51
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Ouellet E, Lausted C, Lin T, Yang CWT, Hood L, Lagally ET. Parallel microfluidic surface plasmon resonance imaging arrays. LAB ON A CHIP 2010; 10:581-8. [PMID: 20162233 DOI: 10.1039/b920589f] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Surface plasmon resonance imaging (SPRi) is a label-free technique used for the quantitation of binding affinities and concentrations for a wide variety of target molecules. Although SPRi is capable of determining binding constants for multiple ligands in parallel, current commercial instruments are limited to a single analyte stream on multiple ligand spots. Measurement of binding kinetics requires the serial introduction of different analyte concentrations; such repeated experiments are conducted manually and are therefore time-intensive. To address these challenges, we have developed an integrated microfluidic array using soft lithography techniques for high-throughput SPRi-based detection and determination of binding affinities of antibodies against protein targets. The device consists of 264 element-addressable chambers isolated by microvalves. The resulting 700 pL chamber volumes, combined with a serial dilution network for simultaneous interrogation of up to six different analyte concentrations, allow for further speeding detection times. To test for device performance, human alpha-thrombin was immobilized on the sensor surface and anti-human alpha-thrombin IgG was injected across the surface at different concentrations. The equilibrium dissociation constant was determined to be 5.0 +/- 1.9 nM, which agrees well with values reported in the literature. The interrogation of multiple ligands to multiple analytes in a single device was also investigated and samples were recovered with no cross-contamination. Since each chamber can be addressed independently, this array is capable of interrogating binding events from up to 264 different immobilized ligands against multiple analytes in a single experiment. The development of high-throughput protein analytic measurements is a critical technology for systems approaches to biology and medicine.
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Affiliation(s)
- Eric Ouellet
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
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52
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Im H, Wittenberg NJ, Lesuffleur A, Lindquist NC, Oh SH. Membrane protein biosensing with plasmonic nanopore arrays and pore-spanning lipid membranes. Chem Sci 2010; 1:688-696. [PMID: 21218136 PMCID: PMC3015192 DOI: 10.1039/c0sc00365d] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Integration of solid-state biosensors and lipid bilayer membranes is important for membrane protein research and drug discovery. In these sensors, it is critical that the solid-state sensing material does not have adverse effects on the conformation or functionality of membrane-bound molecules. In this work, pore-spanning lipid membranes are formed over an array of periodic nanopores in free-standing gold films for surface plasmon resonance (SPR) kinetic binding assays. The ability to perform kinetic assays with a transmembrane protein is demonstrated with α-hemolysin (α-HL). The incorporation of α-HL into the membrane followed by specific antibody binding (anti-α-HL) red-shifts the plasmon resonance of the gold nanopore array, which is optically monitored in real time. Subsequent fluorescence imaging reveals that the antibodies primarily bind in nanopore regions, indicating that α-HL incorporation preferentially occurs into areas of pore-spanning lipid membranes.
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Affiliation(s)
| | | | | | | | - Sang-Hyun Oh
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, Minnesota, 55455, USA. Fax: +1 612 625 4583; Tel: +1 612 625 0125;
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53
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Liao WS, Chen X, Yang T, Castellana ET, Chen J, Cremer PS. Benchtop chemistry for the rapid prototyping of label-free biosensors: Transmission localized surface plasmon resonance platforms. Biointerphases 2009; 4:80-5. [PMID: 20408728 PMCID: PMC3449173 DOI: 10.1116/1.3284738] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Herein, a simple label-free biosensor fabrication method is demonstrated based on transmission localized surface plasmon resonance (T-LSPR). The platform, which consists of a silver nanoparticle array, can be prepared in just a few minutes using benchtop chemistry. The array was made by a templating technique in conjunction with the photoreduction of Ag ions from solution. This metal surface was functionalized with biotin-linked thiol ligands for binding streptavidin molecules from solution. For an array of 19 nm diameter silver nanoparticles, a redshift in the T-LSPR spectrum of 24 nm was observed upon protein-ligand binding at saturation. The binding constant was found to be 2x10(12) M(-1). Platforms were also fabricated with silver nanoparticles of 34, 55, and 72 nm diameters. The maximum LSPR wavelength shift was nanoparticle size dependent and the maximum sensitivity was obtained with the smaller nanoparticles.
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Affiliation(s)
- Wei-Ssu Liao
- Department of Chemistry, Texas A&M University, College Station, Texas 77843
| | - Xin Chen
- Department of Chemistry, Texas A&M University, College Station, Texas 77843
| | - Tinglu Yang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843
| | | | - Jixin Chen
- Department of Chemistry, Texas A&M University, College Station, Texas 77843
| | - Paul S. Cremer
- Department of Chemistry, Texas A&M University, College Station, Texas 77843
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54
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Xia N, Liu L, Yi X, Wang J. Studies of interaction of tumor suppressor p53 with apo-MT using surface plasmon resonance. Anal Bioanal Chem 2009; 395:2569-75. [DOI: 10.1007/s00216-009-3174-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2009] [Revised: 09/18/2009] [Accepted: 09/19/2009] [Indexed: 11/24/2022]
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55
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Rai A, Tsow F, Nassirpour S, Bankers J, Spinatsch M, He MP, Forzani E, Tao NJ. Selective Detection of Sulfur Derivatives Using Microfabricated Tuning Fork-Based Sensors. SENSORS AND ACTUATORS. B, CHEMICAL 2009; 140:490-499. [PMID: 20160943 PMCID: PMC2765673 DOI: 10.1016/j.snb.2009.04.053] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The paper describes an integtrated sensor system that can selectively and reversibly detect sulfur derivatives in the presence of interferent molecules. This is accomplished by integrating analyte-specific sensing materials with optimized filter materials. Microfabricated quartz tuning fork arrays are used to provide fast, accurate and low-cost transduction of the analyte binding events into electronic signals. The concept is demonstrated for detection of three sulfur derivatives - dimethyl disulfide, ethanethiol and methylsulfide.
