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Gin A, Nguyen PD, Melzer JE, Li C, Strzelinski H, Liggett SB, Su J. Label-free, real-time monitoring of membrane binding events at zeptomolar concentrations using frequency-locked optical microresonators. Nat Commun 2024; 15:7445. [PMID: 39198447 PMCID: PMC11358326 DOI: 10.1038/s41467-024-51320-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 08/06/2024] [Indexed: 09/01/2024] Open
Abstract
G-protein coupled receptors help regulate cellular function and communication, and are targets of small molecule drug discovery efforts. Conventional techniques to probe these interactions require labels and large amounts of receptor to achieve satisfactory sensitivity. Here, we use frequency-locked optical microtoroids for label-free characterization of membrane interactions in vitro at zeptomolar concentrations for the kappa opioid receptor and its native agonist dynorphin A 1-13, as well as big dynorphin (dynorphin A and dynorphin B) using a supported biomimetic membrane. The measured affinity of the agonist dynorphin A 1-13 to the κ-opioid receptor was also measured and found to be 3.1 nM. Radioligand assays revealed a dissociation constant in agreement with this value (1.1 nM). The limit of detection for the κOR/DynA 1-13 was calculated as 180 zM. The binding of Cholera Toxin B-monosialotetrahexosyl ganglioside was also monitored in real-time and an equilibrium dissociation constant of 1.53 nM was found. Our biosensing platform provides a method for highly sensitive real-time characterization of membrane embedded protein binding kinetics that is rapid and label-free, for drug discovery and toxin screening among other applications.
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Affiliation(s)
- Adley Gin
- Wyant College of Optical Sciences, The University of Arizona, Tucson, AZ, 85721, USA
| | - Phuong-Diem Nguyen
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ, 85721, USA
| | - Jeffrey E Melzer
- Wyant College of Optical Sciences, The University of Arizona, Tucson, AZ, 85721, USA
| | - Cheng Li
- Wyant College of Optical Sciences, The University of Arizona, Tucson, AZ, 85721, USA
| | - Hannah Strzelinski
- Department of Medicine, University of South Florida Morsani College of Medicine, Tampa, FL, 33612, USA
| | - Stephen B Liggett
- Department of Medicine, University of South Florida Morsani College of Medicine, Tampa, FL, 33612, USA
| | - Judith Su
- Wyant College of Optical Sciences, The University of Arizona, Tucson, AZ, 85721, USA.
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ, 85721, USA.
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2
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Gin A, Nguyen PD, Melzer JE, Li C, Strzelinski H, Liggett SB, Su J. Label-free, real-time monitoring of membrane binding events at zeptomolar concentrations using frequency-locked optical microresonators. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.20.558657. [PMID: 37786702 PMCID: PMC10541581 DOI: 10.1101/2023.09.20.558657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Binding events to elements of the cell membrane act as receptors which regulate cellular function and communication and are the targets of many small molecule drug discovery efforts for agonists and antagonists. Conventional techniques to probe these interactions generally require labels and large amounts of receptor to achieve satisfactory sensitivity. Whispering gallery mode microtoroid optical resonators have demonstrated sensitivity to detect single-molecule binding events. Here, we demonstrate the use of frequency-locked optical microtoroids for characterization of membrane interactions in vitro at zeptomolar concentrations using a supported biomimetic membrane. Arrays of microtoroids were produced using photolithography and subsequently modified with a biomimetic membrane, providing high quality (Q) factors (> 10 6 ) in aqueous environments. Fluorescent recovery after photobleaching (FRAP) experiments confirmed the retained fluidity of the microtoroid supported-lipid membrane with a diffusion coefficient of 3.38 ± 0.26 μm 2 ⋅ s - 1 . Utilizing this frequency-locked membrane-on-a-chip model combined with auto-balanced detection and non-linear post-processing techniques, we demonstrate zeptomolar detection levels The binding of Cholera Toxin B- monosialotetrahexosyl ganglioside (GM1) was monitored in real-time, with an apparent equilibrium dissociation constant k d = 1.53 nM . The measured affiny of the agonist dynorphin A 1-13 to the κ -opioid receptor revealed a k d = 3.1 nM using the same approach. Radioligand binding competition with dynorphin A 1-13 revealed a k d in agreement (1.1 nM) with the unlabeled method. The biosensing platform reported herein provides a highly sensitive real-time characterization of membrane embedded protein binding kinetics, that is rapid and label-free, for toxin screening and drug discovery, among other applications.
