Label-Free Sensing on Microarrays.

Microarrays of biological molecules such as DNAs, proteins, carbohydrates, and small molecules provide a high-throughput platform for screening tens of thousands of biomolecular interactions simultaneously, facilitating the functional characterization of these biomolecules in areas of genomics, proteomics, glycomics, and cytomics. Routinely, analysis of binding reactions between solution-phased probes and surface-immobilized targets involves some kinds of fluorescence-based detection methods. Even though these methods have advantages of high sensitivity and wide dynamic range, labeling probes and/or targets inevitably changes their innate properties and in turn affects probe-target interactions in often uncharacterized ways. Therefore, in recent years, various label-free sensing technologies have been developed for characterizing biomolecular interactions in microarray format. These biosensors, to a certain extent, take the place of fluorescent methods by providing a comparable sensitivity as well as retaining the conformational and functional integrality of biomolecules to be investigated. More importantly, some of these biosensors are capable of real-time monitoring probe-target interactions, providing the binding affinities of these reactions. Using label-free biosensors in microarrays has become a current trend in developing high-throughput screening platforms for drug discoveries and applications in all areas of "-omics." This article is aimed to provide principles and recent developments in label-free sensing technologies applicable to microarrays, with special attentions being paid to surface plasmon resonance microscopy and oblique-incidence reflectivity difference microscopy.

[1]  R. Corn,et al.  SPR imaging measurements of 1-D and 2-D DNA microarrays created from microfluidic channels on gold thin films. , 2001, Analytical chemistry.

[2]  Jian-hui Jiang,et al.  A new aptameric biosensor for cocaine based on surface-enhanced Raman scattering spectroscopy. , 2008, Chemistry.

[3]  Gavin MacBeath,et al.  Protein microarrays and proteomics , 2002, Nature Genetics.

[4]  K. Lam,et al.  A novel high-throughput scanning microscope for label-free detection of protein and small-molecule chemical microarrays. , 2008, The Review of scientific instruments.

[5]  Jean-Pierre Vilcot,et al.  Recent advances in the development of graphene-based surface plasmon resonance (SPR) interfaces , 2013, Analytical and Bioanalytical Chemistry.

[6]  Kit S Lam,et al.  Screening small-molecule compound microarrays for protein ligands without fluorescence labeling with a high-throughput scanning microscope. , 2010, Journal of biomedical optics.

[7]  S.X. Wang,et al.  GMR biosensor arrays: a system perspective. , 2010, Biosensors & bioelectronics.

[8]  Kit S. Lam,et al.  Generating Encoded Compound Libraries for Fabricating Microarrays as a High-Throughput Protein Ligand Discovery Platform , 2014 .

[9]  Hiroshi Kano,et al.  Localized surface plasmon microscope with an illumination system employing a radially polarized zeroth-order Bessel beam. , 2009, Optics letters.

[10]  Gil U. Lee,et al.  A biosensor based on magnetoresistance technology. , 1998, Biosensors & bioelectronics.

[11]  Hui-bin Lu,et al.  General theory of optical reflection from a thin film on a solid and its application to heteroepitaxy , 2007 .

[12]  Hsing-Ying Lin,et al.  Tubular waveguide evanescent field absorption biosensor based on particle plasmon resonance for multiplex label-free detection. , 2013, Biosensors & bioelectronics.

[13]  V. Sanz,et al.  A reagentless optical biosensor based on the intrinsic absorption properties of peroxidase. , 2007, Biosensors & bioelectronics.

[14]  R. Azzam,et al.  Ellipsometry and polarized light : North Holland, Amsterdam, 1987 (ISBN 0-444-87016-4). xvii + 539 pp. Price Dfl. 75.00. , 1987 .

[15]  M. Roukes,et al.  Comparative advantages of mechanical biosensors. , 2011, Nature nanotechnology.

[16]  Junji Tominaga,et al.  Label-free methods of reporting biomolecular interactions by optical biosensors. , 2013, The Analyst.

