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Georgiou CD. Functional Properties of Amino Acid Side Chains as Biomarkers of Extraterrestrial Life. ASTROBIOLOGY 2018; 18:1479-1496. [PMID: 30129781 PMCID: PMC6211371 DOI: 10.1089/ast.2018.1868] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/10/2018] [Indexed: 05/22/2023]
Abstract
The present study proposes to search our solar system (Mars, Enceladus, Europa) for patterns of organic molecules that are universally associated with biological functions and structures. The functions are primarily catalytic because life could only have originated within volume/space-constrained compartments containing chemical reactions catalyzed by certain polymers. The proposed molecular structures are specific groups in the side chains of amino acids with the highest catalytic propensities related to life on Earth, that is, those that most frequently participate as key catalytic groups in the active sites of enzymes such as imidazole, thiol, guanidinium, amide, and carboxyl. Alternatively, these or other catalytic groups can be searched for on non-amino-acid organic molecules, which can be tested for certain hydrolytic catalytic activities. The first scenario assumes that life may have originated in a similar manner as the terrestrial set of α-amino acids, while the second scenario does not set such a requirement. From the catalytic propensity perspective proposed in the first scenario, life must have invented amino acids with high catalytic propensity (His, Cys, Arg) in order to overcome, and be complemented by, the low catalytic propensity of the initially available abiogenic amino acids. The abiogenic and the metabolically invented amino acids with the lowest catalytic propensity can also serve as markers of extraterrestrial life when searching for patterns on the basis of the following functional propensities related to protein secondary/quaternary structure: (1) amino acids that are able to form α-helical intramembrane peptide domains, which can serve as primitive transporters in protocell membrane bilayers and catalysts of simple biochemical reactions; (2) amino acids that tend to accumulate in extremophile proteins of Earth and possibly extraterrestrial life. The catalytic/structural functional propensity approach offers a new perspective in the search for extraterrestrial life and could help unify previous amino acid-based approaches.
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Liang L, Jin L, Ran Y, Sun LP, Guan BO. Fiber Light-Coupled Optofluidic Waveguide (FLOW) Immunosensor for Highly Sensitive Detection of p53 Protein. Anal Chem 2018; 90:10851-10857. [PMID: 30141911 DOI: 10.1021/acs.analchem.8b02123] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Highly sensitive detection of molecular tumor markers is essential for biomarker-based cancer diagnostics. In this work, we showcase the implementation of fiber light-coupled optofluidic waveguide (FLOW) immunosensor for the detection of p53 protein, a typical tumor marker. The FLOW consists of a liquid-core capillary and an accompanying optical fiber, which allows evanescent interaction between light and microfluidic sample. Molecular binding at internal surface of the capillary induces a response in wavelength shift of the transmission spectrum in the optical fiber. To enable highly sensitive molecular detection, the evanescent-wave interaction has been strengthened by enlarging shape factor R via fine geometry control. The proposed FLOW immunosensor works with flowing microfluid, which increases the surface molecular coverage and improves the detection limit. As a result, the FLOW immunosensor presents a log-linear response to the tumor protein at concentrations ranging from 10 fg/mL up to 10 ng/mL. In addition, the nonspecifically adsorbed molecules can be effectively removed by the fluid at an optimal flow rate, which benefits the accuracy of the measurement. Tested in serum samples, the FLOW successfully maintains its sensitivity and specificity on p53 protein, making it suitable for diagnostics applications.