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Affiliation(s)
- Adley Gin
- Wyant College of Optical Sciences, The University of Arizona, Tucson, AZ 85721
| | - Phuong-Diem Nguyen
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721
| | - Jeffrey E. Melzer
- Wyant College of Optical Sciences, The University of Arizona, Tucson, AZ 85721
| | - Cheng Li
- Wyant College of Optical Sciences, The University of Arizona, Tucson, AZ 85721
| | - Hannah Strzelinski
- Department of Medicine, University of South Florida Morsani College of Medicine, Tampa, FL 33612
| | - Stephen B. Liggett
- Department of Medicine, University of South Florida Morsani College of Medicine, Tampa, FL 33612
| | - Judith Su
- Wyant College of Optical Sciences, The University of Arizona, Tucson, AZ 85721
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721
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3
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Puumala LS, Grist SM, Morales JM, Bickford JR, Chrostowski L, Shekhar S, Cheung KC. Biofunctionalization of Multiplexed Silicon Photonic Biosensors. BIOSENSORS 2022; 13:bios13010053. [PMID: 36671887 PMCID: PMC9855810 DOI: 10.3390/bios13010053] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/10/2022] [Accepted: 12/23/2022] [Indexed: 05/28/2023]
Abstract
Silicon photonic (SiP) sensors offer a promising platform for robust and low-cost decentralized diagnostics due to their high scalability, low limit of detection, and ability to integrate multiple sensors for multiplexed analyte detection. Their CMOS-compatible fabrication enables chip-scale miniaturization, high scalability, and low-cost mass production. Sensitive, specific detection with silicon photonic sensors is afforded through biofunctionalization of the sensor surface; consequently, this functionalization chemistry is inextricably linked to sensor performance. In this review, we first highlight the biofunctionalization needs for SiP biosensors, including sensitivity, specificity, cost, shelf-stability, and replicability and establish a set of performance criteria. We then benchmark biofunctionalization strategies for SiP biosensors against these criteria, organizing the review around three key aspects: bioreceptor selection, immobilization strategies, and patterning techniques. First, we evaluate bioreceptors, including antibodies, aptamers, nucleic acid probes, molecularly imprinted polymers, peptides, glycans, and lectins. We then compare adsorption, bioaffinity, and covalent chemistries for immobilizing bioreceptors on SiP surfaces. Finally, we compare biopatterning techniques for spatially controlling and multiplexing the biofunctionalization of SiP sensors, including microcontact printing, pin- and pipette-based spotting, microfluidic patterning in channels, inkjet printing, and microfluidic probes.
