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Wang S, Tsao CY, Motabar D, Li J, Payne GF, Bentley WE. A Redox-Based Autoinduction Strategy to Facilitate Expression of 5xCys-Tagged Proteins for Electrobiofabrication. Front Microbiol 2021; 12:675729. [PMID: 34220759 PMCID: PMC8250426 DOI: 10.3389/fmicb.2021.675729] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/13/2021] [Indexed: 01/17/2023] Open
Abstract
Biofabrication utilizes biological materials and biological means, or mimics thereof, for assembly. When interfaced with microelectronics, electrobiofabricated assemblies enable exquisite sensing and reporting capabilities. We recently demonstrated that thiolated polyethylene glycol (PEG-SH) could be oxidatively assembled into a thin disulfide crosslinked hydrogel at an electrode surface; with sufficient oxidation, extra sulfenic acid groups are made available for covalent, disulfide coupling to sulfhydryl groups of proteins or peptides. We intentionally introduced a polycysteine tag (5xCys-tag) consisting of five consecutive cysteine residues at the C-terminus of a Streptococcal protein G to enable its covalent coupling to an electroassembled PEG-SH film. We found, however, that its expression and purification from E. coli was difficult, owing to the extra cysteine residues. We developed a redox-based autoinduction methodology that greatly enhanced the yield, especially in the soluble fraction of E. coli extracts. The redox component involved the deletion of oxyRS, a global regulator of the oxidative stress response and the autoinduction component integrated a quorum sensing (QS) switch that keys the secreted QS autoinducer-2 to induction. Interestingly, both methods helped when independently employed and further, when used in combination (i.e., autodinduced oxyRS mutant) the results were best—we found the highest total yield and highest yield in the soluble fraction. We hypothesize that the production host was less prone to severe metabolic perturbations that might reduce yield or drive sequestration of the -tagged protein into inclusion bodies. We expect this methodology will be useful for the expression of many such Cys-tagged proteins, ultimately enabling a diverse array of functionalized devices.
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Affiliation(s)
- Sally Wang
- Fischell Department of Bioengineering, University of Maryland, College Park, College Park, MD, United States.,Fischell Institute for Biomedical Devices, University of Maryland, College Park, College Park, MD, United States.,Institute of Bioscience and Biotechnology Research, University of Maryland, College Park, College Park, MD, United States
| | - Chen-Yu Tsao
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, College Park, MD, United States.,Institute of Bioscience and Biotechnology Research, University of Maryland, College Park, College Park, MD, United States
| | - Dana Motabar
- Fischell Department of Bioengineering, University of Maryland, College Park, College Park, MD, United States.,Fischell Institute for Biomedical Devices, University of Maryland, College Park, College Park, MD, United States.,Institute of Bioscience and Biotechnology Research, University of Maryland, College Park, College Park, MD, United States
| | - Jinyang Li
- Fischell Department of Bioengineering, University of Maryland, College Park, College Park, MD, United States.,Fischell Institute for Biomedical Devices, University of Maryland, College Park, College Park, MD, United States.,Institute of Bioscience and Biotechnology Research, University of Maryland, College Park, College Park, MD, United States
| | - Gregory F Payne
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, College Park, MD, United States.,Institute of Bioscience and Biotechnology Research, University of Maryland, College Park, College Park, MD, United States
| | - William E Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, College Park, MD, United States.,Fischell Institute for Biomedical Devices, University of Maryland, College Park, College Park, MD, United States.,Institute of Bioscience and Biotechnology Research, University of Maryland, College Park, College Park, MD, United States
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2
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Application of elastin-based nanoparticles displaying antibody binding domains for a homogeneous immunoassay. Anal Biochem 2018; 544:72-79. [DOI: 10.1016/j.ab.2017.12.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/12/2017] [Accepted: 12/14/2017] [Indexed: 02/08/2023]
