republic of Korea
| | - Joungpyo Lim
- Department of Chemical and Biomolecular EngineeringSogang University 35 Baekbeom‐Ro Mapo‐Gu Seoul 04107 Republic of Korea
| | - Dong Yeon Kim
- Department of Chemical and Biomolecular EngineeringSogang University 35 Baekbeom‐Ro Mapo‐Gu Seoul 04107 Republic of Korea
| | - Taek Lee
- Department of Chemical EngineeringKwangwoon University Wolgye‐dong Nowon‐gu Seoul 01899 Republic of Korea
| | - Jeong‐Woo Choi
- Department of Chemical and Biomolecular EngineeringSogang University 35 Baekbeom‐Ro Mapo‐Gu Seoul 04107 Republic of Korea
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Qi Y, Wang Y, Zhao C, Ma Y, Yang W. Highly Transparent Cyclic Olefin Copolymer Film with a Nanotextured Surface Prepared by One-Step Photografting for High-Density DNA Immobilization. ACS APPLIED MATERIALS & INTERFACES 2019; 11:28690-28698. [PMID: 31322850 DOI: 10.1021/acsami.9b09662] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Compared with conventional glass slides and two-dimensional (2D) planar microarrays, polymer-based support materials and three-dimensional (3D) surface structures have attracted increasing attention in the field of biochips because of their good processability in microfabrication and low cost in mass production, as well as their improved sensitivity and specificity for the detection of biomolecules. In the present study, UV-induced emulsion graft polymerization was carried out on a cyclic olefin copolymer (COC) surface to generate 3D nanotextures composed of loosely stacked nanoparticles with a diameter of approximately 50 nm. The introduction of a hierarchical nanostructure on a COC surface only resulted in a 5% decrease in its transparency at a wavelength of 550 nm but significantly increased the surface area, which markedly improved immobilization density and efficiency of an oligonucleotide probe compared with the functional group and polymer brush-modified substrates. The highest immobilization efficiency of the probes reached 93%, and a limit of detection of 75 pM could be obtained. The hybridization experiment demonstrated that the 3D gene chip exhibited excellent sensitivity for target DNA detection and single-nucleotide polymorphism discrimination. This one-step approach to the construction of nanotextured surfaces on the COC has promising applications in the fields of biochips and immunoassays.
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Hu Y, Niemeyer CM. From DNA Nanotechnology to Material Systems Engineering. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1806294. [PMID: 30767279 DOI: 10.1002/adma.201806294] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/29/2018] [Indexed: 05/25/2023]
Abstract
In the past 35 years, DNA nanotechnology has grown to a highly innovative and vibrant field of research at the interface of chemistry, materials science, biotechnology, and nanotechnology. Herein, a short summary of the state of research in various subdisciplines of DNA nanotechnology, ranging from pure "structural DNA nanotechnology" over protein-DNA assemblies, nanoparticle-based DNA materials, and DNA polymers to DNA surface technology is given. The survey shows that these subdisciplines are growing ever closer together and suggests that this integration is essential in order to initiate the next phase of development. With the increasing implementation of machine-based approaches in microfluidics, robotics, and data-driven science, DNA-material systems will emerge that could be suitable for applications in sensor technology, photonics, as interfaces between technical systems and living organisms, or for biomimetic fabrication processes.
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Affiliation(s)
- Yong Hu
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Christof M Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
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Straightforward Protein-Protein Interaction Interface Mapping via Random Mutagenesis and Mammalian Protein Protein Interaction Trap (MAPPIT). Int J Mol Sci 2019; 20:ijms20092058. [PMID: 31027327 PMCID: PMC6539206 DOI: 10.3390/ijms20092058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 04/08/2019] [Accepted: 04/13/2019] [Indexed: 01/18/2023] Open
Abstract
The MAPPIT (mammalian protein protein interaction trap) method allows high-throughput detection of protein interactions by very simple co-transfection of three plasmids in HEK293T cells, followed by a luciferase readout. MAPPIT detects a large percentage of all protein interactions, including those requiring posttranslational modifications and endogenous or exogenous ligands. Here, we present a straightforward method that allows detailed mapping of interaction interfaces via MAPPIT. The method provides insight into the interaction mechanism and reveals how this is affected by disease-associated mutations. By combining error-prone polymerase chain reaction (PCR) for random mutagenesis, 96-well DNA prepping, Sanger sequencing, and MAPPIT via 384-well transfections, we test the effects of a large number of mutations of a selected protein on its protein interactions. The entire screen takes less than three months and interactions with multiple partners can be studied in parallel. The effect of mutations on the MAPPIT readout is mapped on the protein structure, allowing unbiased identification of all putative interaction sites. We have thus far analysed 6 proteins and mapped their interfaces for 16 different interaction partners. Our method is broadly applicable as the required tools are simple and widely available.
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Deng J, Fu R, Li Q, Wang Y, Hu W, Shen B, Li H, Hu C, Liu M, Zhang L, Liu M, Cao Q, Wang Y. Increased sFRP3 expression correlated to senescence of endothelial cells in the aging process of mice. Am J Transl Res 2019; 11:1810-1818. [PMID: 30972204 PMCID: PMC6456558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 01/23/2019] [Indexed: 06/09/2023]
Abstract
Aging is tightly associated with various diseases, such as cardiovascular diseases; however, there is no effective biomarker to detect and evaluate the aging process in vivo. Therefore, it is critical to identify new aging biomarkers for earlier diagnose of aging-related diseases. This study investigated the profile of cytokines in serum samples of young and aged mice with the purpose of exploring new biomarkers that have remarkable alterations in aging. A solid-phase antibody array was used to screen 200 proteins in the mouse serum, among which 32 cytokines differentially expressed between young and aged mice were screened. The major proteins were secreted frizzled-related protein 3 (sFRP3), Fractalkine, IGFBP-5, IGFBP-6, etc. We select secreted frizzled-related protein 3 (sFRP3) in follow-up study. Then, enzyme-linked immunosorbent assay (ELISA) was used to detect the expression levels of sFRP3. Our results revealed that the expression levels of sFRP3 in serum samples from aged mice were significantly higher than those in samples from young mice. ELISA data were identical to those obtained by the antibody array. Our findings indicated that sFRP3 has remarkable significance in senescence. Furthermore, we detected sFRP3 level in culture supernatants of primary endothelial cells, and the variation trend of sFRP3 levels in culture supernatant was consistent with serum data. We also detected serum sFRP3 amounts in healthy young and elderly individuals. Interestingly, serum sFRP3 amounts in the elderly were significantly increased compared with those of young individuals.