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Affiliation(s)
- Lauren S. Puumala
- School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
- Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Samantha M. Grist
- School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
- Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
- Dream Photonics Inc., Vancouver, BC V6T 0A7, Canada
| | - Jennifer M. Morales
- Army Research Laboratory, US Army Combat Capabilities Development Command, 2800 Powder Mill Rd., Adelphi, MD 20783, USA
| | - Justin R. Bickford
- Army Research Laboratory, US Army Combat Capabilities Development Command, 2800 Powder Mill Rd., Adelphi, MD 20783, USA
| | - Lukas Chrostowski
- Dream Photonics Inc., Vancouver, BC V6T 0A7, Canada
- Department of Electrical and Computer Engineering, University of British Columbia, 2332 Main Mall, Vancouver, BC V6T 1Z4, Canada
- Stewart Blusson Quantum Matter Institute, University of British Columbia, 2355 East Mall, Vancouver, BC V6T 1Z4, Canada
| | - Sudip Shekhar
- Dream Photonics Inc., Vancouver, BC V6T 0A7, Canada
- Department of Electrical and Computer Engineering, University of British Columbia, 2332 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | - Karen C. Cheung
- School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
- Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
- Department of Electrical and Computer Engineering, University of British Columbia, 2332 Main Mall, Vancouver, BC V6T 1Z4, Canada
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4
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Bläsi J, Gerken M. Multiplex optical biosensors based on multi-pinhole interferometry. BIOMEDICAL OPTICS EXPRESS 2021; 12:4265-4275. [PMID: 34457413 PMCID: PMC8367262 DOI: 10.1364/boe.426991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 05/10/2023]
Abstract
The application of new sensor technologies for frequent biomarker monitoring in combination with the leverage of artificial intelligence has great potential to improve the design and safety of health care. With current research efforts, the screening of tens of biomarkers at the point of care and immediate adjustment of therapy is coming within reach. Here we introduce an optical multiplexing approach based on multi-pinhole interference providing inherent differential referencing between a multitude of measurement fields on a surface. A theoretical study of an 11-plex and a 54-plex design is complemented with the experimental demonstration of the technique for a 3-field refractive index measurements and detection of human α-thrombin.
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Impact of Silanization Parameters and Antibody Immobilization Strategy on Binding Capacity of Photonic Ring Resonators. SENSORS 2020; 20:s20113163. [PMID: 32498466 PMCID: PMC7309079 DOI: 10.3390/s20113163] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/29/2020] [Accepted: 05/31/2020] [Indexed: 12/27/2022]
Abstract
Ring resonator-based biosensors have found widespread application as the transducing principle in “lab-on-a-chip” platforms due to their sensitivity, small size and support for multiplexed sensing. Their sensitivity is, however, not inherently selective towards biomarkers, and surface functionalization of the sensors is key in transforming the sensitivity to be specific for a particular biomarker. There is currently no consensus on process parameters for optimized functionalization of these sensors. Moreover, the procedures are typically optimized on flat silicon oxide substrates as test systems prior to applying the procedure to the actual sensor. Here we present what is, to our knowledge, the first comparison of optimization of silanization on flat silicon oxide substrates to results of protein capture on sensors where all parameters of two conjugation protocols are tested on both platforms. The conjugation protocols differed in the chosen silanization solvents and protein immobilization strategy. The data show that selection of acetic acid as the solvent in the silanization step generally yields a higher protein binding capacity for C-reactive protein (CRP) onto anti-CRP functionalized ring resonator sensors than using ethanol as the solvent. Furthermore, using the BS3 linker resulted in more consistent protein binding capacity across the silanization parameters tested. Overall, the data indicate that selection of parameters in the silanization and immobilization protocols harbor potential for improved biosensor binding capacity and should therefore be included as an essential part of the biosensor development process.
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6
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Orlet JD, Bailey RC. Silicon Photonic Microring Resonator Arrays as a Universal Detector for Capillary Electrophoresis. Anal Chem 2020; 92:2331-2338. [PMID: 31829562 DOI: 10.1021/acs.analchem.9b05271] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Electrophoretic separations conventionally rely on chromogenic, fluorogenic, or redox properties for analyte detection that, in many instances, involve chemical modification of samples prior to analysis. For analytes natively lacking chemical signatures, refractive index-based measurements are appealing as a method to detect these molecules without pretreatment. Microring resonators are a type of whispering gallery mode sensor capable of detecting bulk changes in refractive index. Here, we demonstrate the use of silicon photonic microring resonator arrays as a postcolumn detector for capillary electrophoresis. In this approach, we establish the universal detection capabilities of microrings through calibration with analytes lacking unique spectral signatures. Separations of small molecule mixtures are demonstrated using capillary zone electrophoresis. For these separations, the microring resonators maintain a linear response over several orders of magnitude in concentration for three candidate small molecules. Successful separation of three sugars with direct detection is also demonstrated. We further present the successful separation and detection of three model proteins, exemplifying the promise of microring resonators arrays as a biocompatible detector for capillary electrophoresis. Additionally, the spatially offset, array-based nature of the sensing platform enables real-time analysis of analyte mobility and performance characterization-a combination that is not typically provided using single-point detectors.