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3
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Dai Y, Molazemhosseini A, Liu CC. In Vitro Quantified Determination of β-Amyloid 42 Peptides, a Biomarker of Neuro-Degenerative Disorders, in PBS and Human Serum Using a Simple, Cost-Effective Thin Gold Film Biosensor. BIOSENSORS-BASEL 2017; 7:bios7030029. [PMID: 28726727 PMCID: PMC5618035 DOI: 10.3390/bios7030029] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 07/03/2017] [Accepted: 07/18/2017] [Indexed: 02/06/2023]
Abstract
A simple in vitro biosensor for the detection of β-amyloid 42 in phosphate-buffered saline (PBS) and undiluted human serum was fabricated and tested based on our platform sensor technology. The bio-recognition mechanism of this biosensor was based on the effect of the interaction between antibody and antigen of β-amyloid 42 to the redox couple probe of K4Fe(CN)6 and K3Fe(CN)6. Differential pulse voltammetry (DPV) served as the transduction mechanism measuring the current output derived from the redox coupling reaction. The biosensor was a three-electrode electrochemical system, and the working and counter electrodes were 50 nm thin gold film deposited by a sputtering technique. The reference electrode was a thick-film printed Ag/AgCl electrode. Laser ablation technique was used to define the size and structure of the biosensor. Cost-effective roll-to-roll manufacturing process was employed in the fabrication of the biosensor, making it simple and relatively inexpensive. Self-assembled monolayers (SAM) of 3-Mercaptopropionic acid (MPA) was employed to covalently immobilize the thiol group on the gold working electrode. A carbodiimide conjugation approach using N-(3-dimethylaminopropyl)-N′-ethylcarbodiimide hydrochloride (EDC) and N–hydroxysuccinimide (NHS) was undertaken for cross-linking antibody of β-amyloid 42 to the carboxylic groups on one end of the MPA. The antibody concentration of β-amyloid 42 used was 18.75 µg/mL. The concentration range of β-amyloid 42 in this study was from 0.0675 µg/mL to 0.5 µg/mL for both PBS and undiluted human serum. DPV measurements showed excellent response in this antigen concentration range. Interference study of this biosensor was carried out in the presence of Tau protein antigen. Excellent specificity of this β-amyloid 42 biosensor was demonstrated without interference from other species, such as T-tau protein.
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Affiliation(s)
- Yifan Dai
- Department of Chemical & Biomolecular Engineering and Electronics Design Center, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
| | - Alireza Molazemhosseini
- Dip. Chimica Materiali e Ing. Chimica "Giulio Natta", Politecnico di Milano, Via Mancinelli 7, 20131 MIlan, Italy.
| | - Chung Chiun Liu
- Department of Chemical & Biomolecular Engineering and Electronics Design Center, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
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Badiya PK, Srinivasan V, Jayakumar TP, Ramamurthy SS. Ag-CNT Architectures for Attomolar Dopamine Detection and 100-Fold Fluorescence Enhancements with Cellphone-Based Surface Plasmon-Coupled Emission Platform. Chemphyschem 2016; 17:2791-4. [PMID: 27338187 DOI: 10.1002/cphc.201600571] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Indexed: 11/07/2022]
Abstract
We report cellphone-based detection of dopamine with attomolar sensitivity in clinical samples with the use of a surface plasmon-coupled emission (SPCE) platform. To this end, silver-coated carbon nanotubes were used as spacer and cavity materials on SPCE substrates to obtain up to 100-fold fluorescence enhancements. The presence of silver on the carbon nanotubes helped to overcome fluorescence quenching arising due to π-π interactions between the carbon nanotube and rhodamine 6G. The competing adsorption of dopamine versus rhodamine 6G on graphene oxide was utilized to develop this sensing platform.
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Affiliation(s)
- Pradeep Kumar Badiya
- Plasmonics Laboratory, Department of Chemistry, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, 515134, India
| | - Venkatesh Srinivasan
- Plasmonics Laboratory, Department of Chemistry, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, 515134, India
| | - Tejkiran Pindi Jayakumar
- Plasmonics Laboratory, Department of Chemistry, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, 515134, India
| | - Sai Sathish Ramamurthy
- Plasmonics Laboratory, Department of Chemistry, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, 515134, India.