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Affiliation(s)
- Jie Deng
- The Central Laboratory of Medical Research Center, Anhui Provincial Hospital, Anhui Medical UniversityHefei 230001, Anhui, PR China
| | - Rui Fu
- The Central Laboratory of Medical Research Center, Anhui Provincial Hospital, Anhui Medical UniversityHefei 230001, Anhui, PR China
| | - Qing Li
- The Central Laboratory of Medical Research Center, Anhui Provincial Hospital, Anhui Medical UniversityHefei 230001, Anhui, PR China
| | - Yuanmin Wang
- Centre for Kidney Research, Children’s Hospital at WestmeadSydney, NSW, Australia
| | - Wei Hu
- Department of Neurology, Anhui Provincial Hospital, Anhui Medical UniversityHefei 230001, Anhui, PR China
| | - Bing Shen
- School of Basic Medical Sciences, Anhui Medical UniversityHefei 230032, Anhui, PR China
| | - Hongqi Li
- Department of Geriatric Cardiology, Anhui Provincial Hospital, Anhui Medical UniversityHefei 230001, Anhui, PR China
| | - Chaojie Hu
- The Central Laboratory of Medical Research Center, Anhui Provincial Hospital, Anhui Medical UniversityHefei 230001, Anhui, PR China
| | - Manli Liu
- The Central Laboratory of Medical Research Center, Anhui Provincial Hospital, Anhui Medical UniversityHefei 230001, Anhui, PR China
| | - Liang Zhang
- The Central Laboratory of Medical Research Center, Anhui Provincial Hospital, Anhui Medical UniversityHefei 230001, Anhui, PR China
| | - Mengdie Liu
- The Central Laboratory of Medical Research Center, Anhui Provincial Hospital, Anhui Medical UniversityHefei 230001, Anhui, PR China
| | - Qi Cao
- The Centre for Transplantation and Renal Research, Westmead Institute for Medical Research, University of SydneyNSW, Australia
| | - Yiping Wang
- The Centre for Transplantation and Renal Research, Westmead Institute for Medical Research, University of SydneyNSW, Australia
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Philippi M, You C, Richter CP, Schmidt M, Thien J, Liße D, Wollschläger J, Piehler J, Steinhart M. Close-packed silane nanodot arrays by capillary nanostamping coupled with heterocyclic silane ring opening. RSC Adv 2019; 9:24742-24750. [PMID: 35528685 PMCID: PMC9069738 DOI: 10.1039/c9ra03440d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/29/2019] [Indexed: 11/21/2022] Open
Abstract
We report the parallel generation of close-packed ordered silane nanodot arrays with nanodot diameters of few 100 nm and nearest-neighbor distances in the one-micron range.
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Affiliation(s)
- Michael Philippi
- Institute for Chemistry of New Materials
- Center for Cellular Nanoanalytics (CellNanOs)
- Universität Osnabrück
- 49076 Osnabrück
- Germany
| | - Changjiang You
- Department of Biology
- Center for Cellular Nanoanalytics (CellNanOs)
- Universität Osnabrück
- 49076 Osnabrück
- Germany
| | - Christian P. Richter
- Department of Biology
- Center for Cellular Nanoanalytics (CellNanOs)
- Universität Osnabrück
- 49076 Osnabrück
- Germany
| | - Mercedes Schmidt
- Institute for Chemistry of New Materials
- Center for Cellular Nanoanalytics (CellNanOs)
- Universität Osnabrück
- 49076 Osnabrück
- Germany
| | - Jannis Thien
- Department of Physics
- Universität Osnabrück
- 49076 Osnabrück
- Germany
| | - Domenik Liße
- Department of Biology
- Center for Cellular Nanoanalytics (CellNanOs)
- Universität Osnabrück
- 49076 Osnabrück
- Germany
| | | | - Jacob Piehler
- Department of Biology
- Center for Cellular Nanoanalytics (CellNanOs)
- Universität Osnabrück
- 49076 Osnabrück
- Germany
| | - Martin Steinhart
- Institute for Chemistry of New Materials
- Center for Cellular Nanoanalytics (CellNanOs)
- Universität Osnabrück
- 49076 Osnabrück
- Germany
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Schneider A, Niemeyer CM. DNA Surface Technology: From Gene Sensors to Integrated Systems for Life and Materials Sciences. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201811713] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ann‐Kathrin Schneider
- Institute for Biological Interfaces (IBG 1) Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldshafen Germany
| | - Christof M. Niemeyer
- Institute for Biological Interfaces (IBG 1) Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldshafen Germany
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Schneider A, Niemeyer CM. DNA Surface Technology: From Gene Sensors to Integrated Systems for Life and Materials Sciences. Angew Chem Int Ed Engl 2018; 57:16959-16967. [DOI: 10.1002/anie.201811713] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/15/2018] [Indexed: 01/21/2023]
Affiliation(s)
- Ann‐Kathrin Schneider
- Institute for Biological Interfaces (IBG 1) Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldshafen Germany
| | - Christof M. Niemeyer
- Institute for Biological Interfaces (IBG 1) Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldshafen Germany
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15
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Dual-functional polymer-modified magnetic nanoparticles for isolation of lysozyme. Anal Chim Acta 2018; 1035:70-76. [DOI: 10.1016/j.aca.2018.07.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 06/13/2018] [Accepted: 07/07/2018] [Indexed: 12/30/2022]
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Grawe RW, Knotts TA. The effects of tether placement on antibody stability on surfaces. J Chem Phys 2018; 146:215102. [PMID: 28576081 DOI: 10.1063/1.4983705] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Despite their potential benefits, antibody microarrays have fallen short of performing reliably and have not found widespread use outside of the research setting. Experimental techniques have been unable to determine what is occurring on the surface of an atomic level, so molecular simulation has emerged as the primary method of investigating protein/surface interactions. Simulations of small proteins have indicated that the stability of the protein is a function of the residue on the protein where a tether is placed. The purpose of this research is to see whether these findings also apply to antibodies, with their greater size and complexity. To determine this, 24 tethering locations were selected on the antibody Protein Data Bank (PDB) ID: 1IGT. Replica exchange simulations were run on two different surfaces, one hydrophobic and one hydrophilic, to determine the degree to which these tethering sites stabilize or destabilize the antibody. Results showed that antibodies tethered to hydrophobic surfaces were in general less stable than antibodies tethered to hydrophilic surfaces. Moreover, the stability of the antibody was a function of the tether location on hydrophobic surfaces but not hydrophilic surfaces.
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Affiliation(s)
- Rebecca W Grawe
- Department of Chemical Engineering, Brigham Young University, Provo, Utah 84606, USA
| | - Thomas A Knotts
- Department of Chemical Engineering, Brigham Young University, Provo, Utah 84606, USA
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Wasserberg D, Cabanas-Danés J, Prangsma J, O’Mahony S, Cazade PA, Tromp E, Blum C, Thompson D, Huskens J, Subramaniam V, Jonkheijm P. Controlling Protein Surface Orientation by Strategic Placement of Oligo-Histidine Tags. ACS NANO 2017; 11:9068-9083. [PMID: 28850777 PMCID: PMC5618149 DOI: 10.1021/acsnano.7b03717] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 08/29/2017] [Indexed: 05/24/2023]
Abstract
We report oriented immobilization of proteins using the standard hexahistidine (His6)-Ni2+:NTA (nitrilotriacetic acid) methodology, which we systematically tuned to give control of surface coverage. Fluorescence microscopy and surface plasmon resonance measurements of self-assembled monolayers (SAMs) of red fluorescent proteins (TagRFP) showed that binding strength increased by 1 order of magnitude for each additional His6-tag on the TagRFP proteins. All TagRFP variants with His6-tags located on only one side of the barrel-shaped protein yielded a 1.5 times higher surface coverage compared to variants with His6-tags on opposite sides of the so-called β-barrel. Time-resolved fluorescence anisotropy measurements supported by polarized infrared spectroscopy verified that the orientation (and thus coverage and functionality) of proteins on surfaces can be controlled by strategic placement of a His6-tag on the protein. Molecular dynamics simulations show how the differently tagged proteins reside at the surface in "end-on" and "side-on" orientations with each His6-tag contributing to binding. Also, not every dihistidine subunit in a given His6-tag forms a full coordination bond with the Ni2+:NTA SAMs, which varied with the position of the His6-tag on the protein. At equal valency but different tag positions on the protein, differences in binding were caused by probing for Ni2+:NTA moieties and by additional electrostatic interactions between different fractions of the β-barrel structure and charged NTA moieties. Potential of mean force calculations indicate there is no specific single-protein interaction mode that provides a clear preferential surface orientation, suggesting that the experimentally measured preference for the end-on orientation is a supra-protein, not a single-protein, effect.