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Affiliation(s)
- John D Orlet
- Department of Chemistry , University of Michigan , 930 North University Avenue , Ann Arbor , Michigan 48109 , United States
| | - Ryan C Bailey
- Department of Chemistry , University of Michigan , 930 North University Avenue , Ann Arbor , Michigan 48109 , United States
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7
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Photonic ring resonance is a versatile platform for performing multiplex immunoassays in real time. J Immunol Methods 2017; 448:34-43. [DOI: 10.1016/j.jim.2017.05.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 05/07/2017] [Accepted: 05/11/2017] [Indexed: 12/17/2022]
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8
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Muehl EM, Gajsiewicz JM, Medfisch SM, Wiersma ZSB, Morrissey JH, Bailey RC. Multiplexed silicon photonic sensor arrays enable facile characterization of coagulation protein binding to nanodiscs with variable lipid content. J Biol Chem 2017; 292:16249-16256. [PMID: 28801460 DOI: 10.1074/jbc.m117.800938] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/11/2017] [Indexed: 11/06/2022] Open
Abstract
Interactions of soluble proteins with the cell membrane are critical within the blood coagulation cascade. Of particular interest are the interactions of γ-carboxyglutamic acid-rich domain-containing clotting proteins with lipids. Variability among conventional analytical methods presents challenges for comparing clotting protein-lipid interactions. Most previous studies have investigated only a single clotting protein and lipid composition and have yielded widely different binding constants. Herein, we demonstrate that a combination of lipid bilayer nanodiscs and a multiplexed silicon photonic analysis technology enables high-throughput probing of many protein-lipid interactions among blood-clotting proteins. This approach allowed direct comparison of the binding constants of prothrombin, factor X, activated factor VII, and activated protein C to seven different binary lipid compositions. In a single experiment, the binding constants of one protein interacting with all lipid compositions were simultaneously determined. A simple surface regeneration then facilitated similar binding measurements for three other coagulation proteins. As expected, our results indicated that all proteins exhibit tighter binding (lower Kd ) as the proportion of anionic lipid increases. Interestingly, at high proportions of phosphatidylserine, the Kd values of all four proteins began to converge. We also found that although koff values for all four proteins followed trends similar to those observed for the Kd values, the variation among the proteins was much lower, indicating that much of the variation came from the kinetic binding (kon) of the proteins. These findings indicate that the combination of silicon photonic microring resonator arrays and nanodiscs enables rapid interrogation of biomolecular binding interactions at model cell membrane interfaces.
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Affiliation(s)
| | - Joshua M Gajsiewicz
- Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801 and
| | - Sara M Medfisch
- the Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | | | - James H Morrissey
- Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801 and
| | - Ryan C Bailey
- From the Departments of Chemistry and .,the Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
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9
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Pasquardini L, Pancheri L, Potrich C, Ferri A, Piemonte C, Lunelli L, Napione L, Comunanza V, Alvaro M, Vanzetti L, Bussolino F, Pederzolli C. SPAD aptasensor for the detection of circulating protein biomarkers. Biosens Bioelectron 2015; 68:500-507. [PMID: 25636022 DOI: 10.1016/j.bios.2015.01.042] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/08/2015] [Accepted: 01/19/2015] [Indexed: 10/24/2022]
Abstract
The need for decentralized clinical tests together with the concept of time and cost saving are pushing the development of portable, miniaturized, compact biosensors with diagnostic and prognostic purpose. Here, we propose an innovative detection system based on a Single Photon Avalanche Diode (SPAD) with high sensitivity and low noise, crucial features for an efficient chemiluminescence biosensor. The SPAD detector, having 60 µm diameter, has a Photon Detection Efficiency higher than 55% at 425 nm and a Dark Count Rate lower than 100 Hz at room temperature. Our design allows a good optical coupling efficiency between sample and detector. A specific biofunctional surface was implemented taking advantage of aptamers, short DNA sequences having high selectivity and affinity toward their targets. We successfully detected physiological levels of Vascular Endothelial Growth Factor (VEGF), a circulating protein biomarker highly correlated with cancer. The SPAD aptasensor showed a Limit of Detection (LoD) in the pM range, stability (up to 42 days) and re-usability (up to seven cycles). This compact biosensor is therefore a promising step toward the actual use of portable microdevices in diagnostics.