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Borrebaeck CAK, Wingren C. High-throughput proteomics using antibody microarrays: an update. Expert Rev Mol Diagn 2014; 7:673-86. [PMID: 17892372 DOI: 10.1586/14737159.7.5.673] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Antibody-based microarrays are a rapidly emerging technology that has advanced from the first proof-of-concept studies to demanding serum protein profiling applications during recent years, displaying great promise within disease proteomics. Miniaturized micro- and nanoarrays can be fabricated with an almost infinite number of antibodies carrying the desired specificities. While consuming only minute amounts of reagents, multiplexed and ultrasensitive assays can be performed targeting high- as well as low-abundance analytes in complex nonfractionated proteomes. The microarray images generated can then be converted into protein expression profiles or protein atlases, revealing a detailed composition of the sample. The technology will provide unique opportunities for fields such as disease diagnostics, biomarker discovery, patient stratification, predicting disease recurrence and drug target discovery. This review describes an update of high-throughput proteomics, using antibody-based microarrays, focusing on key technological advances and novel applications that have emerged over the last 3 years.
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Affiliation(s)
- Carl A K Borrebaeck
- Lund University, Department of Immunotechnology & CREATE Health, BMC D13, SE-221 84 Lund, Sweden.
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6
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Autonomous bacterial localization and gene expression based on nearby cell receptor density. Mol Syst Biol 2013; 9:636. [PMID: 23340842 PMCID: PMC3564257 DOI: 10.1038/msb.2012.71] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 12/08/2012] [Indexed: 11/09/2022] Open
Abstract
Escherichia coli were genetically modified to enable programmed motility, sensing, and actuation based on the density of features on nearby surfaces. Then, based on calculated feature density, these cells expressed marker proteins to indicate phenotypic response. Specifically, site-specific synthesis of bacterial quorum sensing autoinducer-2 (AI-2) is used to initiate and recruit motile cells. In our model system, we rewired E. coli's AI-2 signaling pathway to direct bacteria to a squamous cancer cell line of head and neck (SCCHN), where they initiate synthesis of a reporter (drug surrogate) based on a threshold density of epidermal growth factor receptor (EGFR). This represents a new type of controller for targeted drug delivery as actuation (synthesis and delivery) depends on a receptor density marking the diseased cell. The ability to survey local surfaces and initiate gene expression based on feature density represents a new area-based switch in synthetic biology that will find use beyond the proposed cancer model here.
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Bae J, Mie M, Kobatake E. Development of a specific siRNA delivery system into HeLa cells using an IgG-binding fusion protein. Biotechnol Lett 2013; 35:2081-9. [DOI: 10.1007/s10529-013-1299-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Accepted: 06/26/2013] [Indexed: 12/01/2022]
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8
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Supported protein G on gold electrode: characterization and immunosensor application. Talanta 2013; 116:84-90. [PMID: 24148377 DOI: 10.1016/j.talanta.2013.04.059] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 04/18/2013] [Accepted: 04/24/2013] [Indexed: 11/21/2022]
Abstract
In this work, we study the electrochemical properties of protein layer grafted on gold electrode for C-reactive protein detection. Two CRP-antibody immobilization methods were used: the first method is based on direct physisorption of CRP-antibody onto the gold surface and the second method is based on oriented CRP-antibody with protein G intermediate layer. The two developed immunosensors were tested against CRP antigen in phosphate buffer saline solution and in human plasma. The electrochemical characterization of each immobilized layers was achieved by cyclic voltammetry and impedance spectroscopy. The morphology of the deposited biomolecules was observed by Atomic Force Microscopy and the roughness was measured. Moreover, contact angle measurement was used for wettability studies. The response of the developed immunosensors was reproducible, rapid, and highly stable and a detection limit of 100 fg/mL and 10 pg/mL antigen was observed with and without protein G respectively. The developed immunosensors was used for CRP detection in human plasma.