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Affiliation(s)
- Anant Rai
- The Biodesign Institute and Department of Electrical Engineering, Arizona State University, Tempe, AZ 85287-5801
| | - Francis Tsow
- The Biodesign Institute and Department of Electrical Engineering, Arizona State University, Tempe, AZ 85287-5801
| | | | - Jeffrey Bankers
- The Dial Corporation, 15501 N. Dial Blvd., Scottsdale, AZ 85260
| | | | - M. Pete He
- The Dial Corporation, 15501 N. Dial Blvd., Scottsdale, AZ 85260
| | - Erica Forzani
- The Biodesign Institute and Department of Electrical Engineering, Arizona State University, Tempe, AZ 85287-5801
| | - N. J. Tao
- The Biodesign Institute and Department of Electrical Engineering, Arizona State University, Tempe, AZ 85287-5801
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56
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Berger MF, Bulyk ML. Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors. Nat Protoc 2009; 4:393-411. [PMID: 19265799 DOI: 10.1038/nprot.2008.195] [Citation(s) in RCA: 268] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Protein-binding microarray (PBM) technology provides a rapid, high-throughput means of characterizing the in vitro DNA-binding specificities of transcription factors (TFs). Using high-density, custom-designed microarrays containing all 10-mer sequence variants, one can obtain comprehensive binding-site measurements for any TF, regardless of its structural class or species of origin. Here, we present a protocol for the examination and analysis of TF-binding specificities at high resolution using such 'all 10-mer' universal PBMs. This procedure involves double-stranding a commercially synthesized DNA oligonucleotide array, binding a TF directly to the double-stranded DNA microarray and labeling the protein-bound microarray with a fluorophore-conjugated antibody. We describe how to computationally extract the relative binding preferences of the examined TF for all possible contiguous and gapped 8-mers over the full range of affinities, from highest affinity sites to nonspecific sites. Multiple proteins can be tested in parallel in separate chambers on a single microarray, enabling the processing of a dozen or more TFs in a single day.
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Affiliation(s)
- Michael F Berger
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
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57
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Im H, Lesuffleur A, Lindquist NC, Oh SH. Plasmonic nanoholes in a multichannel microarray format for parallel kinetic assays and differential sensing. Anal Chem 2009; 81:2854-9. [PMID: 19284776 DOI: 10.1021/ac802276x] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present nanohole arrays in a gold film integrated with a six-channel microfluidic chip for parallel measurements of molecular binding kinetics. Surface plasmon resonance effects in the nanohole arrays enable real-time, label-free measurements of molecular binding events in each channel, while adjacent negative reference channels can record measurement artifacts such as bulk solution index changes, temperature variations, or changing light absorption in the liquid. With the use of this platform, streptavidin-biotin specific binding kinetics are measured at various concentrations with negative controls. A high-density microarray of 252 biosensing pixels is also demonstrated with a packing density of 10(6) sensing elements/cm(2), which can potentially be coupled with a massively parallel array of microfluidic channels for protein microarray applications.
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Affiliation(s)
- Hyungsoon Im
- Laboratory of Nanostructures and Biosensing, Department of Electrical and Computer Engineering, University of Minnesota, Twin Cities, 200 Union Street South East, Minneapolis, Minnesota 55455, USA
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58
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Liu J, Eddings MA, Miles AR, Bukasov R, Gale BK, Shumaker-Parry JS. In Situ Microarray Fabrication and Analysis Using a Microfluidic Flow Cell Array Integrated with Surface Plasmon Resonance Microscopy. Anal Chem 2009; 81:4296-301. [DOI: 10.1021/ac900181f] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jianping Liu
- Department of Chemistry, Department of Bioengineering, and Department of Mechanical Engineering, University of Utah, Salt Lake City, Utah 84112, and Wasatch Microfluidics, 825 N. 300 W. Street NE 129, North Salt Lake City, Utah 84054
| | - Mark A. Eddings
- Department of Chemistry, Department of Bioengineering, and Department of Mechanical Engineering, University of Utah, Salt Lake City, Utah 84112, and Wasatch Microfluidics, 825 N. 300 W. Street NE 129, North Salt Lake City, Utah 84054
| | - Adam R. Miles
- Department of Chemistry, Department of Bioengineering, and Department of Mechanical Engineering, University of Utah, Salt Lake City, Utah 84112, and Wasatch Microfluidics, 825 N. 300 W. Street NE 129, North Salt Lake City, Utah 84054
| | - Rostislav Bukasov
- Department of Chemistry, Department of Bioengineering, and Department of Mechanical Engineering, University of Utah, Salt Lake City, Utah 84112, and Wasatch Microfluidics, 825 N. 300 W. Street NE 129, North Salt Lake City, Utah 84054
| | - Bruce K. Gale
- Department of Chemistry, Department of Bioengineering, and Department of Mechanical Engineering, University of Utah, Salt Lake City, Utah 84112, and Wasatch Microfluidics, 825 N. 300 W. Street NE 129, North Salt Lake City, Utah 84054
| | - Jennifer S. Shumaker-Parry
- Department of Chemistry, Department of Bioengineering, and Department of Mechanical Engineering, University of Utah, Salt Lake City, Utah 84112, and Wasatch Microfluidics, 825 N. 300 W. Street NE 129, North Salt Lake City, Utah 84054
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59
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Qavi AJ, Washburn AL, Byeon JY, Bailey RC. Label-free technologies for quantitative multiparameter biological analysis. Anal Bioanal Chem 2009; 394:121-35. [PMID: 19221722 PMCID: PMC2667559 DOI: 10.1007/s00216-009-2637-8] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Revised: 01/12/2009] [Accepted: 01/20/2009] [Indexed: 11/26/2022]
Abstract
In the postgenomic era, information is king and information-rich technologies are critically important drivers in both fundamental biology and medicine. It is now known that single-parameter measurements provide only limited detail and that quantitation of multiple biomolecular signatures can more fully illuminate complex biological function. Label-free technologies have recently attracted significant interest for sensitive and quantitative multiparameter analysis of biological systems. There are several different classes of label-free sensors that are currently being developed both in academia and in industry. In this critical review, we highlight, compare, and contrast some of the more promising approaches. We describe the fundamental principles of these different methods and discuss advantages and disadvantages that might potentially help one in selecting the appropriate technology for a given bioanalytical application.