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Affiliation(s)
- Laura Pasquardini
- Fondazione Bruno Kessler, Laboratory of Biomolecular Sequence and Structure Analysis for Health, via Sommarive 18, 38123 Povo (Trento), Italy.
| | - Lucio Pancheri
- DII -Department of Industrial Engineering, University of Trento, via Sommarive 9, 38123 Povo (Trento), Italy
| | - Cristina Potrich
- Fondazione Bruno Kessler, Laboratory of Biomolecular Sequence and Structure Analysis for Health, via Sommarive 18, 38123 Povo (Trento), Italy; CNR-Institute of Biophysics, Unit at Trento, via alla Cascata 56, 38123 Povo (Trento), Italy
| | - Alessandro Ferri
- Fondazione Bruno Kessler, Center for Materials and Microsystem (CMM), via Sommarive 18, 38123 Povo (Trento), Italy
| | - Claudio Piemonte
- Fondazione Bruno Kessler, Center for Materials and Microsystem (CMM), via Sommarive 18, 38123 Povo (Trento), Italy
| | - Lorenzo Lunelli
- Fondazione Bruno Kessler, Laboratory of Biomolecular Sequence and Structure Analysis for Health, via Sommarive 18, 38123 Povo (Trento), Italy; CNR-Institute of Biophysics, Unit at Trento, via alla Cascata 56, 38123 Povo (Trento), Italy
| | - Lucia Napione
- Department of Oncology, University of Torino and Institute for Cancer Research at Candiolo (IRCC), Strada Provinciale 142, 10060 Candiolo (Torino), Italy
| | - Valentina Comunanza
- Department of Oncology, University of Torino and Institute for Cancer Research at Candiolo (IRCC), Strada Provinciale 142, 10060 Candiolo (Torino), Italy
| | - Maria Alvaro
- Department of Oncology, University of Torino and Institute for Cancer Research at Candiolo (IRCC), Strada Provinciale 142, 10060 Candiolo (Torino), Italy
| | - Lia Vanzetti
- Fondazione Bruno Kessler, Center for Materials and Microsystem (CMM), via Sommarive 18, 38123 Povo (Trento), Italy
| | - Federico Bussolino
- Department of Oncology, University of Torino and Institute for Cancer Research at Candiolo (IRCC), Strada Provinciale 142, 10060 Candiolo (Torino), Italy
| | - Cecilia Pederzolli
- Fondazione Bruno Kessler, Laboratory of Biomolecular Sequence and Structure Analysis for Health, via Sommarive 18, 38123 Povo (Trento), Italy
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Biomolecular analysis with microring resonators: applications in multiplexed diagnostics and interaction screening. Curr Opin Chem Biol 2013; 17:818-26. [PMID: 23871688 DOI: 10.1016/j.cbpa.2013.06.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 06/06/2013] [Accepted: 06/14/2013] [Indexed: 02/06/2023]
Abstract
Microring optical resonators are a promising class of sensor whose value in bioanalytical applications has only begun to be explored. Utilized in the telecommunication industry for signal processing applications, microring resonators have more recently been re-tasked for biosensing because of their scalability, sensitivity, and versatility. Their sensing modality arises from light/matter interactions--light propagating through the microring and the resultant evanescent field extending beyond the structure is sensitive to the refractive index of the local environment, which modulates resonant wavelength of light supported by the cavity. This sensing capability has recently been utilized for the detection of numerous biological targets including proteins, nucleic acids, viruses, and small molecules. Herein we highlight some of the most exciting recent uses of this technology for biosensing applications, with an eye towards future developments in the field.