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Affiliation(s)
- Dorothee Wasserberg
- Bioinspired
Molecular Engineering Laboratory, MIRA Biomedical Technology
and Technical Medicine Institute, Molecular nanoFabrication Group, MESA+ Institute
for Nanotechnology, and Nanobiophysics Group, MESA+ Institute for Nanotechnology,
and MIRA Biomedical Technology and Technical Medicine Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Jordi Cabanas-Danés
- Bioinspired
Molecular Engineering Laboratory, MIRA Biomedical Technology
and Technical Medicine Institute, Molecular nanoFabrication Group, MESA+ Institute
for Nanotechnology, and Nanobiophysics Group, MESA+ Institute for Nanotechnology,
and MIRA Biomedical Technology and Technical Medicine Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Jord Prangsma
- Bioinspired
Molecular Engineering Laboratory, MIRA Biomedical Technology
and Technical Medicine Institute, Molecular nanoFabrication Group, MESA+ Institute
for Nanotechnology, and Nanobiophysics Group, MESA+ Institute for Nanotechnology,
and MIRA Biomedical Technology and Technical Medicine Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Shane O’Mahony
- Department
of Physics, Bernal Institute, University
of Limerick, Limerick V94 T9PX, Ireland
| | - Pierre-Andre Cazade
- Department
of Physics, Bernal Institute, University
of Limerick, Limerick V94 T9PX, Ireland
| | - Eldrich Tromp
- Bioinspired
Molecular Engineering Laboratory, MIRA Biomedical Technology
and Technical Medicine Institute, Molecular nanoFabrication Group, MESA+ Institute
for Nanotechnology, and Nanobiophysics Group, MESA+ Institute for Nanotechnology,
and MIRA Biomedical Technology and Technical Medicine Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Christian Blum
- Bioinspired
Molecular Engineering Laboratory, MIRA Biomedical Technology
and Technical Medicine Institute, Molecular nanoFabrication Group, MESA+ Institute
for Nanotechnology, and Nanobiophysics Group, MESA+ Institute for Nanotechnology,
and MIRA Biomedical Technology and Technical Medicine Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Damien Thompson
- Department
of Physics, Bernal Institute, University
of Limerick, Limerick V94 T9PX, Ireland
| | - Jurriaan Huskens
- Bioinspired
Molecular Engineering Laboratory, MIRA Biomedical Technology
and Technical Medicine Institute, Molecular nanoFabrication Group, MESA+ Institute
for Nanotechnology, and Nanobiophysics Group, MESA+ Institute for Nanotechnology,
and MIRA Biomedical Technology and Technical Medicine Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Vinod Subramaniam
- Bioinspired
Molecular Engineering Laboratory, MIRA Biomedical Technology
and Technical Medicine Institute, Molecular nanoFabrication Group, MESA+ Institute
for Nanotechnology, and Nanobiophysics Group, MESA+ Institute for Nanotechnology,
and MIRA Biomedical Technology and Technical Medicine Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
- Free
University of Amsterdam, De Boelelaan 1105, 1081 HV Amsterdam, The Netherlands
| | - Pascal Jonkheijm
- Bioinspired
Molecular Engineering Laboratory, MIRA Biomedical Technology
and Technical Medicine Institute, Molecular nanoFabrication Group, MESA+ Institute
for Nanotechnology, and Nanobiophysics Group, MESA+ Institute for Nanotechnology,
and MIRA Biomedical Technology and Technical Medicine Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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18
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Dirscherl C, Springer S. Protein micropatterns printed on glass: Novel tools for protein-ligand binding assays in live cells. Eng Life Sci 2017; 18:124-131. [PMID: 32624894 DOI: 10.1002/elsc.201700010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 08/10/2017] [Accepted: 08/22/2017] [Indexed: 11/09/2022] Open
Abstract
Micrometer-sized patterns of proteins on glass or silica surfaces are in widespread use as protein arrays for probing with ligands or recombinant proteins. More recently, they have been used to capture the surface proteins of mammalian cells seeded onto them, and to arrange these surface proteins into pattern structures. Binding of small molecule ligands or of other proteins, transmembrane or intracellular, to these captured surface proteins can then be quantified. However, reproducible production of protein micropatterns on surfaces can be technically difficult. In this review, we outline the wide potential and the current practical uses of printed protein micropatterns in a historical overview, and we detail some potential pitfalls and difficulties from our own experience, as well as ways to circumvent them.
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Affiliation(s)
- Cindy Dirscherl
- Department of Life Sciences and Chemistry Jacobs University Bremen Germany
| | - Sebastian Springer
- Department of Life Sciences and Chemistry Jacobs University Bremen Germany
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19
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Sekula-Neuner S, de Freitas M, Tröster LM, Jochum T, Levkin PA, Hirtz M, Fuchs H. Phospholipid arrays on porous polymer coatings generated by micro-contact spotting. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2017; 8:715-722. [PMID: 28487815 PMCID: PMC5389190 DOI: 10.3762/bjnano.8.75] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 03/09/2017] [Indexed: 05/08/2023]
Abstract
Nanoporous poly(2-hydroxyethyl methacrylate-co-ethylene dimethacrylate) (HEMA-EDMA) is used as a 3D mesh for spotting lipid arrays. Its porous structure is an ideal matrix for lipid ink to infiltrate, resulting in higher fluorescent signal intensity as compared to similar arrays on strictly 2D substrates like glass. The embedded lipid arrays show high stability against washing steps, while still being accessible for protein and antibody binding. To characterize binding to polymer-embedded lipids we have applied Streptavidin as well as biologically important biotinylated androgen receptor binding onto 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-(cap biotinyl) (Biotinyl Cap PE) and anti-DNP IgE recognition of 2,4-dinitrophenyl[1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-[6-[(2,4-dinitrophenyl)amino]hexanoyl] (DNP)] antigen. This approach adds lipid arrays to the range of HEMA polymer applications and makes this solid substrate a very attractive platform for a variety of bio-applications.
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Affiliation(s)
- Sylwia Sekula-Neuner
- Institute of Nanotechnology (INT) and Karlsruhe Nano Micro Facility (KNMF) Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Monica de Freitas
- Institute for Photon Science and Synchrotron Radiation (IPS), Laboratory for Applications of Synchrotron Radiation (LAS), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Lea-Marie Tröster
- Institute for Photon Science and Synchrotron Radiation (IPS), Laboratory for Applications of Synchrotron Radiation (LAS), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Tobias Jochum
- Institute for Photon Science and Synchrotron Radiation (IPS), Laboratory for Applications of Synchrotron Radiation (LAS), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Pavel A Levkin
- Institute of Toxicology and Genetics (ITG), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany
| | - Michael Hirtz
- Institute of Nanotechnology (INT) and Karlsruhe Nano Micro Facility (KNMF) Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Harald Fuchs
- Institute of Nanotechnology (INT) and Karlsruhe Nano Micro Facility (KNMF) Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
- Physikalisches Institut and Center for Nanotechnology (CeNTech), Universität Münster, 48149 Münster, Germany
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20
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21
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Schulte-Zweckel J, Rosi F, Sreenu D, Schröder H, Niemeyer CM, Triola G. High Affinity Immobilization of Proteins Using the CrAsH/TC Tag. Molecules 2016; 21:molecules21060750. [PMID: 27338319 PMCID: PMC6273389 DOI: 10.3390/molecules21060750] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 06/02/2016] [Accepted: 06/03/2016] [Indexed: 02/03/2023] Open
Abstract
Protein microarrays represent important tools for biomedical analysis. We have recently described the use of the biarsenical-tetracysteine (TC) tag for the preparation of protein microarrays. The unique feature of this tag enables the site-specific immobilization of TC-containing proteins on biarsenical-modified surfaces, resulting in a fluorescence enhancement that allows the direct quantification of the immobilized proteins. Moreover, the reversibility of the binding upon incubation with large quantities of thiols permits the detachment of the proteins from the surface, thereby enabling recovery of the substrate to extend the life time of the slide. Herein, we describe our recent results that further extend the applicability of the CrAsH/TC tag to the fabrication of biochips. With this aim, the immobilization of proteins on surfaces has been investigated using two different spacers and two TC tags, the minimal TC sequence (CCPGCC) and an optimized motif (FLNCCPGCCMEP). While the minimal peptide motif enables a rapid recycling of the slide, the optimized TC sequence reveals an increased affinity due to its greater resistance to displacement by thiols. Moreover, the developed methodology was applied to the immobilization of proteins via on-chip ligation of recombinant protein thioesters.