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9
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Bae J, Mie M, Kobatake E. Targeted Gene Delivery via PEI Complexed with an Antibody. Appl Biochem Biotechnol 2012; 168:2184-90. [DOI: 10.1007/s12010-012-9928-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 10/03/2012] [Indexed: 10/27/2022]
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10
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Terrell JL, Gordonov T, Cheng Y, Wu HC, Sampey D, Luo X, Tsao CY, Ghodssi R, Rubloff GW, Payne GF, Bentley WE. Integrated biofabrication for electro-addressed in-film bioprocessing. Biotechnol J 2012; 7:428-39. [DOI: 10.1002/biot.201100181] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 11/14/2011] [Accepted: 12/22/2011] [Indexed: 01/17/2023]
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11
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Protected immobilization of Taq DNA polymerase by active site masking on self-assembled monolayers of ω-functionalized thiols. Anal Biochem 2011; 419:205-10. [DOI: 10.1016/j.ab.2011.08.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 08/09/2011] [Accepted: 08/11/2011] [Indexed: 01/02/2023]
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12
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Akter F, Mie M, Kobatake E. Immuno-rolling circle amplification using a multibinding fusion protein. Anal Biochem 2011; 416:174-9. [DOI: 10.1016/j.ab.2011.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 05/02/2011] [Accepted: 05/03/2011] [Indexed: 10/18/2022]
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13
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Kumar S, Ch R, Rath D, Panda S. Densities and orientations of antibodies on nano-textured silicon surfaces. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2011. [DOI: 10.1016/j.msec.2010.10.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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14
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Yoon M, Hwang HJ, Kim JH. Immobilization of antibodies on the self-assembled monolayer by antigen-binding site protection and immobilization kinetic control. ACTA ACUST UNITED AC 2011. [DOI: 10.4236/jbise.2011.44033] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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15
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Nakamura M, Mie M, Kobatake E. Construction of a functional IgG-binding luciferase fusion protein for the rapid detection of specific bacterial strains. Analyst 2011; 136:71-2. [DOI: 10.1039/c0an00460j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Liu Y, Kim E, Ghodssi R, Rubloff GW, Culver JN, Bentley WE, Payne GF. Biofabrication to build the biology–device interface. Biofabrication 2010; 2:022002. [DOI: 10.1088/1758-5082/2/2/022002] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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17
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Immobilization of Anti-Galectin-3 onto Polysiloxane–Polyvinyl Alcohol Disks for Tumor Prostatic Diseases Diagnosis. Appl Biochem Biotechnol 2009; 160:2198-207. [DOI: 10.1007/s12010-009-8753-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2009] [Accepted: 08/17/2009] [Indexed: 10/20/2022]
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18
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A Chimeric Fusion Protein Engineered with Disparate Functionalities—Enzymatic Activity and Self–assembly. J Mol Biol 2009; 392:129-42. [DOI: 10.1016/j.jmb.2009.06.075] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2009] [Revised: 06/09/2009] [Accepted: 06/29/2009] [Indexed: 11/30/2022]
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19
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Wu HC, Shi XW, Tsao CY, Lewandowski AT, Fernandes R, Hung CW, DeShong P, Kobatake E, Valdes JJ, Payne GF, Bentley WE. Biofabrication of antibodies and antigens via IgG-binding domain engineered with activatable pentatyrosine pro-tag. Biotechnol Bioeng 2009; 103:231-40. [DOI: 10.1002/bit.22238] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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20
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Yang X, Shi XW, Liu Y, Bentley WE, Payne GF. Orthogonal enzymatic reactions for the assembly of proteins at electrode addresses. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:338-44. [PMID: 19115870 DOI: 10.1021/la802618q] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The ability to interface proteins to device surfaces is important for a range of applications. Here, we enlist the unique capabilities of enzymes and biologically derived polymers to assemble target proteins to electrode addresses. First, the stimuli-responsive aminopolysaccharide chitosan is directed to assemble at the electrode address in response to electrode-imposed signals. The electrodeposited chitosan film serves as the biodevice interface for subsequent protein assembly. Next, tyrosinase is used to catalyze grafting of a protein or peptide tether to the chitosan film. Finally, microbial transglutaminase (mTG) catalyzes the assembly of target proteins to the tether. mTG covalently links proteins through their glutamine (Gln) and lysine (Lys) residues. Since Gln and Lys residues of globular proteins are often inaccessible to mTG, we engineered our target proteins to have fusion tags with added Gln or Lys residues. This assembly method employs the electrical signal to confer spatial selectivity (during chitosan electrodeposition) and employs the enzymes to confer chemical selectivity (i.e., amino acid residue selectivity). Further, this method is mild, since no reactive reagents or protection steps are required, and all steps are performed in aqueous solution. These results demonstrate the potential for employing biological materials and mechanisms to biofabricate the biodevice interface.