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11
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Kuhnline Sloan CD, Marty MT, Sligar SG, Bailey RC. Interfacing lipid bilayer nanodiscs and silicon photonic sensor arrays for multiplexed protein-lipid and protein-membrane protein interaction screening. Anal Chem 2013; 85:2970-6. [PMID: 23425255 PMCID: PMC3600637 DOI: 10.1021/ac3037359] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Soluble proteins are key mediators of many biochemical signaling pathways via direct interaction with the lipid bilayer and via membrane-bound receptors. Components of the cell membrane are involved in many important biological processes, including viral infection, blood clotting, and signal transduction, and as such, they are common targets of therapeutic agents. Therefore, the development of analytical approaches to study interactions at the cell membrane is of critical importance. Herein, we integrate two key technologies, silicon photonic microring resonator arrays and phospholipid bilayer nanodiscs, which together allow multiplexed screening of soluble protein interactions with lipid and membrane-embedded targets. Microring resonator arrays are an intrinsically multiplexable, label-free analysis platform that has previously been applied to studying protein-protein, protein-nucleic acid, and nucleic acid-nucleic acid interactions. Nanodiscs are protein-stabilized lipid assemblies that represent a convenient construct to mimic the native phospholipid bilayer, investigate the effects of membrane composition, and solubilize membrane-embedded targets. Exploiting the natural affinity of nanodisc-supported lipid bilayers for oxide-passivated silicon, we assembled single and multiplex sensor arrays via direct physisorption, characterizing electrostatic effects on the nanodisc attachment. Using model systems, we demonstrate the applicability of this platform for the parallel screening of protein interactions with nanodisc-embedded lipids, glycolipids, and membrane proteins.
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Affiliation(s)
| | - Michael T. Marty
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801
| | - Stephen G. Sligar
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801
| | - Ryan C. Bailey
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801
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12
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Bañuls MJ, Puchades R, Maquieira Á. Chemical surface modifications for the development of silicon-based label-free integrated optical (IO) biosensors: a review. Anal Chim Acta 2013; 777:1-16. [PMID: 23622959 DOI: 10.1016/j.aca.2013.01.025] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 01/03/2013] [Accepted: 01/04/2013] [Indexed: 12/29/2022]
Abstract
Increasing interest has been paid to label-free biosensors in recent years. Among them, refractive index (RI) optical biosensors enable high density and the chip-scale integration of optical components. This makes them more appealing to help develop lab-on-a-chip devices. Today, many RI integrated optical (IO) devices are made using silicon-based materials. A key issue in their development is the biofunctionalization of sensing surfaces because they provide a specific, sensitive response to the analyte of interest. This review critically discusses the biofunctionalization procedures, assay formats and characterization techniques employed in setting up IO biosensors. In addition, it provides the most relevant results obtained from using these devices for real sample biosensing. Finally, an overview of the most promising future developments in the fields of chemical surface modification and capture agent attachment for IO biosensors follows.
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Affiliation(s)
- María-José Bañuls
- Centro de Reconocimiento Molecular y Desarrollo Tecnológico, Departamento de Química, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain.
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13
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Marty MT, Sloan CDK, Bailey RC, Sligar SG. Nonlinear analyte concentration gradients for one-step kinetic analysis employing optical microring resonators. Anal Chem 2012; 84:5556-64. [PMID: 22686186 DOI: 10.1021/ac300478f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Conventional methods to probe the binding kinetics of macromolecules at biosensor surfaces employ a stepwise titration of analyte concentrations and measure the association and dissociation to the immobilized ligand at each concentration level. It has previously been shown that kinetic rates can be measured in a single step by monitoring binding as the analyte concentration increases over time in a linear gradient. We report here the application of nonlinear analyte concentration gradients for determining kinetic rates and equilibrium binding affinities in a single experiment. A versatile nonlinear gradient maker is presented, which is easily applied to microfluidic systems. Simulations validate that accurate kinetic rates can be extracted for a wide range of association and dissociation rates, gradient slopes, and curvatures, and with models for mass transport. The nonlinear analyte gradient method is demonstrated with a silicon photonic microring resonator platform to measure prostate specific antigen-antibody binding kinetics.