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Affiliation(s)
- Abraham J. Qavi
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL 61801
| | - Adam L. Washburn
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL 61801
| | - Ji-Yeon Byeon
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL 61801
| | - Ryan C. Bailey
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL 61801
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60
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Eftekhari F, Escobedo C, Ferreira J, Duan X, Girotto EM, Brolo AG, Gordon R, Sinton D. Nanoholes As Nanochannels: Flow-through Plasmonic Sensing. Anal Chem 2009; 81:4308-11. [DOI: 10.1021/ac900221y] [Citation(s) in RCA: 243] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fatemeh Eftekhari
- Electrical and Computer Engineering, Mechanical Engineering, and Chemistry, University of Victoria, Victoria, British Columbia, Canada, Universidade Estadual de Maringa, Maringa, PR, Brazil, and British Columbia Cancer Agency, Trev & Joyce Deeley Research Centre, Victoria, British Columbia, Canada
| | - Carlos Escobedo
- Electrical and Computer Engineering, Mechanical Engineering, and Chemistry, University of Victoria, Victoria, British Columbia, Canada, Universidade Estadual de Maringa, Maringa, PR, Brazil, and British Columbia Cancer Agency, Trev & Joyce Deeley Research Centre, Victoria, British Columbia, Canada
| | - Jacqueline Ferreira
- Electrical and Computer Engineering, Mechanical Engineering, and Chemistry, University of Victoria, Victoria, British Columbia, Canada, Universidade Estadual de Maringa, Maringa, PR, Brazil, and British Columbia Cancer Agency, Trev & Joyce Deeley Research Centre, Victoria, British Columbia, Canada
| | - Xiaobo Duan
- Electrical and Computer Engineering, Mechanical Engineering, and Chemistry, University of Victoria, Victoria, British Columbia, Canada, Universidade Estadual de Maringa, Maringa, PR, Brazil, and British Columbia Cancer Agency, Trev & Joyce Deeley Research Centre, Victoria, British Columbia, Canada
| | - Emerson M. Girotto
- Electrical and Computer Engineering, Mechanical Engineering, and Chemistry, University of Victoria, Victoria, British Columbia, Canada, Universidade Estadual de Maringa, Maringa, PR, Brazil, and British Columbia Cancer Agency, Trev & Joyce Deeley Research Centre, Victoria, British Columbia, Canada
| | - Alexandre G. Brolo
- Electrical and Computer Engineering, Mechanical Engineering, and Chemistry, University of Victoria, Victoria, British Columbia, Canada, Universidade Estadual de Maringa, Maringa, PR, Brazil, and British Columbia Cancer Agency, Trev & Joyce Deeley Research Centre, Victoria, British Columbia, Canada
| | - Reuven Gordon
- Electrical and Computer Engineering, Mechanical Engineering, and Chemistry, University of Victoria, Victoria, British Columbia, Canada, Universidade Estadual de Maringa, Maringa, PR, Brazil, and British Columbia Cancer Agency, Trev & Joyce Deeley Research Centre, Victoria, British Columbia, Canada
| | - David Sinton
- Electrical and Computer Engineering, Mechanical Engineering, and Chemistry, University of Victoria, Victoria, British Columbia, Canada, Universidade Estadual de Maringa, Maringa, PR, Brazil, and British Columbia Cancer Agency, Trev & Joyce Deeley Research Centre, Victoria, British Columbia, Canada
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61
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Lindquist NC, Lesuffleur A, Im H, Oh SH. Sub-micron resolution surface plasmon resonance imaging enabled by nanohole arrays with surrounding Bragg mirrors for enhanced sensitivity and isolation. LAB ON A CHIP 2009; 9:382-7. [PMID: 19156286 DOI: 10.1039/b816735d] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
We present nanohole arrays in thin gold films as sub-micron resolution surface plasmon resonance (SPR) imaging pixels in a microarray format. With SPR imaging, the resolution is not limited by diffraction, but by the propagation of surface plasmon waves to adjacent sensing areas, or nanohole arrays, causing unwanted interference. For ultimate scalability, several issues need to be addressed, including: (1) as several nanohole arrays are brought close to each other, surface plasmon interference introduces large sources of error; and (2) as the size of the nanohole array is reduced, i.e. fewer holes, detection sensitivity suffers. To address these scalability issues, we surround each biosensing pixel (a 3-by-3 nanohole array) with plasmonic Bragg mirrors, blocking interference between adjacent SPR sensing pixels for high-density packing, while maintaining the sensitivity of a 50 x larger footprint pixel (a 16-by-16 nanohole array). We measure real-time, label-free streptavidin-biotin binding kinetics with a microarray of 600 sub-micron biosensing pixels at a packing density of more than 10(7) per cm(2).
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Affiliation(s)
- Nathan C Lindquist
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN 55455, USA
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62
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Yao J, Stewart ME, Maria J, Lee TW, Gray SK, Rogers JA, Nuzzo RG. Seeing molecules by eye: surface plasmon resonance imaging at visible wavelengths with high spatial resolution and submonolayer sensitivity. Angew Chem Int Ed Engl 2008; 47:5013-7. [PMID: 18512212 DOI: 10.1002/anie.200800501] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Jimin Yao
- Department of Chemistry, University of Illinois, South Mathews Avenue, Urbana, IL 61801, USA
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63
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Chan LL, Pineda M, Heeres JT, Hergenrother PJ, Cunningham BT. A general method for discovering inhibitors of protein-DNA interactions using photonic crystal biosensors. ACS Chem Biol 2008; 3:437-48. [PMID: 18582039 DOI: 10.1021/cb800057j] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Protein-DNA interactions are essential for fundamental cellular processes such as transcription, DNA damage repair, and apoptosis. As such, small molecule disruptors of these interactions could be powerful tools for investigation of these biological processes, and such compounds would have great potential as therapeutics. Unfortunately, there are few methods available for the rapid identification of compounds that disrupt protein-DNA interactions. Here we show that photonic crystal (PC) technology can be utilized to detect protein-DNA interactions, and can be used in a high-throughput screening mode to identify compounds that prevent protein-DNA binding. The PC technology is used to detect binding between protein-DNA interactions that are DNA-sequence-dependent (the bacterial toxin-antitoxin system MazEF) and those that are DNA-sequence-independent (the human apoptosis inducing factor (AIF)). The PC technology was further utilized in a screen for inhibitors of the AIF-DNA interaction, and through this screen aurin tricarboxylic acid was identified as the first in vitro inhibitor of AIF. The generality and simplicity of the photonic crystal method should enable this technology to find broad utility for identification of compounds that inhibit protein-DNA binding.