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Affiliation(s)
- Janine Schulte-Zweckel
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany.
| | - Federica Rosi
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany.
| | - Domalapally Sreenu
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany.
| | - Hendrik Schröder
- Chimera Biotec GmbH, Emil-Figge-Str., 76 A, D-44227 Dortmund, Germany.
| | - Christof M Niemeyer
- Institute of Biological Interfaces (IBG1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz Platz, D-76344 Eggenstein-Leopoldshafen, Germany.
| | - Gemma Triola
- Department of Biomedicinal Chemistry, Institute of Advanced Chemistry of Catalonia, Jordi Girona 18-26, 08034 Barcelona, Spain.
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22
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Lei Z, Gao J, Liu X, Liu D, Wang Z. Poly(glycidyl methacrylate-co-2-hydroxyethyl methacrylate) Brushes as Peptide/Protein Microarray Substrate for Improving Protein Binding and Functionality. ACS APPLIED MATERIALS & INTERFACES 2016; 8:10174-10182. [PMID: 27049528 DOI: 10.1021/acsami.6b01156] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We developed a three-dimensional (3D) polymer-brush substrate for protein and peptide microarray fabrication, and this substrate was facilely prepared by copolymerization of glycidyl methacrylate (GMA) and 2-hydroxyethyl methacrylate (HEMA) monomers via surface-initiated atom transfer radical polymerization (SI-ATRP) on a glass slide. The performance of obtained poly(glycidyl methacrylate-co-2-hydroxyethyl methacrylate) (P(GMA-HEMA)) brush substrate was assessed by binding of human IgG with rabbit antihuman IgG antibodies on a protein microarray and by the determination of matrix metalloproteinase (MMP) activities on a peptide microarray. The P(GMA-HEMA) brush substrate exhibited higher immobilization capacities for proteins and peptides than those of a two-dimensional (2D) planar epoxy slide. Furthermore, the sensitivity of the P(GMA-HEMA) brush-based microarray on rabbit antihuman IgG antibody detection was much higher than that of its 2D counterpart. The enzyme activities of MMPs were determined specifically with a low detection limit of 6.0 pg mL(-1) for MMP-2 and 5.7 pg mL(-1) for MMP-9. By taking advantage of the biocompatibility of PHEMA, the P(GMA-HEMA) brush-based peptide microarray was also employed to evaluate the secretion of MMP-2 and MMP-9 by cells cultured off the chip or directly on the chip, and satisfactory results were obtained.
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Affiliation(s)
- Zhen Lei
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun 130022, P. R. China
- University of Chinese Academy of Sciences , Beijing 100049, P. R. China
| | - Jiaxue Gao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun 130022, P. R. China
- University of Chinese Academy of Sciences , Beijing 100049, P. R. China
| | - Xia Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun 130022, P. R. China
| | - Dianjun Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun 130022, P. R. China
| | - Zhenxin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun 130022, P. R. China
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23
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Wu J, Hou Y, Wang P, Wang Z, Li Y, Wang S, Yang M. Detection of lysozyme with aptasensor based on fluorescence resonance energy transfer from carbon dots to graphene oxide. LUMINESCENCE 2016. [DOI: 10.1002/bio.3092] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Jing Wu
- School of Chemistry and Chemical Engineering; Liaoning Normal University; Dalian 116029 China
| | - Yu Hou
- School of Chemistry and Chemical Engineering; Liaoning Normal University; Dalian 116029 China
| | - Peiyao Wang
- School of Chemistry and Chemical Engineering; Liaoning Normal University; Dalian 116029 China
| | - Zhenni Wang
- School of Chemistry and Chemical Engineering; Liaoning Normal University; Dalian 116029 China
| | - Yanjie Li
- School of Chemistry and Chemical Engineering; Liaoning Normal University; Dalian 116029 China
| | - Shan Wang
- School of Chemistry and Chemical Engineering; Liaoning Normal University; Dalian 116029 China
| | - Mei Yang
- School of Chemistry and Chemical Engineering; Liaoning Normal University; Dalian 116029 China
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24
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Wang Y, Li H, Xu D. Aptamers-based sandwich assay for silver-enhanced fluorescence multiplex detection. Anal Chim Acta 2015; 905:149-55. [PMID: 26755149 DOI: 10.1016/j.aca.2015.12.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 12/04/2015] [Accepted: 12/12/2015] [Indexed: 12/26/2022]
Abstract
In this work, aptamers-modified silver nanoparticles (AgNPs) were prepared as capture substrate, and fluorescent dyes-modified aptamers were synthesized as detection probes. The sandwich assay was based on dual aptamers, which was aimed to accomplish the highly sensitive detection of single protein and multiplex detection of proteins on one-spot. We found that aptamers-modified AgNPs based microarray was much superior to the aptamer based microarray in fluorescence detection of proteins. The result shows that the detection limit of the sandwich assay using AgNPs probes for thrombin or platelet-derived growth factor-BB (PDGF-BB) is 80 or 8 times lower than that of aptamers used directly. For multiplex detection of proteins, the detection limit was 625 pM for PDGF-BB and 21 pM for thrombin respectively. The sandwich assay based on dual aptamers and AgNPs was sensitive and specific.
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Affiliation(s)
- Ying Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China; School of Environmental Science, Nanjing Xiaozhuang University, China.
| | - Hui Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China.
| | - Danke Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China.