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Affiliation(s)
- Michael T Marty
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
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14
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Shang J, Cheng F, Dubey M, Kaplan JM, Rawal M, Jiang X, Newburg DS, Sullivan PA, Andrade RB, Ratner DM. An organophosphonate strategy for functionalizing silicon photonic biosensors. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:3338-44. [PMID: 22220731 PMCID: PMC3291497 DOI: 10.1021/la2043153] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Silicon photonic microring resonators have established their potential for label-free and low-cost biosensing applications. However, the long-term performance of this optical sensing platform requires robust surface modification and biofunctionalization. Herein, we demonstrate a conjugation strategy based on an organophosphonate surface coating and vinyl sulfone linker to biofunctionalize silicon resonators for biomolecular sensing. To validate this method, a series of glycans, including carbohydrates and glycoconjugates, were immobilized on divinyl sulfone (DVS)/organophosphonate-modified microrings and used to characterize carbohydrate-protein and norovirus particle interactions. This biofunctional platform was able to orthogonally detect multiple specific carbohydrate-protein interactions simultaneously. Additionally, the platform was capable of reproducible binding after multiple regenerations by high-salt, high-pH, or low-pH solutions and after 1 month storage in ambient conditions. This remarkable stability and durability of the organophosphonate immobilization strategy will facilitate the application of silicon microring resonators in various sensing conditions, prolong their lifetime, and minimize the cost for storage and delivery; these characteristics are requisite for developing biosensors for point-of-care and distributed diagnostics and other biomedical applications. In addition, the platform demonstrated its ability to characterize carbohydrate-mediated host-virus interactions, providing a facile method for discovering new antiviral agents to prevent infectious disease.
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Affiliation(s)
- Jing Shang
- Department of Bioengineering, University of Washington, 3720 15th AVE NE, Seattle, WA, 98195, USA
| | - Fang Cheng
- Department of Bioengineering, University of Washington, 3720 15th AVE NE, Seattle, WA, 98195, USA
| | - Manish Dubey
- National ESCA and Surface Analysis Center for Biomedical Problems, University of Washington, Box 351750, Seattle, WA, 98195, USA
| | - Justin M. Kaplan
- Department of Chemistry, Temple University, Beury Hall 130, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Meghana Rawal
- Department of Chemistry, University of Washington, 36 Bagley Hall, Seattle, WA, 98195, USA
| | - Xi Jiang
- Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, Ohio, 45229-3039, USA
| | - David S. Newburg
- Program in Glycobiology, Higgins Hall 140 Commonwealth Avenue, Boston College, Chestnut Hill, MA, 02467-3961, USA
| | - Philip A. Sullivan
- Department of Chemistry, University of Washington, 36 Bagley Hall, Seattle, WA, 98195, USA
| | - Rodrigo B. Andrade
- Department of Chemistry, Temple University, Beury Hall 130, 1901 N. 13th Street, Philadelphia, PA, 19122, USA
| | - Daniel M. Ratner
- Department of Bioengineering, University of Washington, 3720 15th AVE NE, Seattle, WA, 98195, USA
- Corresponding author. . Tel: +1 206 543 1071. Fax: +1 206 685 3925. Address: Department of Bioengineering, University of Washington, 3720 15th AVE NE, Seattle, WA, 98195, USA
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15
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Affiliation(s)
- Matthew S. Luchansky
- 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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16
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Limpoco FT, Bailey RC. Real-time monitoring of surface-initiated atom transfer radical polymerization using silicon photonic microring resonators: implications for combinatorial screening of polymer brush growth conditions. J Am Chem Soc 2011; 133:14864-7. [PMID: 21899288 DOI: 10.1021/ja205358g] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We directly monitor in parallel and in real time the temporal profiles of polymer brushes simultaneously grown via multiple ATRP reaction conditions on a single substrate using arrays of silicon photonic microring resonators. In addition to probing relative polymerization rates, we show the ability to evaluate the dynamic properties of the in situ grown polymers. This presents a powerful new platform for studying modified interfaces that may allow for the combinatorial optimization of surface-initiated polymerization conditions.