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Affiliation(s)
- Lili Liang
- Guangdong Provincial Key Laboratory of Optical Fiber Sensing and Communication, Institute of Photonics Technology , Jinan University , Guangzhou 510632 , China
| | - Long Jin
- Guangdong Provincial Key Laboratory of Optical Fiber Sensing and Communication, Institute of Photonics Technology , Jinan University , Guangzhou 510632 , China
| | - Yang Ran
- Guangdong Provincial Key Laboratory of Optical Fiber Sensing and Communication, Institute of Photonics Technology , Jinan University , Guangzhou 510632 , China.,Department of Biomedical Engineering , Duke University , Durham , 27708 , United States
| | - Li-Peng Sun
- Guangdong Provincial Key Laboratory of Optical Fiber Sensing and Communication, Institute of Photonics Technology , Jinan University , Guangzhou 510632 , China
| | - Bai-Ou Guan
- Guangdong Provincial Key Laboratory of Optical Fiber Sensing and Communication, Institute of Photonics Technology , Jinan University , Guangzhou 510632 , China
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3
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Ozcelik D, Stott MA, Parks JW, Black JA, Wall TA, Hawkins AR, Schmidt H. Signal-to-noise Enhancement in Optical Detection of Single Viruses with Multi-spot Excitation. IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS : A PUBLICATION OF THE IEEE LASERS AND ELECTRO-OPTICS SOCIETY 2016; 22:4402406. [PMID: 27524876 PMCID: PMC4978512 DOI: 10.1109/jstqe.2015.2503321] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
We present fluorescence detection of single H1N1 viruses with enhanced signal to noise ratio (SNR) achieved by multi-spot excitation in liquid-core anti-resonant reflecting optical waveguides (ARROWs). Solid-core Y-splitting ARROW waveguides are fabricated orthogonal to the liquid-core section of the chip, creating multiple excitation spots for the analyte. We derive expressions for the SNR increase after signal processing, and analyze its dependence on signal levels and spot number. Very good agreement between theoretical calculations and experimental results is found. SNR enhancements up to 5x104 are demonstrated.
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Affiliation(s)
- Damla Ozcelik
- School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064 USA
| | - Matthew A. Stott
- Department of Electrical and Computer Engineering, Brigham Young University, Provo, UT 84602 USA
| | - Joshua W. Parks
- School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064 USA
| | - Jennifer A. Black
- School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064 USA
| | - Thomas A. Wall
- Department of Electrical and Computer Engineering, Brigham Young University, Provo, UT 84602 USA
| | - Aaron R. Hawkins
- Department of Electrical and Computer Engineering, Brigham Young University, Provo, UT 84602 USA
| | - Holger Schmidt
- School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064 USA
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4
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Testa G, Persichetti G, Bernini R. Liquid Core ARROW Waveguides: A Promising Photonic Structure for Integrated Optofluidic Microsensors. MICROMACHINES 2016; 7:mi7030047. [PMID: 30407419 PMCID: PMC6190334 DOI: 10.3390/mi7030047] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 02/29/2016] [Accepted: 03/07/2016] [Indexed: 12/11/2022]
Abstract
In this paper, we introduce a liquid core antiresonant reflecting optical waveguide (ARROW) as a novel optofluidic device that can be used to create innovative and highly functional microsensors. Liquid core ARROWs, with their dual ability to guide the light and the fluids in the same microchannel, have shown great potential as an optofluidic tool for quantitative spectroscopic analysis. ARROWs feature a planar architecture and, hence, are particularly attractive for chip scale integrated system. Step by step, several improvements have been made in recent years towards the implementation of these waveguides in a complete on-chip system for highly-sensitive detection down to the single molecule level. We review applications of liquid ARROWs for fluids sensing and discuss recent results and trends in the developments and applications of liquid ARROW in biomedical and biochemical research. The results outlined show that the strong light matter interaction occurring in the optofluidic channel of an ARROW and the versatility offered by the fabrication methods makes these waveguides a very promising building block for optofluidic sensor development.
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Affiliation(s)
- Genni Testa
- Istituto per il Rilevamento Elettromagnetico dell'Ambiente, Consiglio Nazionale delle Ricerche (IREA-CNR), Via Diocleziano 328, 80124 Naples, Italy.
| | - Gianluca Persichetti
- Istituto per il Rilevamento Elettromagnetico dell'Ambiente, Consiglio Nazionale delle Ricerche (IREA-CNR), Via Diocleziano 328, 80124 Naples, Italy.
| | - Romeo Bernini
- Istituto per il Rilevamento Elettromagnetico dell'Ambiente, Consiglio Nazionale delle Ricerche (IREA-CNR), Via Diocleziano 328, 80124 Naples, Italy.