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25
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Angelin A, Weigel S, Garrecht R, Meyer R, Bauer J, Kumar RK, Hirtz M, Niemeyer CM. Multiscale Origami Structures as Interface for Cells. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201509772] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Alessandro Angelin
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann‐von‐Helmholtz‐Platz, 76344 Eggenstein‐Leopoldshafen (Germany)
| | - Simone Weigel
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann‐von‐Helmholtz‐Platz, 76344 Eggenstein‐Leopoldshafen (Germany)
| | - Ruben Garrecht
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann‐von‐Helmholtz‐Platz, 76344 Eggenstein‐Leopoldshafen (Germany)
| | - Rebecca Meyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann‐von‐Helmholtz‐Platz, 76344 Eggenstein‐Leopoldshafen (Germany)
| | - Jens Bauer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann‐von‐Helmholtz‐Platz, 76344 Eggenstein‐Leopoldshafen (Germany)
| | - Ravi Kapoor Kumar
- Karlsruhe Institute of Technology (KIT), Institute for Nanotechnology (INT) & Karlsruhe Nano Micro Facility (KNMF), Hermann‐von‐Helmholtz‐Platz, 76344 Eggenstein‐Leopoldshafen (Germany)
| | - Michael Hirtz
- Karlsruhe Institute of Technology (KIT), Institute for Nanotechnology (INT) & Karlsruhe Nano Micro Facility (KNMF), Hermann‐von‐Helmholtz‐Platz, 76344 Eggenstein‐Leopoldshafen (Germany)
| | - Christof M. Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann‐von‐Helmholtz‐Platz, 76344 Eggenstein‐Leopoldshafen (Germany)
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26
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Angelin A, Weigel S, Garrecht R, Meyer R, Bauer J, Kumar RK, Hirtz M, Niemeyer CM. Multiscale Origami Structures as Interface for Cells. Angew Chem Int Ed Engl 2015; 54:15813-7. [DOI: 10.1002/anie.201509772] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 11/12/2015] [Indexed: 01/07/2023]
Affiliation(s)
- Alessandro Angelin
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann‐von‐Helmholtz‐Platz, 76344 Eggenstein‐Leopoldshafen (Germany)
| | - Simone Weigel
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann‐von‐Helmholtz‐Platz, 76344 Eggenstein‐Leopoldshafen (Germany)
| | - Ruben Garrecht
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann‐von‐Helmholtz‐Platz, 76344 Eggenstein‐Leopoldshafen (Germany)
| | - Rebecca Meyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann‐von‐Helmholtz‐Platz, 76344 Eggenstein‐Leopoldshafen (Germany)
| | - Jens Bauer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann‐von‐Helmholtz‐Platz, 76344 Eggenstein‐Leopoldshafen (Germany)
| | - Ravi Kapoor Kumar
- Karlsruhe Institute of Technology (KIT), Institute for Nanotechnology (INT) & Karlsruhe Nano Micro Facility (KNMF), Hermann‐von‐Helmholtz‐Platz, 76344 Eggenstein‐Leopoldshafen (Germany)
| | - Michael Hirtz
- Karlsruhe Institute of Technology (KIT), Institute for Nanotechnology (INT) & Karlsruhe Nano Micro Facility (KNMF), Hermann‐von‐Helmholtz‐Platz, 76344 Eggenstein‐Leopoldshafen (Germany)
| | - Christof M. Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann‐von‐Helmholtz‐Platz, 76344 Eggenstein‐Leopoldshafen (Germany)
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27
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Bosmans RPG, Hendriksen WE, Verheijden M, Eelkema R, Jonkheijm P, van Esch JH, Brunsveld L. Supramolecular Protein Immobilization on Lipid Bilayers. Chemistry 2015; 21:18466-73. [DOI: 10.1002/chem.201502461] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Indexed: 01/08/2023]
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28
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Shetty D, Khedkar JK, Park KM, Kim K. Can we beat the biotin-avidin pair?: cucurbit[7]uril-based ultrahigh affinity host-guest complexes and their applications. Chem Soc Rev 2015; 44:8747-61. [PMID: 26434388 DOI: 10.1039/c5cs00631g] [Citation(s) in RCA: 307] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The design of synthetic, monovalent host-guest molecular recognition pairs is still challenging and of particular interest to inquire into the limits of the affinity that can be achieved with designed systems. In this regard, cucurbit[7]uril (CB[7]), an important member of the host family cucurbit[n]uril (CB[n], n = 5-8, 10, 14), has attracted much attention because of its ability to form ultra-stable complexes with multiple guests. The strong hydrophobic effect between the host cavity and guests, ion-dipole and dipole-dipole interactions of guests with CB portals helps in cooperative and multiple noncovalent interactions that are essential for realizing such strong complexations. These highly selective, strong yet dynamic interactions can be exploited in many applications including affinity chromatography, biomolecule immobilization, protein isolation, biological catalysis, and sensor technologies. In this review, we summarize the progress in the development of high affinity guests for CB[7], factors affecting the stability of complexes, theoretical insights, and the utility of these high affinity pairs in different challenging applications.
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Affiliation(s)
- Dinesh Shetty
- Center for Self-assembly and Complexity (CSC), Institute for Basic Science (IBS), Pohang 37673, Republic of Korea.
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29
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Samarth RM, Samarth M, Matsumoto Y. Utilization of cytogenetic biomarkers as a tool for assessment of radiation injury and evaluation of radiomodulatory effects of various medicinal plants - a review. Drug Des Devel Ther 2015; 9:5355-72. [PMID: 26451089 PMCID: PMC4590411 DOI: 10.2147/dddt.s91299] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Systematic biological measurement of “cytogenetic endpoints” has helped phenomenally in assessment of risks associated with radiation exposure. There has been a surge in recent times for the usage of radioactive materials in health care, agriculture, industrial, and nuclear power sectors. The likelihood of radiation exposure from accidental or occupational means is always higher in an overburdened ecosystem that is continuously challenged to meet the population demands. Risks associated with radiation exposure in this era of modern industrial growth are minimal as international regulations for maintaining the safety standards are stringent and strictly adhered to, however, a recent disaster like “Fukushima” impels us to think beyond. The major objective of radiobiology is the development of an orally effective radio-modifier that provides protection from radiation exposure. Once available for mass usage, these compounds will not only be useful for providing selective protection against accidental and occupational radiation exposure but also help to permit use of higher doses of radiation during treatment of various malignancies curtailing unwarranted adverse effects imposed on normal tissues. Bio-active compounds isolated from natural sources enriched with antioxidants possess unique immune-modulating properties, thus providing a double edged benefit over synthetic radioprotectors. We aim to provide here a comprehensive overview of the various agents originating from plant sources that portrayed promising radioprotection in various experimental models with special emphasis on studies that used cytogenetic biomarkers. The agents will include crude extracts of various medicinal plants, purified fractions, and herbal preparations.
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Affiliation(s)
- Ravindra M Samarth
- Department of Research, Bhopal Memorial Hospital and Research Centre (ICMR), Bhopal, India ; National Institute for Research in Environmental Health (NIREH), Indian Council of Medical Research, Bhopal, India
| | - Meenakshi Samarth
- Department of Zoology, Centre for Advanced Studies, University of Rajasthan, Jaipur, India
| | - Yoshihisa Matsumoto
- Research Laboratory for Nuclear Reactors, Tokyo Institute of Technology, Tokyo, Japan
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Sato S, Ikemi M, Kikuchi T, Matsumura S, Shiba K, Fujita M. Bridging Adhesion of a Protein onto an Inorganic Surface Using Self-Assembled Dual-Functionalized Spheres. J Am Chem Soc 2015; 137:12890-6. [PMID: 26190770 DOI: 10.1021/jacs.5b06184] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
For the bridging adhesion of different classes of materials in their intact functional states, the adhesion of biomolecules onto inorganic surfaces is a necessity. A new molecular design strategy for bridging adhesion was demonstrated by the introduction of two independent recognition groups on the periphery of spherical complexes self-assembled from metal ions (M) and bidentate ligands (L). These dual-functionalized M12L24 spheres were quantitatively synthesized in one step from two ligands, bearing either a biotin for streptavidin recognition or a titania-binding aptamer, and Pd(II) ions. The selective recognition of titania surfaces was achieved by ligands with hexapeptide aptamers (Arg-Lys-Leu-Pro-Asp-Ala: minTBP-1), whose fixation ability was enhanced by the accumulation effect on the surface of the M12L24 spheres. These well-defined spherical structures can be specifically tailored to promote interactions with both titania and streptavidin simultaneously without detrimentally affecting either recognition motif. The irreversible immobilization of the spheres onto titania was revealed quantitatively by quartz crystal microbalance measurements, and the adhesion of streptavidin to the titania surface mediated by the biotin surrounding the spheres was visually demonstrated by lithographic patterning experiments.