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Affiliation(s)
- F Ted Limpoco
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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17
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Qavi AJ, Kindt JT, Gleeson MA, Bailey RC. Anti-DNA:RNA antibodies and silicon photonic microring resonators: increased sensitivity for multiplexed microRNA detection. Anal Chem 2011; 83:5949-56. [PMID: 21711056 PMCID: PMC3146633 DOI: 10.1021/ac201340s] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In this paper, we present a method for the sensitive detection of microRNAs (miRNAs) utilizing an antibody that specifically recognizes DNA:RNA heteroduplexes and a silicon photonic microring resonator array transduction platform. Microring resonator arrays are covalently functionalized with DNA capture probes that are complementary to solution phase miRNA targets. Following hybridization on the sensor, the anti-DNA:RNA antibody is introduced and binds selectively to the heteroduplexes, giving a larger signal than the original miRNA hybridization due to the increased mass of the antibody, as compared to the 22-mer oligoribonucleotide. Furthermore, the secondary recognition step is performed in neat buffer solution and at relatively higher antibody concentrations, facilitating the detection of miRNAs of interest. The intrinsic sensitivity of the microring resonator platform coupled with the amplification provided by the anti-DNA:RNA antibodies allows for the detection of microRNAs at concentrations as low as 10 pM (350 amol). The simplicity and sequence generality of this amplification method position it as a promising tool for high-throughput, multiplexed miRNA analysis as well as a range of other RNA based detection applications.
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Affiliation(s)
- Abraham J. Qavi
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Illinois, 61801
| | - Jared T. Kindt
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Illinois, 61801
| | - Martin A. Gleeson
- Genalyte, Inc., 11099 North Torrey Pines Road, Suite 170, La Jolla, California, 92037
| | - Ryan C. Bailey
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Illinois, 61801
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18
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Washburn AL, Gomez J, Bailey RC. DNA-encoding to improve performance and allow parallel evaluation of the binding characteristics of multiple antibodies in a surface-bound immunoassay format. Anal Chem 2011; 83:3572-80. [PMID: 21438633 PMCID: PMC3098033 DOI: 10.1021/ac200317z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
High affinity capture agents against protein targets are essential components for immunoassays, regardless of specific analysis format. Here, we describe the use of DNA-encoded antibodies for rapidly screening the kinetic and equilibrium binding properties of twelve commercial antibodies in a parallel analysis format using a multiplexed array of microring optical resonators. We show that DNA-encoding offers advantages in terms of antigen binding capacity, compared to covalently tethered antibodies; we also demonstrate that this linkage modality facilitates the rapid self-assembly of multiplexed arrays on account of complementarity between the DNA sequences on the antibodies and sensor array, respectively. Furthermore, DNA-encoded antibodies also allow for sensor array regeneration and reprogramming, as chaotropic agents can be used to disrupt the DNA-DNA duplexes that link the capture agents to the sensor without harming the underlying DNA on the surface, which can subsequently be reloaded with antibodies either targeting the same or different antigens.
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Affiliation(s)
- Adam L. Washburn
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Joseph Gomez
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Ryan C. Bailey
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
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19
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Washburn AL, Luchansky MS, McClellan MS, Bailey RC. Label-free, multiplexed biomolecular analysis using arrays of silicon photonic microring resonators. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.proeng.2011.12.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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