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5
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Liu S, Hawkins AR, Schmidt H. Optofluidic devices with integrated solid-state nanopores. Mikrochim Acta 2016; 183:1275-1287. [PMID: 27046940 DOI: 10.1007/s00604-016-1758-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This review (with 90 refs.) covers the state of the art in optofluidic devices with integrated solid-state nanopores for use in detection and sensing. Following an introduction into principles of optofluidics and solid-state nanopore technology, we discuss features of solid-state nanopore based assays using optofluidics. This includes the incorporation of solid-state nanopores into optofluidic platforms based on liquid-core anti-resonant reflecting optical waveguides (ARROWs), methods for their fabrication, aspects of single particle detection and particle manipulation. We then describe the new functionalities provided by solid-state nanopores integrated into optofluidic chips, in particular acting as smart gates for correlated electro-optical detection and discrimination of nanoparticles. This enables the identification of viruses and λ-DNA, particle trajectory simulations, enhancing sensitivity by tuning the shape of nanopores. The review concludes with a summary and an outlook.
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Affiliation(s)
- Shuo Liu
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Aaron R Hawkins
- ECEn Department, 459 Clyde Building, Brigham Young University, Provo, UT 84602, USA
| | - Holger Schmidt
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
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6
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Liu S, Wall TA, Ozcelik D, Parks JW, Hawkins AR, Schmidt H. Electro-optical detection of single λ-DNA. Chem Commun (Camb) 2015; 51:2084-7. [PMID: 25533516 PMCID: PMC4304986 DOI: 10.1039/c4cc07591a] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Single λ-DNA molecules are detected on a nanopore-gated optofluidic chip electrically and optically. Statistical variations in the single particle trajectories are used to predict the intensity distribution of the fluorescence signals.
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Affiliation(s)
- Shuo Liu
- School of Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
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7
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Coskun AF, Cetin AE, Galarreta BC, Alvarez DA, Altug H, Ozcan A. Lensfree optofluidic plasmonic sensor for real-time and label-free monitoring of molecular binding events over a wide field-of-view. Sci Rep 2014; 4:6789. [PMID: 25346102 DOI: 10.1038/lsa.2014.3] [Citation(s) in RCA: 159] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 08/21/2013] [Accepted: 10/06/2014] [Indexed: 05/28/2023] Open
Abstract
We demonstrate a high-throughput biosensing device that utilizes microfluidics based plasmonic microarrays incorporated with dual-color on-chip imaging toward real-time and label-free monitoring of biomolecular interactions over a wide field-of-view of >20 mm(2). Weighing 40 grams with 8.8 cm in height, this biosensor utilizes an opto-electronic imager chip to record the diffraction patterns of plasmonic nanoapertures embedded within microfluidic channels, enabling real-time analyte exchange. This plasmonic chip is simultaneously illuminated by two different light-emitting-diodes that are spectrally located at the right and left sides of the plasmonic resonance mode, yielding two different diffraction patterns for each nanoaperture array. Refractive index changes of the medium surrounding the near-field of the nanostructures, e.g., due to molecular binding events, induce a frequency shift in the plasmonic modes of the nanoaperture array, causing a signal enhancement in one of the diffraction patterns while suppressing the other. Based on ratiometric analysis of these diffraction images acquired at the detector-array, we demonstrate the proof-of-concept of this biosensor by monitoring in real-time biomolecular interactions of protein A/G with immunoglobulin G (IgG) antibody. For high-throughput on-chip fabrication of these biosensors, we also introduce a deep ultra-violet lithography technique to simultaneously pattern thousands of plasmonic arrays in a cost-effective manner.