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Affiliation(s)
- Xiaohua Yang
- Center for Biosystems Research, University of Maryland Biotechnology Institute, 5115 Plant Sciences Building, College Park, Maryland 20742, USA
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21
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Antibody orientation enhanced by selective polymer–protein noncovalent interactions. Anal Bioanal Chem 2008; 393:1531-8. [DOI: 10.1007/s00216-008-2567-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Revised: 11/26/2008] [Accepted: 12/05/2008] [Indexed: 10/21/2022]
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22
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Smith DS, Kostov Y, Rao G. Signal enhancement of surface plasmon-coupled directional emission by a conical mirror. APPLIED OPTICS 2008; 47:5229-5234. [PMID: 18830315 DOI: 10.1364/ao.47.005229] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A simple strategy for increasing the collection efficiency of surface plasmon-coupled emission (SPCE) is demonstrated. SPCE is a near-field phenomenon occurring when excited fluorophores are in close proximity to a subwavelength metal film. The energy of the fluorophores induces surface plasmons that radiate the coupled energy at highly specific angles. In an attempt to maximize the collected emission, a conical mirror was placed around the coupling prism. The result was a nearly 500 fold enhancement over the free space signal as detected from a single point from a poly(vinyl alcohol) layer doped with ruthenium. Coupling this large enhancement with LED excitation could lead to the development of inexpensive, handheld fluorescent devices with high sensitivity.
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Affiliation(s)
- Derek S Smith
- Center for Advanced Sensor Technology and Department of Chemical and Biochemical Engineering, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, USA
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Shi XW, Wu HC, Liu Y, Tsao CY, Wang K, Kobatake E, Bentley WE, Payne GF. Chitosan Fibers: Versatile Platform for Nickel-Mediated Protein Assembly. Biomacromolecules 2008; 9:1417-23. [DOI: 10.1021/bm800072e] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xiao-Wen Shi
- Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, Maryland 20742, Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, and Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku Yokohama 226-8501, Japan
| | - Hsuan-Chen Wu
- Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, Maryland 20742, Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, and Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku Yokohama 226-8501, Japan
| | - Yi Liu
- Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, Maryland 20742, Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, and Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku Yokohama 226-8501, Japan
| | - Chen-Yu Tsao
- Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, Maryland 20742, Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, and Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku Yokohama 226-8501, Japan
| | - Kai Wang
- Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, Maryland 20742, Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, and Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku Yokohama 226-8501, Japan
| | - Eiry Kobatake
- Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, Maryland 20742, Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, and Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku Yokohama 226-8501, Japan
| | - William E. Bentley
- Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, Maryland 20742, Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, and Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku Yokohama 226-8501, Japan
| | - Gregory F. Payne
- Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, Maryland 20742, Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, and Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku Yokohama 226-8501, Japan
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24
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Controlled antibody immobilization onto immunoanalytical platforms by synthetic peptide. Anal Biochem 2008; 374:99-105. [DOI: 10.1016/j.ab.2007.10.022] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2007] [Revised: 10/11/2007] [Accepted: 10/16/2007] [Indexed: 11/22/2022]
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25
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Flanagin S, Nelson JD, Castner DG, Denisenko O, Bomsztyk K. Microplate-based chromatin immunoprecipitation method, Matrix ChIP: a platform to study signaling of complex genomic events. Nucleic Acids Res 2008; 36:e17. [PMID: 18203739 PMCID: PMC2241906 DOI: 10.1093/nar/gkn001] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The chromatin immunoprecipitation (ChIP) assay is a major tool in the study of genomic processes in vivo. This and other methods are revealing that control of gene expression, cell division and DNA repair involves multiple proteins and great number of their modifications. ChIP assay is traditionally done in test tubes limiting the ability to study signaling of the complex genomic events. To increase the throughput and to simplify the assay we have developed a microplate-based ChIP (Matrix ChIP) method, where all steps from immunoprecipitation to DNA purification are done in microplate wells without sample transfers. This platform has several important advantages over the tube-based assay including very simple sample handling, high throughput, improved sensitivity and reproducibility, and potential for automation. 96 ChIP measurements including PCR can be done by one researcher in one day. We illustrate the power of Matrix ChIP by parallel profiling 80 different chromatin and transcription time-course events along an inducible gene including transient recruitment of kinases.