[17]  G. Emmerson,et al.  Label-free monitoring of antibody-antigen interactions using optical microchip biosensors. , 2010, Journal of immunological methods.

[18]  David A. Russell,et al.  Surface plasmon resonance imaging for real-time, label-free analysis of protein interactions with carbohydrate microarrays , 2007, Glycoconjugate Journal.

[19]  Yuliya Semenova,et al.  Hybrid plasmonic biosensor for simultaneous measurement of both thickness and refractive index , 2013 .

[20]  Piet Bergveld,et al.  Thirty years of ISFETOLOGY ☆: What happened in the past 30 years and what may happen in the next 30 years , 2003 .

[21]  J P Landry,et al.  Measuring affinity constants of 1450 monoclonal antibodies to peptide targets with a microarray-based label-free assay platform. , 2015, Journal of immunological methods.

[22]  Patrick Ducoroy,et al.  Immuno-MALDI-MS in Human Plasma and On-Chip Biomarker Characterizations at the Femtomole Level , 2012, Sensors.

[23]  Ye Fang Guest Editor’s Introduction: Label-free optical biosensors to cell biology and drug discovery , 2009, Journal of receptor and signal transduction research.

[24]  C Bechinger,et al.  Imaging of cell/substrate contacts of living cells with surface plasmon resonance microscopy. , 1999, Biophysical journal.

[25]  Gregory W. Auner,et al.  Dual-mode acoustic wave biosensors microarrays , 2003, SPIE Microtechnologies.

[26]  D. Nedelkov,et al.  Development of surface plasmon resonance mass spectrometry array platform. , 2007, Analytical chemistry.

[27]  Per E Andrén,et al.  Coupling surface plasmon resonance to mass spectrometry to discover novel protein–protein interactions , 2009, Nature Protocols.

[28]  Ping Zhang,et al.  Magnetically Labeled GMR Biosensor With a Single Immobilized Ferrimagnetic Particle Agent for the Detection of Extremely Low Concentration of Biomolecules , 2011, IEEE Sensors Journal.

[29]  Ravi F. Saraf,et al.  An approach to sequence DNA without tagging , 2002 .

[30]  Kofi A. A. Makinwa,et al.  A 256 Pixel Magnetoresistive Biosensor Microarray in 0.18 µm CMOS , 2013, IEEE Journal of Solid-State Circuits.

[31]  R. Corn,et al.  Surface plasmon resonance imaging measurements of DNA and RNA hybridization adsorption onto DNA microarrays. , 2001, Analytical chemistry.

[32]  Vikramjeet Singh,et al.  Small molecule microarray screening methodology based on surface plasmon resonance imaging , 2015 .

[33]  Zhiping Lin,et al.  Multiplex spectral surface plasmon resonance imaging (SPRI) sensor based on the polarization control scheme. , 2011, Optics express.

[34]  Kazuki Inamori,et al.  SPR imaging of photo-cross-linked small-molecule arrays on gold. , 2006, Analytical chemistry.

[35]  Xiangdong Zhu,et al.  An ellipsometry-based biosensor for label-free, real-time, and in-situ detection of DNA-DNA and DNA-protein interactions , 2014 .

[36]  Xiangdong Zhu,et al.  Discovering small molecule ligands of vascular endothelial growth factor that block VEGF-KDR binding using label-free microarray-based assays. , 2013, Assay and drug development technologies.

[37]  Yung-Shin Sun,et al.  Ellipsometry-Based Biosensor for Label-Free Detection of Biomolecular Interactions in Microarray Format , 2013 .

[38]  Wojtek Wlodarski,et al.  Acoustic wave sensors: design, sensing mechanisms and applications , 1997 .

[39]  Gary S. Calabrese,et al.  Surface acoustic wave devices as chemical sensors in liquids. Evidence disputing the importance of Rayleigh wave propagation , 1987 .