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Affiliation(s)
- Sota Sato
- Department of Applied Chemistry, School of Engineering, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Masatoshi Ikemi
- Department of Applied Chemistry, School of Engineering, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takashi Kikuchi
- Department of Applied Chemistry, School of Engineering, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Sachiko Matsumura
- Division of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research , 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Kiyotaka Shiba
- Division of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research , 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Makoto Fujita
- Department of Applied Chemistry, School of Engineering, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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31
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Cheng G, Hao SJ, Yu X, Zheng SY. Nanostructured microfluidic digestion system for rapid high-performance proteolysis. LAB ON A CHIP 2015; 15:650-4. [PMID: 25511010 PMCID: PMC4304898 DOI: 10.1039/c4lc01165a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A novel microfluidic protein digestion system with a nanostructured and bioactive inner surface was constructed by an easy biomimetic self-assembly strategy for rapid and effective proteolysis in 2 minutes, which is faster than the conventional overnight digestion methods. It is expected that this work would contribute to rapid online digestion in future high-throughput proteomics.
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Affiliation(s)
- Gong Cheng
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA.
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Li HM, Guo K, Yu Z, Feng R, Xu P. Diagnostic value of protein chips constructed by lung-cancer-associated markers selected by the T7 phage display library. Thorac Cancer 2015; 6:469-74. [PMID: 26273403 PMCID: PMC4511326 DOI: 10.1111/1759-7714.12215] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 11/05/2014] [Indexed: 12/17/2022] Open
Abstract
Background Traditional diagnostic technology with tumor biomarkers is inefficient, expensive and requires a large number of serum samples. The purpose of this study was to construct human lung cancer protein chips with new lung cancer biomarkers screened by the T7-phage display library, and improve the early diagnosis rate of lung cancer. Methods A T7-phage cDNA display library was constructed of fresh samples from 30 lung cancer patients. With biopanning and high-throughput screening, we gained the immunogenic phage clones from the cDNA library. The insert of selected phage was blasted at GeneBank for alignment to find the exact or the most similar known genes. Protein chips were then constructed and used to assay their expression level in lung cancer serum from 217 cases of lung cancer groups:80 cases of benign lung disease and 220 healthy controls. Results After four rounds of Biopanning and two rounds of enzyme-linked immunosorbent assay, 12 phage monoclonal samples were selected from 2880 phage monoclonal samples. After blasting at GeneBank, six similar genes were used to construct diagnostic protein chips. The protein chips were then used to assay expression level in lung cancer serum. The expression level of six genes in lung cancer groups was significantly higher than those in the other two groups (P < 0.05). Conclusions In this study, we successfully constructed diagnostic protein chips with biomarkers selected from the lung cancer T7-phage cDNA library, which can be used for the early screening of lung cancer patients.
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Affiliation(s)
- Hong-Mei Li
- Cancer Center, The Affiliated Hospital of Qingdao University Qingdao, China
| | - Kang Guo
- Cancer Center, The Affiliated Hospital of Qingdao University Qingdao, China
| | - Zhuang Yu
- Cancer Center, The Affiliated Hospital of Qingdao University Qingdao, China
| | - Rui Feng
- Cancer Center, The Affiliated Hospital of Qingdao University Qingdao, China
| | - Ping Xu
- Cancer Center, The Affiliated Hospital of Qingdao University Qingdao, China
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Functionalized Amphipols: A Versatile Toolbox Suitable for Applications of Membrane Proteins in Synthetic Biology. J Membr Biol 2014; 247:815-26. [DOI: 10.1007/s00232-014-9663-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 03/27/2014] [Indexed: 10/25/2022]
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35
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Phenylboronic acid polymer brush-enabled oriented and high density antibody immobilization for sensitive microarray immunoassay. Colloids Surf B Biointerfaces 2014; 121:21-6. [DOI: 10.1016/j.colsurfb.2014.05.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 05/18/2014] [Accepted: 05/20/2014] [Indexed: 12/30/2022]
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36
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Winssinger N, Gorska K, Ciobanu M, Daguer JP, Barluenga S. Assembly of PNA-tagged small molecules, peptides, and carbohydrates onto DNA templates: programming the combinatorial pairing and inter-ligand distance. Methods Mol Biol 2014; 1050:95-110. [PMID: 24297353 DOI: 10.1007/978-1-62703-553-8_8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The biochemical stability and desirable hybridization properties of peptide nucleic acids (PNA) coupled to the robustness of the peptidic chemistry involved in their oligomerization make them an attractive nucleic acid tag to encode molecules and program their assembly into higher order oligomers. The ability to program the dimerization of ligands with controlled distance between the ligands has important applications in emulating multimeric interactions. Additionally, the ability to program different permutations of ligand assemblies in a combinatorial fashion provides access to a broad diversity and offers a rapid screening method for fragment based approaches to drug discovery. Herein, we describe protocols to covalently link diverse carbohydrates, peptides, or small molecules to PNA and combinatorially assemble them in solution onto libraries of DNA templates or onto DNA microarrays using a commercial platform without recourse to specialized equipment or heavy upfront investment.
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Affiliation(s)
- Nicolas Winssinger
- Laboratoire de Chemie Organique et Bioorganique, Institut de Science et d'Ingénierie Supramoléculaires, Université Louis Pasteur, Strasbourg, France
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37
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Forsberg EM, Sicard C, Brennan JD. Solid-phase biological assays for drug discovery. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2014; 7:337-359. [PMID: 25000820 DOI: 10.1146/annurev-anchem-071213-020241] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In the past 30 years, there has been a significant growth in the use of solid-phase assays in the area of drug discovery, with a range of new assays being used for both soluble and membrane-bound targets. In this review, we provide some basic background to typical drug targets and immobilization protocols used in solid-phase biological assays (SPBAs) for drug discovery, with emphasis on particularly labile biomolecular targets such as kinases and membrane-bound receptors, and highlight some of the more recent approaches for producing protein microarrays, bioaffinity columns, and other devices that are central to small molecule screening by SPBA. We then discuss key applications of such assays to identify drug leads, with an emphasis on the screening of mixtures. We conclude by highlighting specific advantages and potential disadvantages of SPBAs, particularly as they relate to particular assay formats.
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Affiliation(s)
- Erica M Forsberg
- Biointerfaces Institute, McMaster University, Hamilton, Ontario L8S 4L8, Canada;
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38
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Wang HC, Yu CC, Liang CF, Huang LD, Hwu JR, Lin CC. Site-Selective Protein Immobilization through 2-Cyanobenzothiazole-Cysteine Condensation. Chembiochem 2014; 15:829-35. [DOI: 10.1002/cbic.201300800] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Indexed: 11/10/2022]
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39
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Meyer R, Giselbrecht S, Rapp BE, Hirtz M, Niemeyer CM. Advances in DNA-directed immobilization. Curr Opin Chem Biol 2014; 18:8-15. [DOI: 10.1016/j.cbpa.2013.10.023] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 10/01/2013] [Indexed: 12/18/2022]
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40
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Cabanas-Danés J, Huskens J, Jonkheijm P. Chemical strategies for the presentation and delivery of growth factors. J Mater Chem B 2014; 2:2381-2394. [DOI: 10.1039/c3tb20853b] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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41
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Li H, Wang M, Qiang W, Hu H, Li W, Xu D. Metal-enhanced fluorescent detection for protein microarrays based on a silver plasmonic substrate. Analyst 2014; 139:1653-60. [DOI: 10.1039/c3an01875j] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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42
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Arrabito G, Reisewitz S, Dehmelt L, Bastiaens PI, Pignataro B, Schroeder H, Niemeyer CM. Biochips for cell biology by combined dip-pen nanolithography and DNA-directed protein immobilization. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:4243-4249. [PMID: 23881817 DOI: 10.1002/smll.201300941] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Indexed: 06/02/2023]
Abstract
A general methodology for patterning of multiple protein ligands with lateral dimensions below those of single cells is described. It employs dip pen nanolithography (DPN) patterning of DNA oligonucleotides which are then used as capture strands for DNA-directed immobilization (DDI) of oligonucleotide-tagged proteins. This study reports the development and optimization of PEG-based liquid ink, used as carrier for the immobilization of alkylamino-labeled DNA oligomers on chemically activated glass surfaces. The resulting DNA arrays have typical spot sizes of 4-5 μm with a pitch of 12 μm micrometer. It is demonstrated that the arrays can be further functionalized with covalent DNA-streptavidin (DNA-STV) conjugates bearing ligands recognized by cells. To this end, biotinylated epidermal growth factor (EGF) is coupled to the DNA-STV conjugates, the resulting constructs are hybridized with the DNA arrays and the resulting surfaces used for the culturing of MCF-7 (human breast adenocarcinoma) cells. Owing to the lateral diffusion of transmembrane proteins in the cell's plasma membrane, specific recruitment and concentration of EGF receptor can be induced specifically at the sites where the ligands are bound on the solid substrate. This is a clear demonstration that this method is suitable for precise functional manipulations of subcellular areas within living cells.