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Affiliation(s)
- Ahmet F Coskun
- 1] Departments of Electrical Engineering and Bioengineering, University of California, Los Angeles (UCLA), CA 90095, USA [2] Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125
| | - Arif E Cetin
- 1] Department of Electrical and Computer Engineering, Boston University, MA 02215, USA [2] Bioengineering Department, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne CH-1015 Switzerland
| | - Betty C Galarreta
- 1] Department of Electrical and Computer Engineering, Boston University, MA 02215, USA [2] Pontificia Universidad Catolica del Peru, Departamento de Ciencias-Quimica, Avenida Universitaria 1801, Lima 32, Peru
| | | | - Hatice Altug
- 1] Department of Electrical and Computer Engineering, Boston University, MA 02215, USA [2] Bioengineering Department, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne CH-1015 Switzerland
| | - Aydogan Ozcan
- 1] Departments of Electrical Engineering and Bioengineering, University of California, Los Angeles (UCLA), CA 90095, USA [2] California NanoSystems Institute, University of California, Los Angeles (UCLA), CA 90095, USA
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8
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Parks JW, Olson MA, Kim J, Ozcelik D, Cai H, Carrion R, Patterson JL, Mathies RA, Hawkins AR, Schmidt H. Integration of programmable microfluidics and on-chip fluorescence detection for biosensing applications. BIOMICROFLUIDICS 2014; 8:054111. [PMID: 25584111 PMCID: PMC4290670 DOI: 10.1063/1.4897226] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 09/24/2014] [Indexed: 05/05/2023]
Abstract
We describe the integration of an actively controlled programmable microfluidic sample processor with on-chip optical fluorescence detection to create a single, hybrid sensor system. An array of lifting gate microvalves (automaton) is fabricated with soft lithography, which is reconfigurably joined to a liquid-core, anti-resonant reflecting optical waveguide (ARROW) silicon chip fabricated with conventional microfabrication. In the automaton, various sample handling steps such as mixing, transporting, splitting, isolating, and storing are achieved rapidly and precisely to detect viral nucleic acid targets, while the optofluidic chip provides single particle detection sensitivity using integrated optics. Specifically, an assay for detection of viral nucleic acid targets is implemented. Labeled target nucleic acids are first captured and isolated on magnetic microbeads in the automaton, followed by optical detection of single beads on the ARROW chip. The combination of automated microfluidic sample preparation and highly sensitive optical detection opens possibilities for portable instruments for point-of-use analysis of minute, low concentration biological samples.
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Affiliation(s)
- J W Parks
- School of Engineering, University of California Santa Cruz , Santa Cruz, California 95064, USA
| | - M A Olson
- Department of Electrical and Computer Engineering, Brigham Young University , Provo, Utah 84602, USA
| | | | - D Ozcelik
- School of Engineering, University of California Santa Cruz , Santa Cruz, California 95064, USA
| | - H Cai
- School of Engineering, University of California Santa Cruz , Santa Cruz, California 95064, USA
| | - R Carrion
- Department of Virology and Immunology, Texas Biomedical Research Institute , 7620 NW Loop 410, San Antonio, Texas 78227, USA
| | - J L Patterson
- Department of Virology and Immunology, Texas Biomedical Research Institute , 7620 NW Loop 410, San Antonio, Texas 78227, USA
| | - R A Mathies
- Department of Chemistry, University of California Berkeley , Berkeley, California 94720, USA
| | - A R Hawkins
- Department of Electrical and Computer Engineering, Brigham Young University , Provo, Utah 84602, USA
| | - H Schmidt
- School of Engineering, University of California Santa Cruz , Santa Cruz, California 95064, USA
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9
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Coupling of fluorescence correlation spectroscopy with capillary and microchannel analytical systems and its applications. Electrophoresis 2014; 35:2267-78. [DOI: 10.1002/elps.201300648] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 03/10/2014] [Accepted: 03/21/2014] [Indexed: 02/03/2023]
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10
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Parks JW, Cai H, Zempoaltecatl L, Yuzvinsky TD, Leake K, Hawkins AR, Schmidt H. Hybrid optofluidic integration. LAB ON A CHIP 2013; 13:4118-23. [PMID: 23969694 PMCID: PMC3818110 DOI: 10.1039/c3lc50818h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Complete integration of microfluidic and optical functions in a single lab-on-chip device is one goal of optofluidics. Here, we demonstrate the hybrid integration of a PDMS-based fluid handling layer with a silicon-based optical detection layer in a single optofluidic system. The optical layer consists of a liquid-core antiresonant reflecting optical waveguide (ARROW) chip that is capable of single particle detection and interfacing with optical fiber. Integrated devices are reconfigurable and able to sustain high pressures despite the small dimensions of the liquid-core waveguide channels. We show the combination of salient sample preparation capabilities-particle mixing, distribution, and filtering-with single particle fluorescence detection. Specifically, we demonstrate fluorescent labelling of λ-DNA, followed by flow-based single-molecule detection on a single device. This points the way towards amplification-free detection of nucleic acids with low-complexity biological sample preparation on a chip.