[40]  Jong Seol Yuk,et al.  Sensitivity enhancement of a grating-based surface plasmon-coupled emission (SPCE) bionsor chip using gold thickness. , 2014, Chemical physics letters.

[41]  Hyunmin Cho,et al.  Nanogap biosensors for electrical and label-free detection of biomolecular interactions , 2009, Nanotechnology.

[42]  Nader Pourmand,et al.  Giant magnetoresistive biochip for DNA detection and HPV genotyping. , 2008, Biosensors & bioelectronics.

[43]  I. Pockrand,et al.  Surface plasma oscillations at silver surfaces with thin transparent and absorbing coatings , 1978 .

[44]  Robert L White,et al.  Multiplex protein assays based on real-time magnetic nanotag sensing , 2008, Proceedings of the National Academy of Sciences.

[45]  J P Landry,et al.  Protein reactions with surface-bound molecular targets detected by oblique-incidence reflectivity difference microscopes. , 2008, Applied optics.

[46]  Andreas Nitsche,et al.  Electrical microarrays for highly sensitive detection of multiplex PCR products from biological agents. , 2009, Biosensors & bioelectronics.

[47]  Min-Gon Kim,et al.  Surface plasmon resonance imaging protein arrays for analysis of triple protein interactions of HPV, E6, E6AP, and p53 , 2006, Proteomics.

[48]  Kai-Yin Lo,et al.  Label-free detection of surface markers on stem cells by oblique-incidence reflectivity difference microscopy. , 2011, BioTechniques.

[49]  Xi Chen,et al.  An optics-based variable-temperature assay system for characterizing thermodynamics of biomolecular reactions on solid support. , 2013, The Review of scientific instruments.

[50]  Xiangdong Zhu Oblique-incidence optical reflectivity difference from a rough film of crystalline material , 2004 .

[51]  Xi Chen,et al.  Characterization of Receptor Binding Profiles of Influenza A Viruses Using An Ellipsometry-Based Label-Free Glycan Microarray Assay Platform , 2015, Biomolecules.

[52]  L. Sousa,et al.  Femtomolar limit of detection with a magnetoresistive biochip. , 2009, Biosensors & bioelectronics.

[53]  A. G. Mendoza-Madrigal,et al.  BIOSENSORES MECÁNICOS EN EL ÁREA BIOLÓGICA Y ALIMENTARIA: UNA REVISIÓN , 2013 .

[54]  Ruedi Aebersold,et al.  Microspotting streptavidin and double-stranded DNA arrays on gold for high-throughput studies of protein-DNA interactions by surface plasmon resonance microscopy. , 2004, Analytical chemistry.

[55]  Carles Cané,et al.  Comparison of two types of acoustic biosensors to detect immunoreactions: Love-wave sensor working in dynamic mode and QCM working in static mode , 2013 .

[56]  Byoungho Lee,et al.  Overview of the Characteristics of Micro- and Nano-Structured Surface Plasmon Resonance Sensors , 2011, Sensors.

[57]  María-Isabel Rocha-Gaso,et al.  Surface Generated Acoustic Wave Biosensors for the Detection of Pathogens: A Review , 2009, Sensors.

[58]  Peng Li,et al.  Label-Free Electrical Biosensor Arrays: A New Challenge for TFT Technology , 2009 .

[59]  Mark E. Thompson,et al.  Label-free, electrical detection of the SARS virus N-protein with nanowire biosensors utilizing antibody mimics as capture probes. , 2009, ACS nano.

[60]  Yung-Shin Sun,et al.  Fluorescent labeling agents change binding profiles of glycan-binding proteins. , 2011, Molecular bioSystems.

[61]  C. Lebrilla,et al.  Use of real-time, label-free analysis in revealing low-affinity binding to blood group antigens by Helicobacter pylori. , 2011, Analytical chemistry.

[62]  Salvador M. Fernandez,et al.  Grating‐coupled surface plasmon resonance: A cell and protein microarray platform , 2005, Proteomics.