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Affiliation(s)
- Leo L. Chan
- Department of Electrical and Computer Engineering
| | | | | | - Paul J. Hergenrother
- Department of Biochemistry
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
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64
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Yao J, Stewart M, Maria J, Lee TW, Gray S, Rogers J, Nuzzo R. Seeing Molecules by Eye: Surface Plasmon Resonance Imaging at Visible Wavelengths with High Spatial Resolution and Submonolayer Sensitivity. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200800501] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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65
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66
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Monot J, Petit M, Lane SM, Guisle I, Léger J, Tellier C, Talham DR, Bujoli B. Towards Zirconium Phosphonate-Based Microarrays for Probing DNA−Protein Interactions: Critical Influence of the Location of the Probe Anchoring Groups. J Am Chem Soc 2008; 130:6243-51. [DOI: 10.1021/ja711427q] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Julien Monot
- Université de Nantes, CNRS, UMR 6230, Chimie Et Interdisciplinarité: Synthèse Analyse Modélisation (CEISAM), UFR Sciences et Techniques, 2, rue de la Houssinière, BP 92208, 44322 NANTES Cedex 3, Department of Chemistry, University of Florida, Gainesville, Florida, 32611-7200, USA, U INSERM 533, UFR de Médecine Physiologie, 1 rue Gaston Veil, BP 53508, 44035 NANTES Cedex 1, France, and Nantes Atlantique Universités, CNRS, UMR 6204, Laboratoire de Biotechnologie, Biocatalyse et Biorégulation, 2 Rue de la
| | - Marc Petit
- Université de Nantes, CNRS, UMR 6230, Chimie Et Interdisciplinarité: Synthèse Analyse Modélisation (CEISAM), UFR Sciences et Techniques, 2, rue de la Houssinière, BP 92208, 44322 NANTES Cedex 3, Department of Chemistry, University of Florida, Gainesville, Florida, 32611-7200, USA, U INSERM 533, UFR de Médecine Physiologie, 1 rue Gaston Veil, BP 53508, 44035 NANTES Cedex 1, France, and Nantes Atlantique Universités, CNRS, UMR 6204, Laboratoire de Biotechnologie, Biocatalyse et Biorégulation, 2 Rue de la
| | - Sarah M. Lane
- Université de Nantes, CNRS, UMR 6230, Chimie Et Interdisciplinarité: Synthèse Analyse Modélisation (CEISAM), UFR Sciences et Techniques, 2, rue de la Houssinière, BP 92208, 44322 NANTES Cedex 3, Department of Chemistry, University of Florida, Gainesville, Florida, 32611-7200, USA, U INSERM 533, UFR de Médecine Physiologie, 1 rue Gaston Veil, BP 53508, 44035 NANTES Cedex 1, France, and Nantes Atlantique Universités, CNRS, UMR 6204, Laboratoire de Biotechnologie, Biocatalyse et Biorégulation, 2 Rue de la
| | - Isabelle Guisle
- Université de Nantes, CNRS, UMR 6230, Chimie Et Interdisciplinarité: Synthèse Analyse Modélisation (CEISAM), UFR Sciences et Techniques, 2, rue de la Houssinière, BP 92208, 44322 NANTES Cedex 3, Department of Chemistry, University of Florida, Gainesville, Florida, 32611-7200, USA, U INSERM 533, UFR de Médecine Physiologie, 1 rue Gaston Veil, BP 53508, 44035 NANTES Cedex 1, France, and Nantes Atlantique Universités, CNRS, UMR 6204, Laboratoire de Biotechnologie, Biocatalyse et Biorégulation, 2 Rue de la
| | - Jean Léger
- Université de Nantes, CNRS, UMR 6230, Chimie Et Interdisciplinarité: Synthèse Analyse Modélisation (CEISAM), UFR Sciences et Techniques, 2, rue de la Houssinière, BP 92208, 44322 NANTES Cedex 3, Department of Chemistry, University of Florida, Gainesville, Florida, 32611-7200, USA, U INSERM 533, UFR de Médecine Physiologie, 1 rue Gaston Veil, BP 53508, 44035 NANTES Cedex 1, France, and Nantes Atlantique Universités, CNRS, UMR 6204, Laboratoire de Biotechnologie, Biocatalyse et Biorégulation, 2 Rue de la
| | - Charles Tellier
- Université de Nantes, CNRS, UMR 6230, Chimie Et Interdisciplinarité: Synthèse Analyse Modélisation (CEISAM), UFR Sciences et Techniques, 2, rue de la Houssinière, BP 92208, 44322 NANTES Cedex 3, Department of Chemistry, University of Florida, Gainesville, Florida, 32611-7200, USA, U INSERM 533, UFR de Médecine Physiologie, 1 rue Gaston Veil, BP 53508, 44035 NANTES Cedex 1, France, and Nantes Atlantique Universités, CNRS, UMR 6204, Laboratoire de Biotechnologie, Biocatalyse et Biorégulation, 2 Rue de la
| | - Daniel R. Talham
- Université de Nantes, CNRS, UMR 6230, Chimie Et Interdisciplinarité: Synthèse Analyse Modélisation (CEISAM), UFR Sciences et Techniques, 2, rue de la Houssinière, BP 92208, 44322 NANTES Cedex 3, Department of Chemistry, University of Florida, Gainesville, Florida, 32611-7200, USA, U INSERM 533, UFR de Médecine Physiologie, 1 rue Gaston Veil, BP 53508, 44035 NANTES Cedex 1, France, and Nantes Atlantique Universités, CNRS, UMR 6204, Laboratoire de Biotechnologie, Biocatalyse et Biorégulation, 2 Rue de la
| | - Bruno Bujoli
- Université de Nantes, CNRS, UMR 6230, Chimie Et Interdisciplinarité: Synthèse Analyse Modélisation (CEISAM), UFR Sciences et Techniques, 2, rue de la Houssinière, BP 92208, 44322 NANTES Cedex 3, Department of Chemistry, University of Florida, Gainesville, Florida, 32611-7200, USA, U INSERM 533, UFR de Médecine Physiologie, 1 rue Gaston Veil, BP 53508, 44035 NANTES Cedex 1, France, and Nantes Atlantique Universités, CNRS, UMR 6204, Laboratoire de Biotechnologie, Biocatalyse et Biorégulation, 2 Rue de la
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67
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Homola J. Surface plasmon resonance sensors for detection of chemical and biological species. Chem Rev 2008; 108:462-93. [PMID: 18229953 DOI: 10.1021/cr068107d] [Citation(s) in RCA: 1754] [Impact Index Per Article: 109.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jirí Homola
- Institute of Photonics and Electronics ASCR, Chaberská 57, 182 51 Prague 8, Czech Republic.