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Affiliation(s)
- Steve Flanagin
- UW Medicine Lake Union, Department of Medicine, University of Washington, Seattle, WA 98109, USA
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26
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Kopf E, Zharhary D. Antibody arrays--an emerging tool in cancer proteomics. Int J Biochem Cell Biol 2007; 39:1305-17. [PMID: 17600752 DOI: 10.1016/j.biocel.2007.04.029] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2006] [Revised: 04/26/2007] [Accepted: 04/27/2007] [Indexed: 10/23/2022]
Abstract
Cancer is a result of complex changes that occur in normal cells as they transform to become malignant and further when they become metastatic. These changes are not a consequence of a single protein but rather involve multiple proteins that function in pathways and networks. Thus, profiling cancer-associated changes requires simultaneous measurement of many proteins in a single sample. Identifying these changes may lead to the discovery of cancer-associated biomarkers that may assist in diagnosis, prognosis, patient monitoring and possibly for therapeutic purposes. Antibody arrays are a relatively new technology that enables one to perform multiplex high-throughput protein expression profiling. This review describes current technologies in antibody array and assay design, and presents a survey of the current literature on the use of these arrays in cancer research.
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Affiliation(s)
- Eliezer Kopf
- Sigma-Aldrich Israel Ltd., 3 Plaut Street, Park Rabin, Rehovot 76100, Israel
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Lee HJ, Nedelkov D, Corn RM. Surface plasmon resonance imaging measurements of antibody arrays for the multiplexed detection of low molecular weight protein biomarkers. Anal Chem 2007; 78:6504-10. [PMID: 16970327 DOI: 10.1021/ac060881d] [Citation(s) in RCA: 146] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This paper describes a simple methodology for the creation of high-density multiplexed antibody arrays on gold surfaces that can be used to detect low molecular weight protein biomarkers with surface plasmon resonance imaging (SPRI). A one-step carbonyldiimidazole (CDI) surface reaction was utilized to attach antibodies onto alkanethiol-modified gold surfaces and characterized with polarization modulation FT-IR reflection absorption spectroscopy. The CDI chemistry was then employed to create an antibody microarray with array element sizes varying from 750 microm down to 200 microm. As a demonstration, a three-component antibody array was employed to detect two clinically important protein biomarkers, beta2-microglobulin (11.8 kDa) and cystatin C (13.4 kDa). SPRI measurements could simultaneously detect both of these small unlabeled proteins with no cross talk at solution concentrations from 300 nM down to 1 nM. In addition, the adsorption strengths of these biomarkers onto an antibody array were measured with SPRI and compared to those obtained from the kinetic analysis of single-channel angle shift SPR measurements.
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Affiliation(s)
- Hye Jin Lee
- Department of Chemistry, University of California-Irvine, Irvine, California 92697, USA
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Abstract
In the past few years, protein biochips have emerged as promising proteomic and diagnostic tools for obtaining information about protein functions and interactions. Important technological innovations have been made. However, considerable development is still required, especially regarding protein immobilization, in order to fully realize the potential of protein biochips. In fact, protein immobilization is the key to the success of microarray technology. Proteins need to be immobilized onto surfaces with high density in order to allow the usage of small amount of sample solution. Nonspecific protein adsorption needs to be avoided or at least minimized in order to improve detection performances. Moreover, full retention of protein conformation and activity is a challenging task to be accomplished. Although a large number of review papers on protein biochips have been published in recent years, few have focused on protein immobilization technology. In this review, current protein immobilization strategies, including physical, covalent, and bioaffinity immobilization for the fabrication of protein biochips, are described. Particular consideration has been given to oriented immobilization, also referred to as site-specific immobilization, which is believed will improve homogeneous surface covering and accessibility of the active site.
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Affiliation(s)
- Federica Rusmini
- Department of Polymer Chemistry and Biomaterials (PBM), Institute for Biomedical Technology (BMTI), Faculty of Science and Technology, University of Twente, Enschede, 7500 AE, The Netherlands
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