[63]  Kit S. Lam,et al.  DETECTION OF FORMATION AND DISINTEGRATION OF MICELLES BY OBLIQUE-INCIDENCE REFLECTIVITY DIFFERENCE MICROSCOPY , 2013 .

[64]  Wolfgang Lindner,et al.  Optical resonance-enhanced absorption-based near-field immunochip biosensor for allergen detection. , 2008, Analytical chemistry.

[65]  Xiangdong Zhu,et al.  AN OBLIQUE-INCIDENCE REFLECTIVITY DIFFERENCE STUDY OF THE DEPENDENCE OF PROBE-TARGET REACTION CONSTANTS ON SURFACE TARGET DENSITY USING STREPTAVIDIN-BIOTIN REACTIONS AS A MODEL , 2013 .

[66]  R. Schasfoort,et al.  Angle-scanning SPR imaging for detection of biomolecular interactions on microarrays. , 2008, Biosensors & bioelectronics.

[67]  Xiangdong Zhu,et al.  Comparison of two optical techniques for label-free detection of biomolecular microarrays on solids , 2006 .

[68]  Bastian E. Rapp,et al.  Surface acoustic wave biosensors: a review , 2008, Analytical and bioanalytical chemistry.

[69]  Zhang Yingying,et al.  Determination of effective complex refractive index of a turbid liquid with surface plasmon resonance phase detection. , 2009, Applied optics.

[70]  Malcolm Buckle,et al.  Rapid coupling of Surface Plasmon Resonance (SPR and SPRi) and ProteinChip™ based mass spectrometry for the identification of proteins in nucleoprotein interactions , 2007, Nucleic acids research.

[71]  J P Landry,et al.  Label-free detection of microarrays of biomolecules by oblique-incidence reflectivity difference microscopy. , 2004, Optics letters.

[72]  Xiliang Luo,et al.  Electrical biosensors and the label free detection of protein disease biomarkers. , 2013, Chemical Society reviews.

[73]  Christopher Lausted,et al.  Parallel microfluidic surface plasmon resonance imaging arrays. , 2010, Lab on a chip.

[74]  Wenchao Zhou,et al.  Gold nanoparticle amplified optical microfiber evanescent wave absorption biosensor for cancer biomarker detection in serum. , 2014, Talanta.

[75]  R. Schasfoort,et al.  Biomolecular interaction monitoring of autoantibodies by scanning surface plasmon resonance microarray imaging. , 2007, Journal of the American Chemical Society.

[76]  Matthew R Fleming,et al.  Use of label-free optical biosensors to detect modulation of potassium channels by G-protein coupled receptors. , 2014, Journal of visualized experiments : JoVE.

[77]  V. Konopsky,et al.  A biosensor based on photonic crystal surface waves with an independent registration of the liquid refractive index. , 2010, Biosensors & bioelectronics.

[78]  Jong Seol Yuk,et al.  Highly sensitive grating coupler-based surface plasmon-coupled emission (SPCE) biosensor for immunoassay. , 2013, The Analyst.

[79]  G Gauglitz,et al.  Affinity detection of low molecular weight analytes. , 1996, Analytical chemistry.

[80]  Kenzo Maehashi,et al.  Label-Free Electrical Detection Using Carbon Nanotube-Based Biosensors , 2009, Sensors.

[81]  David A. Russell,et al.  Surface plasmon resonance imaging of glycoarrays identifies novel and unnatural carbohydrate-based ligands for potential ricin sensor development , 2011 .

[82]  T Neumann,et al.  SPR-based fragment screening: advantages and applications. , 2007, Current topics in medicinal chemistry.

[83]  R. Corn,et al.  Surface plasmon resonance imaging measurements of antibody arrays for the multiplexed detection of low molecular weight protein biomarkers. , 2006, Analytical chemistry.