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68
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Electroless-plated gold films for sensitive surface plasmon resonance detection of white spot syndrome virus. Biosens Bioelectron 2007; 23:1200-7. [PMID: 18023170 DOI: 10.1016/j.bios.2007.10.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2007] [Revised: 09/24/2007] [Accepted: 10/08/2007] [Indexed: 11/23/2022]
Abstract
The paper describes the rapid and label-free detection of the white spot syndrome virus (WSSV) using a surface plasmon resonance (SPR) device based on gold films prepared by electroless plating. The plating condition for obtaining films suitable for SPR measurements was optimized. Gold nanoparticles adsorbed on glass slides were characterized by transmission electron microscopy (TEM). Detection of the WSSV was performed through the binding between WSSV in solution and the anti-WSSV single chain variable fragment (scFv antibody) preimmobilized onto the sensor surface. Morphologies of the as-prepared gold films, gold films modified with self-assembled alkanethiol monolayers, and films covered with antibody were examined using an atomic force microscope (AFM). To demonstrate the viability of the method for real sample analysis, WSSV of different concentrations present in a shrimp hemolymph matrix was determined upon optimizing the surface density of the antibody molecules. The SPR device based on the electroless-plated gold films is capable of detecting concentration of WSSV as low as 2.5 ng/mL in 2% shrimp hemolymph, which is one to two orders of magnitude lower than the level measurable by enzyme-linked immunosorbant assays.
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69
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Abstract
DNA-protein interactions are fundamental to many biological processes, including the regulation of gene expression. Determining the binding affinities of transcription factors (TFs) to different DNA sequences allows the quantitative modeling of transcriptional regulatory networks and has been a significant technical challenge in molecular biology for many years. A recent paper by Maerkl and Quake1 demonstrated the use of microfluidic technology for the analysis of DNA-protein interactions. An array of short DNA sequences was spotted onto a glass slide, which was then covered with a microfluidic device allowing each spot to be within a chamber into which the flow of materials was controlled by valves. By trapping the DNA-protein complexes on the surface and measuring their concentrations microscopically, they could determine the binding affinity to a large number of DNA sequences that were varied systematically. They studied four TFs from the basic helix-loop-helix family of proteins, all of which bind to E-box sites with the consensus CAnnTG (where "n" can be any base), and showed that variations in affinity for different sites allows each TF to regulate different genes.
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Affiliation(s)
- Gary D Stormo
- Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA.
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70
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Wang Z, Wilkop T, Xu D, Dong Y, Ma G, Cheng Q. Surface plasmon resonance imaging for affinity analysis of aptamer-protein interactions with PDMS microfluidic chips. Anal Bioanal Chem 2007; 389:819-25. [PMID: 17673982 DOI: 10.1007/s00216-007-1510-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2007] [Revised: 07/02/2007] [Accepted: 07/12/2007] [Indexed: 01/03/2023]
Abstract
We report on the use of PDMS multichannels for affinity studies of DNA aptamer-human Immunoglobulin E (IgE) interactions by surface plasmon resonance imaging (SPRi). The sensing surface was prepared with thiol-terminated aptamers through a self-assembling process in the PDMS channels defined on a gold substrate. Cysteamine was codeposited with the thiol aptamers to promote proper spatial arrangement of the aptamers and thus maintain their optimal binding efficiencies. Four aptamers with different nucleic acid sequences were studied to test their interaction affinity toward IgE, and the results confirmed that aptamer I (5'-SH-GGG GCA CGT TTA TCC GTC CCT CCT AGT GGC GTG CCC C-3') has the strongest binding affinity. Control experiments were conducted with a PEG-functionalized surface and IgG was used to replace IgE in order to verify the selective binding of aptamer I to the IgE molecules. A linear concentration-dependent relationship between IgE and aptamer I was obtained, and a 2-nM detection limit was achieved. SPRi data were further analyzed by global fitting, and the dissociation constant of aptamer I-IgE complex was found to be 2.7 x 10(-7) M, which agrees relatively well with the values reported in the literature. Aptamer affinity screening by SPR imaging demonstrates marked advantages over competing methods because it does not require labeling, can be used in real-time, and is potentially high-throughput. The ability to provide both qualitative and quantitative results on a multichannel chip further establishes SPRi as a powerful tool for the study of biological interactions in a multiplexed format.
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Affiliation(s)
- Zhuangzhi Wang
- Department of Chemistry, University of California, Riverside, CA 92521, USA
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71
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Lee CY, Harbers GM, Grainger DW, Gamble LJ, Castner DG. Fluorescence, XPS, and TOF-SIMS surface chemical state image analysis of DNA microarrays. J Am Chem Soc 2007; 129:9429-38. [PMID: 17625851 PMCID: PMC2533279 DOI: 10.1021/ja071879m] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Performance improvements in DNA-modified surfaces required for microarray and biosensor applications rely on improved capabilities to accurately characterize the chemistry and structure of immobilized DNA molecules on micropatterned surfaces. Recent innovations in imaging X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (TOF-SIMS) now permit more detailed studies of micropatterned surfaces. We have exploited the complementary information provided by imaging XPS and imaging TOF-SIMS to detail the chemical composition, spatial distribution, and hybridization efficiency of amine-terminated single-stranded DNA (ssDNA) bound to commercial polyacrylamide-based, amine-reactive microarray slides, immobilized in both macrospot and microarray diagnostic formats. Combinations of XPS imaging and small spot analysis were used to identify micropatterned DNA spots within printed DNA arrays on slide surfaces and quantify DNA elements within individual microarray spots for determination of probe immobilization and hybridization efficiencies. This represents the first report of imaging XPS of DNA immobilization and hybridization efficiencies for arrays fabricated on commercial microarray slides. Imaging TOF-SIMS provided distinct analytical data on the lateral distribution of DNA within single array microspots before and after target hybridization. Principal component analysis (PCA) applied to TOF-SIMS imaging datasets demonstrated that the combination of these two techniques provides information not readily observable in TOF-SIMS images alone, particularly in identifying species associated with array spot nonuniformities (e.g., "halo" or "donut" effects often observed in fluorescence images). Chemically specific spot images were compared to conventional fluorescence scanned images in microarrays to provide new information on spot-to-spot DNA variations that affect current diagnostic reliability, assay variance, and sensitivity.