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Affiliation(s)
- Joshua W Parks
- School of Engineering, University of CA Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
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11
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Ozcelik D, Phillips BS, Parks JW, Measor P, Gulbransen D, Hawkins AR, Schmidt H. Dual-core optofluidic chip for independent particle detection and tunable spectral filtering. LAB ON A CHIP 2012; 12:3728-3733. [PMID: 22864667 DOI: 10.1039/c2lc40700k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We present the first integration of fluidically tunable filters with a separate particle detection channel on a single planar, optofluidic chip. Two optically connected, but fluidically isolated liquid-core antiresonant reflecting optical waveguide (ARROW) segments serve as analyte and spectral filter sections, respectively. Ultrasensitive detection of fluorescent nanobeads with high signal-to-noise ratio provided by a fluidically tuned excitation notch filter is demonstrated. In addition, reconfigurable filter response is demonstrated using both core index tuning and bulk liquid tuning. Notch filters with 43 dB rejection ratio and a record 90 nm tuning range are implemented by using different mixtures of ethylene glycol and water in the filter section. Moreover, absorber dyes and liquids with pH-dependent transmission in the filter channel provide additional spectral control independent of the waveguide response. Using both core index and pH control, independent filter tuning at multiple wavelengths is demonstrated for the first time. This extensive on-chip control over spectral filtering as one of the fundamental components of optical particle detection techniques offers significant advantages in terms of compactness, cost, and simplicity, and opens new opportunities for waveguide-based optofluidic analysis systems.
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Affiliation(s)
- Damla Ozcelik
- School of Engineering, University of CA Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
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12
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Chang TY, Huang M, Yanik AA, Tsai HY, Shi P, Aksu S, Yanik MF, Altug H. Large-scale plasmonic microarrays for label-free high-throughput screening. LAB ON A CHIP 2011; 11:3596-602. [PMID: 21901194 DOI: 10.1039/c1lc20475k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Microarrays allowing simultaneous analysis of thousands of parameters can significantly accelerate screening of large libraries of pharmaceutical compounds and biomolecular interactions. For large-scale studies on diverse biomedical samples, reliable, label-free, and high-content microarrays are needed. In this work, using large-area plasmonic nanohole arrays, we demonstrate for the first time a large-scale label-free microarray technology with over one million sensors on a single microscope slide. A dual-color filter imaging method is introduced to dramatically increase the accuracy, reliability, and signal-to-noise ratio of the sensors in a highly multiplexed manner. We used our technology to quantitatively measure protein-protein interactions. Our platform, which is highly compatible with the current microarray scanning systems can enable a powerful screening technology and facilitate diagnosis and treatment of diseases.
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Affiliation(s)
- Tsung-Yao Chang
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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13
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Rudenko MI, Holmes MR, Ermolenko DN, Lunt EJ, Gerhardt S, Noller HF, Deamer DW, Hawkins A, Schmidt H. Controlled gating and electrical detection of single 50S ribosomal subunits through a solid-state nanopore in a microfluidic chip. Biosens Bioelectron 2011; 29:34-9. [DOI: 10.1016/j.bios.2011.07.047] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2011] [Revised: 07/17/2011] [Accepted: 07/19/2011] [Indexed: 10/17/2022]
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14
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Fan X, White IM. Optofluidic Microsystems for Chemical and Biological Analysis. NATURE PHOTONICS 2011; 5:591-597. [PMID: 22059090 PMCID: PMC3207487 DOI: 10.1038/nphoton.2011.206] [Citation(s) in RCA: 399] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Optofluidics - the synergistic integration of photonics and microfluidics - has recently emerged as a new analytical field that provides a number of unique characteristics for enhanced sensing performance and simplification of microsystems. In this review, we describe various optofluidic architectures developed in the past five years, emphasize the mechanisms by which optofluidics enhances bio/chemical analysis capabilities, including sensing and the precise control of biological micro/nanoparticles, and envision new research directions to which optofluidics leads.