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Affiliation(s)
- Giuseppe Arrabito
- Technische Universität Dortmund, Fakultät Chemie, Biologisch-Chemische Mikrostrukturtechnik, Otto Hahn Str. 6, 44227 Dortmund, Germany; Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz, D-76344 Eggenstein-Leopoldshafen, Germany; Scuola Superiore di Catania, Via Valdisavoia 9, 95123 Catania, Italy
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43
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Rostgaard KR, Frederiksen RS, Liu YCC, Berthing T, Madsen MH, Holm J, Nygård J, Martinez KL. Vertical nanowire arrays as a versatile platform for protein detection and analysis. NANOSCALE 2013; 5:10226-35. [PMID: 24062006 DOI: 10.1039/c3nr03113f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Protein microarrays are valuable tools for protein assays. Reducing spot sizes from micro- to nano-scale facilitates miniaturization of platforms and consequently decreased material consumption, but faces inherent challenges in the reduction of fluorescent signals and compatibility with complex solutions. Here we show that vertical arrays of nanowires (NWs) can overcome several bottlenecks of using nanoarrays for extraction and analysis of proteins. The high aspect ratio of the NWs results in a large surface area available for protein immobilization and renders passivation of the surface between the NWs unnecessary. Fluorescence detection of proteins allows quantitative measurements and spatial resolution, enabling us to track individual NWs through several analytical steps, thereby allowing multiplexed detection of different proteins immobilized on different regions of the NW array. We use NW arrays for on-chip extraction, detection and functional analysis of proteins on a nano-scale platform that holds great promise for performing protein analysis on minute amounts of material. The demonstration made here on highly ordered arrays of indium arsenide (InAs) NWs is generic and can be extended to many high aspect ratio nanostructures.
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Affiliation(s)
- Katrine R Rostgaard
- Bio-Nanotechnology and Nanomedicine Laboratory, Department of Chemistry & Nano-Science Center, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark.
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44
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Fors BP, Poelma JE, Menyo MS, Robb MJ, Spokoyny DM, Kramer JW, Waite JH, Hawker CJ. Fabrication of Unique Chemical Patterns and Concentration Gradients with Visible Light. J Am Chem Soc 2013; 135:14106-9. [DOI: 10.1021/ja408467b] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Brett P. Fors
- Materials Research Laboratory, California NanoSystems Institute, Materials Department, Department of Chemistry
and Biochemistry, and Biomolecular Science
and Engineering, University of California, Santa Barbara, California 93106, United States
- The Dow Chemical Company, Midland, Michigan 48667, United States
| | - Justin E. Poelma
- Materials Research Laboratory, California NanoSystems Institute, Materials Department, Department of Chemistry
and Biochemistry, and Biomolecular Science
and Engineering, University of California, Santa Barbara, California 93106, United States
- The Dow Chemical Company, Midland, Michigan 48667, United States
| | - Matthew S. Menyo
- Materials Research Laboratory, California NanoSystems Institute, Materials Department, Department of Chemistry
and Biochemistry, and Biomolecular Science
and Engineering, University of California, Santa Barbara, California 93106, United States
- The Dow Chemical Company, Midland, Michigan 48667, United States
| | - Maxwell J. Robb
- Materials Research Laboratory, California NanoSystems Institute, Materials Department, Department of Chemistry
and Biochemistry, and Biomolecular Science
and Engineering, University of California, Santa Barbara, California 93106, United States
- The Dow Chemical Company, Midland, Michigan 48667, United States
| | - Daniel M. Spokoyny
- Materials Research Laboratory, California NanoSystems Institute, Materials Department, Department of Chemistry
and Biochemistry, and Biomolecular Science
and Engineering, University of California, Santa Barbara, California 93106, United States
- The Dow Chemical Company, Midland, Michigan 48667, United States
| | - John W. Kramer
- Materials Research Laboratory, California NanoSystems Institute, Materials Department, Department of Chemistry
and Biochemistry, and Biomolecular Science
and Engineering, University of California, Santa Barbara, California 93106, United States
- The Dow Chemical Company, Midland, Michigan 48667, United States
| | - J. Herbert Waite
- Materials Research Laboratory, California NanoSystems Institute, Materials Department, Department of Chemistry
and Biochemistry, and Biomolecular Science
and Engineering, University of California, Santa Barbara, California 93106, United States
- The Dow Chemical Company, Midland, Michigan 48667, United States
| | - Craig J. Hawker
- Materials Research Laboratory, California NanoSystems Institute, Materials Department, Department of Chemistry
and Biochemistry, and Biomolecular Science
and Engineering, University of California, Santa Barbara, California 93106, United States
- The Dow Chemical Company, Midland, Michigan 48667, United States
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45
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Lü F, Feng X, Liu L, Wang S. Protein-assisted conjugated polymer microarray: Fabrication and sensing applications. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s11434-013-6025-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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46
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Paulo TDF, de Sousa TP, de Abreu DS, Felício NH, Bernhardt PV, Lopes LGDF, Sousa EHS, Diógenes ICN. Electrochemistry, surface plasmon resonance, and quartz crystal microbalance: an associative study on cytochrome c adsorption on pyridine tail-group monolayers on gold. J Phys Chem B 2013; 117:8673-80. [PMID: 23819458 DOI: 10.1021/jp400694k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quartz crystal microbalance (QCM), surface plasmon resonance (SPR), and electrochemistry techniques were used to study the electron-transfer (ET) reaction of cytochrome c (Cyt c) on gold surfaces modified with thionicotinamide, thioisonicotinamide, 4-mercaptopyridine, 5-(4-pyridyl)-1,3,4-oxadiazole-2-thiol, 5-phenyl-1,3,4-oxadiazole-2-thiol, 4,4'-bipyridine, and 4,4'-dithiopyridine. The electrochemical results showed that the ET process is complex, being chiefly diffusional with steps depending on the orientation of the pyridine or phenyl tail group of the modifiers. The correlation between the electrochemical results and those acquired by SPR and QCM indicated the presence of an adlayer of Cyt c adsorbed on the thiolate SAMs. This adlayer, although being not electroactive, is essential to assess the ET reaction of Cyt c in solution. The results presented in this work are consistent with the statement (Feng, Z. Q.; Imabayashi, S.; Kakiuchi, T.; Niki, K. J. Electroanal. Chem. 1995, 394, 149-154) that the ET reaction of Cyt c can be explained in terms of the through-bond tunneling mechanism.