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Affiliation(s)
- Chi-Ying Lee
- National ESCA and Surface Analysis Center for Biomedical Problems, Box 351750 University of Washington, Seattle, WA 98195-1750
- Department of Chemical Engineering, Box 351750 University of Washington, Seattle, WA 98195-1750
| | - Gregory M. Harbers
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT 84112-5820
- Department of Bioengineering, University of Utah, Salt Lake City, UT 84112-5820
| | - David W. Grainger
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT 84112-5820
- Department of Bioengineering, University of Utah, Salt Lake City, UT 84112-5820
| | - Lara J. Gamble
- National ESCA and Surface Analysis Center for Biomedical Problems, Box 351750 University of Washington, Seattle, WA 98195-1750
- Department of Bioengineering, Box 351750 University of Washington, Seattle, WA 98195-1750
| | - David G. Castner
- National ESCA and Surface Analysis Center for Biomedical Problems, Box 351750 University of Washington, Seattle, WA 98195-1750
- Department of Bioengineering, Box 351750 University of Washington, Seattle, WA 98195-1750
- Department of Chemical Engineering, Box 351750 University of Washington, Seattle, WA 98195-1750
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72
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Lee CY, Nguyen PCT, Grainger DW, Gamble LJ, Castner DG. Structure and DNA hybridization properties of mixed nucleic acid/maleimide-ethylene glycol monolayers. Anal Chem 2007; 79:4390-400. [PMID: 17492838 PMCID: PMC2518630 DOI: 10.1021/ac0703395] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The surface structure and DNA hybridization performance of thiolated single-strand DNA (HS-ssDNA) covalently attached to a maleimide-ethylene glycol disulfide (MEG) monolayer on gold have been investigated. Monolayer immobilization chemistry and surface coverage of reactive ssDNA probes were studied by X-ray photoelectron spectroscopy and time-of-flight secondary ion mass spectrometry. Orientation of the ssDNA probes was determined by near-edge X-ray absorption fine structure (NEXAFS). Target DNA hybridization on the DNA-MEG probe surfaces was measured by surface plasmon resonance (SPR) to demonstrate the utility of these probe surfaces for detection of DNA targets from both purified target DNA samples and complex biological mixtures such as blood serum. Data from complementary techniques showed that immobilized ssDNA density is strongly dependent on the spotted bulk DNA concentration and buffer ionic strength. Variation of the immobilized ssDNA density had a profound influence on the DNA probe orientation at the surface and subsequent target hybridization efficiency. With increasing surface probe density, NEXAFS polarization dependence results (followed by monitoring the N 1s --> pi* transition) indicate that the immobilized ssDNA molecules reorient toward a more upright position on the MEG monolayer. SPR assays of DNA targets from buffer and serum showed that DNA hybridization efficiency increased with decreasing surface probe density. However, target detection in serum was better on the "high-density" probe surface than on the "high-efficiency" probe surface. The amounts of target detected for both ssDNA surfaces were several orders of magnitude poorer in serum than in purified DNA samples due to nonspecific serum protein adsorption onto the sensing surface.
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Affiliation(s)
- Chi-Ying Lee
- National ESCA and Surface Analysis Center for Biomedical Problems, Box 351750 University of Washington, Seattle, WA 98195-1750
- Departments of Pharmaceutics, University of Utah, Salt Lake City, UT 84112-5820
| | - Phuong-Cac T. Nguyen
- National ESCA and Surface Analysis Center for Biomedical Problems, Box 351750 University of Washington, Seattle, WA 98195-1750
- Departments of Bioengineering and Chemical Engineering, Box 351750 University of Washington, Seattle, WA 98195-1750
| | - David W. Grainger
- Departments of Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT 84112-5820
- Departments of Bioengineering, University of Utah, Salt Lake City, UT 84112-5820
| | - Lara J. Gamble
- National ESCA and Surface Analysis Center for Biomedical Problems, Box 351750 University of Washington, Seattle, WA 98195-1750
- Departments of Bioengineering and Chemical Engineering, Box 351750 University of Washington, Seattle, WA 98195-1750
| | - David G. Castner
- National ESCA and Surface Analysis Center for Biomedical Problems, Box 351750 University of Washington, Seattle, WA 98195-1750
- Departments of Bioengineering and Chemical Engineering, Box 351750 University of Washington, Seattle, WA 98195-1750
- Departments of Pharmaceutics, University of Utah, Salt Lake City, UT 84112-5820
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73
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Abstract
With the growth of the "-omics" such as functional genomics and proteomics, one of the foremost challenges in biotechnologies has become the development of novel methods to monitor biological process and acquire the information of biomolecular interactions in a systematic manner. To fully understand the roles of newly discovered genes or proteins, it is necessary to elucidate the functions of these molecules in their interaction network. Microarray technology is becoming the method of choice for such a task. Although protein microarray can provide a high throughput analytical platform for protein profiling and protein-protein interaction, most of the current reports are limited to labeled detection using fluorescence or radioisotope techniques. These limitations deflate the potential of the method and prevent the technology from being adapted in a broader range of proteomics applications. In recent years, label-free analytical approaches have gone through intensified development and have been coupled successfully with protein microarray. In many examples of label-free study, the microarray has not only offered the high throughput detection in real time, but also provided kinetics information as well as in situ identification. This article reviews the most significant label-free detection methods for microarray technology, including surface plasmon resonance imaging, atomic force microscope, electrochemical impedance spectroscopy and MS and their applications in proteomics research.