[84]  Laura L Kiessling,et al.  Surface plasmon resonance imaging studies of protein-carbohydrate interactions. , 2003, Journal of the American Chemical Society.

[85]  Zheng Zheng,et al.  Stable and sensitive silver surface plasmon resonance imaging sensor using trilayered metallic structures. , 2014, Analytical chemistry.

[86]  Xiangdong Zhu,et al.  Simultaneous measurement of 10,000 protein-ligand affinity constants using microarray-based kinetic constant assays. , 2012, Assay and drug development technologies.

[87]  R. Karlsson,et al.  Kinetic analysis of monoclonal antibody-antigen interactions with a new biosensor based analytical system. , 1991, Journal of immunological methods.

[88]  J P Landry,et al.  Macromolecular scaffolds for immobilizing small molecule microarrays in label-free detection of protein-ligand interactions on solid support. , 2009, Analytical chemistry.

[89]  Sung June Kim,et al.  Design optimization of nano-grating surface plasmon resonance sensors. , 2006, Optics express.

[90]  J P Landry,et al.  Incidence-angle dependence of optical reflectivity difference from an ultrathin film on solid surface. , 2006, Optics letters.

[91]  M. Famulok,et al.  A Love-wave biosensor using nucleic acids as ligands , 2004 .

[92]  James F Rusling,et al.  Ultrasensitive carbohydrate-peptide SPR imaging microarray for diagnosing IgE mediated peanut allergy. , 2014, The Analyst.

[93]  Kit S. Lam,et al.  Oblique-incidence reflectivity difference microscope for label-free high-throughput detection of biochemical reactions in a microarray format. , 2007 .

[94]  Jinsong Zhu Retraction: 3D small molecule microarray with enhanced sensitivity and immobilization capacity monitored by surface plasmon resonance imaging , 2014 .

[95]  M. Mascini,et al.  Surface plasmon resonance imaging for affinity-based biosensors. , 2010, Biosensors & bioelectronics.

[96]  A. Hillier,et al.  Surface plasmon resonance imaging of biomolecular interactions on a grating-based sensor array. , 2006, Analytical chemistry.

[97]  Ruedi Aebersold,et al.  Parallel, quantitative measurement of protein binding to a 120-element double-stranded DNA array in real time using surface plasmon resonance microscopy. , 2004, Analytical chemistry.

[98]  Chuan He,et al.  Design of an emission ratiometric biosensor from MerR family proteins: a sensitive and selective sensor for Hg2+. , 2007, Journal of the American Chemical Society.

[99]  Timothy Londergan,et al.  Looking towards label-free biomolecular interaction analysis in a high-throughput format: a review of new surface plasmon resonance technologies. , 2006, Current opinion in biotechnology.

[100]  Dafu Cui,et al.  A hard-soft microfluidic-based biosensor flow cell for SPR imaging application. , 2010, Biosensors & bioelectronics.

[101]  Philippe M. Fauchet,et al.  Electrical Porous Silicon Microarray for dna Hybridization Detection , 2003 .

[102]  Yung-Shin Sun,et al.  OPTICAL BIOSENSORS FOR LABEL-FREE DETECTION OF BIOMOLECULAR INTERACTIONS , 2014 .

[103]  Hamid Latifi,et al.  Measuring bacterial growth by refractive index tapered fiber optic biosensor. , 2010, Journal of photochemistry and photobiology. B, Biology.

[104]  Y.S. Sun,et al.  Effect of fluorescently labeling protein probes on kinetics of protein-ligand reactions , 2008, 2008 Conference on Lasers and Electro-Optics and 2008 Conference on Quantum Electronics and Laser Science.

[105]  S. Haxha,et al.  Design and optimization of a novel surface plasmon resonance biosensor based on Otto configuration. , 2009, Optics express.

[106]  Gibum Kim,et al.  SPR microscopy and its applications to high-throughput analyses of biomolecular binding events and their kinetics. , 2007, Biomaterials.