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Affiliation(s)
- Tércio de F Paulo
- Departamento de Química Orgânica e Inorgânica, Universidade Federal do Ceará, Cx. Postal 6021, Fortaleza, Ceará, Brasil 60455-970
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47
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Kaigala GV, Lovchik RD, Delamarche E. Microfluidics in the "open space" for performing localized chemistry on biological interfaces. Angew Chem Int Ed Engl 2013; 51:11224-40. [PMID: 23111955 DOI: 10.1002/anie.201201798] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Local interactions between (bio)chemicals and biological interfaces play an important role in fields ranging from surface patterning to cell toxicology. These interactions can be studied using microfluidic systems that operate in the "open space", that is, without the need for the sealed channels and chambers commonly used in microfluidics. This emerging class of techniques localizes chemical reactions on biological interfaces or specimens without imposing significant "constraints" on samples, such as encapsulation, pre-processing steps, or the need for scaffolds. They therefore provide new opportunities for handling, analyzing, and interacting with biological samples. The motivation for performing localized chemistry is discussed, as are the requirements imposed on localization techniques. Three classes of microfluidic systems operating in the open space, based on microelectrochemistry, multiphase transport, and hydrodynamic flow confinement of liquids are presented.
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48
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Wasserberg D, Nicosia C, Tromp EE, Subramaniam V, Huskens J, Jonkheijm P. Oriented Protein Immobilization using Covalent and Noncovalent Chemistry on a Thiol-Reactive Self-Reporting Surface. J Am Chem Soc 2013; 135:3104-11. [DOI: 10.1021/ja3102133] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dorothee Wasserberg
- Molecular Nanofabrication Group,
MESA+ Institute for Nanotechnology, Department of Science
and Technology, University of Twente, 7500
AE, Enschede, Netherlands
- Nanobiophysics Group, MESA+ Institute for Nanotechnology
and MIRA Institute for Biomedical
Technology and Technical Medicine, Department of Science and Technology, University of Twente, 7500 AE, Enschede, Netherlands
| | - Carlo Nicosia
- Molecular Nanofabrication Group,
MESA+ Institute for Nanotechnology, Department of Science
and Technology, University of Twente, 7500
AE, Enschede, Netherlands
| | - Eldrich E. Tromp
- Molecular Nanofabrication Group,
MESA+ Institute for Nanotechnology, Department of Science
and Technology, University of Twente, 7500
AE, Enschede, Netherlands
- Nanobiophysics Group, MESA+ Institute for Nanotechnology
and MIRA Institute for Biomedical
Technology and Technical Medicine, Department of Science and Technology, University of Twente, 7500 AE, Enschede, Netherlands
| | - Vinod Subramaniam
- Nanobiophysics Group, MESA+ Institute for Nanotechnology
and MIRA Institute for Biomedical
Technology and Technical Medicine, Department of Science and Technology, University of Twente, 7500 AE, Enschede, Netherlands
| | - Jurriaan Huskens
- Molecular Nanofabrication Group,
MESA+ Institute for Nanotechnology, Department of Science
and Technology, University of Twente, 7500
AE, Enschede, Netherlands
| | - Pascal Jonkheijm
- Molecular Nanofabrication Group,
MESA+ Institute for Nanotechnology, Department of Science
and Technology, University of Twente, 7500
AE, Enschede, Netherlands
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49
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Wasserberg D, Uhlenheuer DA, Neirynck P, Cabanas-Danés J, Schenkel JH, Ravoo BJ, An Q, Huskens J, Milroy LG, Brunsveld L, Jonkheijm P. Immobilization of Ferrocene-Modified SNAP-Fusion Proteins. Int J Mol Sci 2013; 14:4066-80. [PMID: 23429193 PMCID: PMC3588085 DOI: 10.3390/ijms14024066] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 02/04/2013] [Accepted: 02/04/2013] [Indexed: 12/16/2022] Open
Abstract
The supramolecular assembly of proteins on surfaces has been investigated via the site-selective incorporation of a supramolecular moiety on proteins. To this end, fluorescent proteins have been site-selectively labeled with ferrocenes, as supramolecular guest moieties, via SNAP-tag technology. The assembly of guest-functionalized SNAP-fusion proteins on cyclodextrin- and cucurbit[7]uril-coated surfaces yielded stable monolayers. The binding of all ferrocene fusion proteins is specific as determined by surface plasmon resonance. Micropatterns of the fusion proteins, on patterned cyclodextrin and cucurbituril surfaces, have been visualized using fluorescence microscopy. The SNAP-fusion proteins were also immobilized on cyclodextrin vesicles. The supramolecular SNAP-tag labeling of proteins, thus, allows for the assembly of modified proteins via supramolecular host-guest interaction on different surfaces in a controlled manner. These findings extend the toolbox of fabricating supramolecular protein patterns on surfaces taking advantage of the high labeling efficiency of the SNAP-tag with versatile supramolecular moieties.
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Affiliation(s)
- Dorothee Wasserberg
- Molecular NanoFabrication Group, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE, Enschede, The Netherlands; E-Mails: (D.W.); (J.C.-D.); (Q.A.); (J.H.)
| | - Dana A. Uhlenheuer
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands; E-Mails: (D.A.U.); (P.N.); (L.-G.M.)
| | - Pauline Neirynck
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands; E-Mails: (D.A.U.); (P.N.); (L.-G.M.)
| | - Jordi Cabanas-Danés
- Molecular NanoFabrication Group, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE, Enschede, The Netherlands; E-Mails: (D.W.); (J.C.-D.); (Q.A.); (J.H.)
| | - Jan Hendrik Schenkel
- Institute of Organic Chemistry, Westfaelische Wilhelms-Universität Muenster, Corrensstrasse 40, 48149 Münster, Germany; E-Mails: (J.H.S.); (B.J.R.)
| | - Bart Jan Ravoo
- Institute of Organic Chemistry, Westfaelische Wilhelms-Universität Muenster, Corrensstrasse 40, 48149 Münster, Germany; E-Mails: (J.H.S.); (B.J.R.)
| | - Qi An
- Molecular NanoFabrication Group, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE, Enschede, The Netherlands; E-Mails: (D.W.); (J.C.-D.); (Q.A.); (J.H.)
| | - Jurriaan Huskens
- Molecular NanoFabrication Group, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE, Enschede, The Netherlands; E-Mails: (D.W.); (J.C.-D.); (Q.A.); (J.H.)
| | - Lech-Gustav Milroy
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands; E-Mails: (D.A.U.); (P.N.); (L.-G.M.)
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands; E-Mails: (D.A.U.); (P.N.); (L.-G.M.)
- Authors to whom correspondence should be addressed; E-Mails: (L.B.); (P.J.); Tel.: +31-53-489-2987 (P.J.); Fax: +31-53-489-4546 (P.J.)
| | - Pascal Jonkheijm
- Molecular NanoFabrication Group, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE, Enschede, The Netherlands; E-Mails: (D.W.); (J.C.-D.); (Q.A.); (J.H.)
- Authors to whom correspondence should be addressed; E-Mails: (L.B.); (P.J.); Tel.: +31-53-489-2987 (P.J.); Fax: +31-53-489-4546 (P.J.)
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SHA S, YIN Y, GAO XL, HUANG ZR, YU T, ZHENG XD. A New Method of Immobilizing Antibody Probes on Immunochips Based on DNA Hybridization. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2013. [DOI: 10.1016/s1872-2040(13)60627-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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