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Affiliation(s)
- Xiaobo Yu
- Department of Biochemistry, Beijing Institute of Radiation Medicine, Beijing Proteome Research Center, Beijing, PR China
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Stewart ME, Mack NH, Malyarchuk V, Soares JANT, Lee TW, Gray SK, Nuzzo RG, Rogers JA. Quantitative multispectral biosensing and 1D imaging using quasi-3D plasmonic crystals. Proc Natl Acad Sci U S A 2006; 103:17143-8. [PMID: 17085594 PMCID: PMC1634412 DOI: 10.1073/pnas.0606216103] [Citation(s) in RCA: 294] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2006] [Indexed: 11/18/2022] Open
Abstract
We developed a class of quasi-3D plasmonic crystal that consists of multilayered, regular arrays of subwavelength metal nanostructures. The complex, highly sensitive structure of the optical transmission spectra of these crystals makes them especially well suited for sensing applications. Coupled with quantitative electrodynamics modeling of their optical response, they enable full multiwavelength spectroscopic detection of molecular binding events with sensitivities that correspond to small fractions of a monolayer. The high degree of spatial uniformity of the crystals, formed by a soft nanoimprint technique, provides the ability to image binding events over large areas with micrometer spatial resolution. These features, together with compact form factors, low-cost fabrication procedures, simple readout apparatus, and ability for direct integration into microfluidic networks and arrays, suggest promise for these devices in label-free bioanalytical detection systems.
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Affiliation(s)
- Matthew E. Stewart
- Departments of *Chemistry and
- Frederick Seitz Materials Research Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801; and
| | - Nathan H. Mack
- Departments of *Chemistry and
- Frederick Seitz Materials Research Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801; and
| | - Viktor Malyarchuk
- Materials Science and Engineering
- Frederick Seitz Materials Research Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801; and
| | - Julio A. N. T. Soares
- Frederick Seitz Materials Research Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801; and
| | - Tae-Woo Lee
- Chemistry Division and Center for Nanoscale Materials, Argonne National Laboratory, Argonne, IL 60439
| | - Stephen K. Gray
- Chemistry Division and Center for Nanoscale Materials, Argonne National Laboratory, Argonne, IL 60439
| | - Ralph G. Nuzzo
- Departments of *Chemistry and
- Materials Science and Engineering
- Frederick Seitz Materials Research Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801; and
| | - John A. Rogers
- Departments of *Chemistry and
- Materials Science and Engineering
- Frederick Seitz Materials Research Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801; and
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75
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Boozer C, Kim G, Cong S, Guan H, Londergan T. Looking towards label-free biomolecular interaction analysis in a high-throughput format: a review of new surface plasmon resonance technologies. Curr Opin Biotechnol 2006; 17:400-5. [PMID: 16837183 DOI: 10.1016/j.copbio.2006.06.012] [Citation(s) in RCA: 198] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2006] [Revised: 06/02/2006] [Accepted: 06/30/2006] [Indexed: 11/19/2022]
Abstract
Surface plasmon resonance (SPR) biosensors have enabled a wide range of applications in which researchers can monitor biomolecular interactions in real time. Owing to the fact that SPR can provide affinity and kinetic data, unique features in applications ranging from protein-peptide interaction analysis to cellular ligation experiments have been demonstrated. Although SPR has historically been limited by its throughput, new methods are emerging that allow for the simultaneous analysis of many thousands of interactions. When coupled with new protein array technologies, high-throughput SPR methods give users new and improved methods to analyze pathways, screen drug candidates and monitor protein-protein interactions.
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76
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Yao X, Li X, Toledo F, Zurita-Lopez C, Gutova M, Momand J, Zhou F. Sub-attomole oligonucleotide and p53 cDNA determinations via a high-resolution surface plasmon resonance combined with oligonucleotide-capped gold nanoparticle signal amplification. Anal Biochem 2006; 354:220-8. [PMID: 16762306 DOI: 10.1016/j.ab.2006.04.011] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2006] [Revised: 03/29/2006] [Accepted: 04/07/2006] [Indexed: 11/30/2022]
Abstract
Oligonucleotide (ODN)-capped gold nanoparticles (Au-NPs) were used in a sandwich assay of ODN or polynucleotide by a flow injection surface plasmon resonance (SPR). A carboxylated dextran film was immobilized onto the SPR sensor surface to eliminate nonspecific adsorption of ODN-capped Au-NPs. The tandem use of signal amplification via the adlayer of the ODN-capped Au-NPs and the differential signal detection by the bicell detector on the SPR resulted in a remarkable DNA detection level. A 39-mer target at a quantity as low as 2.1 x 10(-20)mol, corresponding to 1.38 fM in a 15 microl solution, can be measured. To our knowledge, both the concentration and quantity detection levels are the lowest among all the gene analyses conducted with SPR to this point. The method is shown to be reproducible (relative standard deviation values <16%) and to possess high sequence specificity. It is also demonstrated to be viable for sequence-specific p53 cDNA analysis. The successful elimination of nonspecific adsorption of, and the signal amplification by, ODN-capped Au-NPs renders the SPR attractive for cases where the DNA concentration is extremely low and the sample availability is severely limited.
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Affiliation(s)
- Xin Yao
- College of Chemistry and Chemical Engineering, Graduate School, Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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77
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Huang H, Chen Y. Surface Plasmon Resonance Imaging Studies for Proteolytic Hydrolysis of Proteins. CHEM LETT 2006. [DOI: 10.1246/cl.2006.372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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78
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Bally M, Halter M, Vörös J, Grandin HM. Optical microarray biosensing techniques. SURF INTERFACE ANAL 2006. [DOI: 10.1002/sia.2375] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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79
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Möhrle BP, Kumpf M, Gauglitz G. Determination of affinity constants of locked nucleic acid (LNA) and DNA duplex formation using label free sensor technology. Analyst 2005; 130:1634-8. [PMID: 16284662 DOI: 10.1039/b507728a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Locked nucleic acid (LNA) is a nucleic acid analogue containing 2'-O,4'-C-methylene-beta-D-ribofuranosyl nucleotides, which have a bicyclic furanose unit locked in a RNA mimicking sugar conformation. Oligonucleotides containing LNA monomers show an enhanced thermal stability and robustness against nuclease mediated cleavage. Therefore special tailored LNA is a versatile tool for gene array analysis and single nucleotide polymorphism (SNP) analysis. The higher melting temperatures result from a higher affinity between the LNA and its complementary base. This was verified by the determination of the affinity constants of the duplex formation of 3 oligonucleotides: DNA, L-DNA, in which all thymidines are substituted by LNA, and a fully modified LNA, to their complementary DNA strand. Affinity constants were calculated to be 1.5 x 10(9), 4.0 x 10(9) and >10(12) L mol(-1). This was done using the label free and time resolved sensing technology reflectometric interference spectroscopy (RIfS), in an assay format similar to a titration called binding inhibition assay.
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Affiliation(s)
- Bernd P Möhrle
- Eberhard-Karls-University of Tübingen, Institute of Physical and Theoretical Chemistry, Auf der Morgenstelle 8, D-72076 Tübingen, Germany.
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80
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Special-Purpose Modifications and Immobilized Functional Nucleic Acids for Biomolecular Interactions. Top Curr Chem (Cham) 2005. [DOI: 10.1007/b136673] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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81
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Homola J, Vaisocherová H, Dostálek J, Piliarik M. Multi-analyte surface plasmon resonance biosensing. Methods 2005; 37:26-36. [PMID: 16199172 DOI: 10.1016/j.ymeth.2005.05.003] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2005] [Accepted: 05/01/2005] [Indexed: 10/25/2022] Open
Abstract
Surface plasmon resonance (SPR) biosensors are affinity sensing devices exploiting a special mode of electromagnetic field-surface plasmon-polariton-to detect the binding of analyte molecules from a liquid sample to biomolecular recognition elements immobilized on the surface of the sensor. In this paper, we review advances of SPR biosensor technology towards detection systems for the simultaneous detection of multiple analytes (multi-analyte detection). In addition, we report application of a recently developed multichannel SPR sensor based on spectroscopy of surface plasmons and wavelength division multiplexing of sensing channels to multi-analyte detection.
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Affiliation(s)
- Jirí Homola
- Institute of Radio Engineering and Electronics, Academy of Sciences of the Czech Republic, Chaberská 57, 18251 Prague, Czech Republic.
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82
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Piliarik M, Vaisocherová H, Homola J. A new surface plasmon resonance sensor for high-throughput screening applications. Biosens Bioelectron 2005; 20:2104-10. [PMID: 15741081 DOI: 10.1016/j.bios.2004.09.025] [Citation(s) in RCA: 138] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2004] [Revised: 09/20/2004] [Accepted: 09/29/2004] [Indexed: 12/28/2022]
Abstract
We report a new high-throughput surface plasmon resonance (SPR) sensor based on combination of SPR imaging with polarization contrast and a spatially patterned multilayer SPR structure. We demonstrate that this approach offers numerous advantageous features including high-contrast SPR images suitable for automated computer analysis, minimum crosstalk between neighboring sensing channels and inherent compensation for light level fluctuations. Applications of a laboratory prototype of the high-throughput SPR sensor with 108 sensing channels for refractometry and biosensing are described. In refractometric experiments, the noise-limited refractive index resolution of the system has been established to be 3 x 10(-6) refractive index unit (RIU). Experimental data on detection of human choriogonadotropin (hCG) suggest that in conjunction with monoclonal antibodies against hCG, the reported SPR imaging sensor is capable of detecting hCG at concentrations lower than 500 ng/ml.
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Affiliation(s)
- Marek Piliarik
- Institute of Radio Engineering and Electronics, Academy of Sciences of the Czech Republic, Chaberská 57, 18251 Prague, Czech Republic
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83
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Pröll F, Möhrle B, Kumpf M, Gauglitz G. Label-free characterisation of oligonucleotide hybridisation using reflectometric interference spectroscopy. Anal Bioanal Chem 2005; 382:1889-94. [PMID: 15995861 DOI: 10.1007/s00216-005-3301-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2005] [Revised: 04/27/2005] [Accepted: 05/02/2005] [Indexed: 10/25/2022]
Abstract
The potential of a label-free detection method, reflectometric interference spectroscopy (RIfS), for temperature-dependent DNA hybridisation experiments (for example in single nucleotide polymorphism (SNP) analysis) is investigated. Hybridisations of DNA, peptide nucleic acid (PNA), and locked nucleic acid (LNA) to a single stranded DNA were measured for several temperatures, and the melting curves and temperatures were calculated from the changes in optical thickness obtained. These measurements were performed by hybridising surface-immobilised single stranded oligomers with their complementary ssDNA or with ssDNA containing SNPs at different temperatures. DNA was compared to its analogue oligomers PNA and LNA due to their stability against nuclease. A comparison of melting temperatures demonstrated the higher binding affinities of the DNA analogues. Moreover, a continuous melting curve was obtained by first hybridising the functionalised surface with its complementary DNA at room temperature and then heating up in-flow. Measurement of the continuous melting curve was only possible due to the insensitivity of the RIfS method towards temperature changes. This is an advantage over other label-free detection methods, which are based on determining the refractive index.
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Affiliation(s)
- Florian Pröll
- Institute of Physical and Theoretical Chemistry, Eberhard-Karls-University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
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84
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Bujoli B, Lane SM, Nonglaton G, Pipelier M, Léger J, Talham DR, Tellier C. Metal Phosphonates Applied to Biotechnologies: A Novel Approach to Oligonucleotide Microarrays. Chemistry 2005; 11:1980-8. [PMID: 15669062 DOI: 10.1002/chem.200400960] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A new process for preparing oligonucleotide arrays is described that uses surface grafting chemistry which is fundamentally different from the electrostatic adsorption and organic covalent binding methods normally employed. Solid supports are modified with a mixed organic/inorganic zirconium phosphonate monolayer film providing a stable, well-defined interface. Oligonucleotide probes terminated with phosphate are spotted directly on to the zirconated surface forming a covalent linkage. Specific binding of terminal phosphate groups with minimal binding of the internal phosphate diesters has been demonstrated. The mixed organic/inorganic thin films have also been extended for use arraying DNA duplex probes, and therefore represent a viable general approach to DNA-based bioarrays. Ideas for interfacing mixed organic/inorganic interfaces to other bioapplications are also discussed.
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Affiliation(s)
- Bruno Bujoli
- Laboratoire de Synthèse Organique, UMR CNRS 6513 & FR CNRS 2465, 2 Rue de la Houssinière, BP92208, 44322 Nantes Cedex 03, France.
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