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Affiliation(s)
- Xudong Fan
- Biomedical Engineering Department, University of Michigan, Ann Arbor, MI 48109, USA
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15
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Vasdekis AE, Laporte GP. Enhancing single molecule imaging in optofluidics and microfluidics. Int J Mol Sci 2011; 12:5135-56. [PMID: 21954349 PMCID: PMC3179156 DOI: 10.3390/ijms12085135] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 05/23/2011] [Accepted: 07/25/2011] [Indexed: 12/25/2022] Open
Abstract
Microfluidics and optofluidics have revolutionized high-throughput analysis and chemical synthesis over the past decade. Single molecule imaging has witnessed similar growth, due to its capacity to reveal heterogeneities at high spatial and temporal resolutions. However, both resolution types are dependent on the signal to noise ratio (SNR) of the image. In this paper, we review how the SNR can be enhanced in optofluidics and microfluidics. Starting with optofluidics, we outline integrated photonic structures that increase the signal emitted by single chromophores and minimize the excitation volume. Turning then to microfluidics, we review the compatible functionalization strategies that reduce noise stemming from non-specific interactions and architectures that minimize bleaching and blinking.
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Affiliation(s)
- Andreas E. Vasdekis
- Optics Laboratory, School of Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland; E-Mail:
| | - Gregoire P.J. Laporte
- Optics Laboratory, School of Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland; E-Mail:
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16
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Chen A, Eberle MM, Lunt EJ, Liu S, Leake K, Rudenko MI, Hawkins AR, Schmidt H. Dual-color fluorescence cross-correlation spectroscopy on a planar optofluidic chip. LAB ON A CHIP 2011; 11:1502-1506. [PMID: 21340094 DOI: 10.1039/c0lc00401d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Fluorescence cross-correlation spectroscopy (FCCS) is a highly sensitive fluorescence technique with distinct advantages in many bioanalytical applications involving interaction and binding of multiple components. Due to the use of multiple beams, bulk optical FCCS setups require delicate and complex alignment procedures. We demonstrate the first implementation of dual-color FCCS on a planar, integrated optofluidic chip based on liquid-core waveguides that can guide liquid and light simultaneously. In this configuration, the excitation beams are delivered in predefined locations and automatically aligned within the excitation waveguides. We implement two canonical applications of FCCS in the optofluidic lab-on-chip environment: particle colocalization and binding/dissociation dynamics. Colocalization is demonstrated in the detection and discrimination of single-color and double-color fluorescently labeled nanobeads. FCCS in combination with fluorescence resonance energy transfer (FRET) is used to detect the denaturation process of double-stranded DNA at nanomolar concentration.
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Affiliation(s)
- A Chen
- School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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17
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Measor P, Phillips BS, Chen A, Hawkins AR, Schmidt H. Tailorable integrated optofluidic filters for biomolecular detection. LAB ON A CHIP 2011; 11:899-904. [PMID: 21221449 PMCID: PMC3064503 DOI: 10.1039/c0lc00496k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Spectral filtering is an essential component of biophotonic methods such as fluorescence and Raman spectroscopy. Predominantly utilized in bulk microscopy, filters require efficient and selective transmission or removal of signals at one or more wavelength bands. However, towards highly sensitive and fully self-contained lab-on-chip systems, the integration of spectral filters is an essential step. In this work, a novel optofluidic solution is presented in which a liquid-core optical waveguide both transports sample analytes and acts as an efficient filter for advanced spectroscopy. To this end, the wavelength dependent nature of interference-based antiresonant reflecting optical waveguide technology is exploited. An extinction of 37 dB, a narrow rejection band of only 2.5 nm and a free spectral range of 76 nm using three specifically designed dielectric layers are demonstrated. These parameters result in an 18.4-fold increase in the signal-to-noise ratio for on-chip fluorescence detection. In addition, liquid-core waveguide filters with three operating wavelengths were designed for Förster resonance energy transfer detection and demonstrated using doubly labeled oligonucleotides. Incorporation of high-performance spectral processing illustrates the power of the optofluidic concept where fluidic channels also perform optical functions to create innovative and highly integrated lab-on-chip devices.
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Affiliation(s)
- Philip Measor
- School of Engineering, University of CA Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | | | - Aiqing Chen
- School of Engineering, University of CA Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Aaron R. Hawkins
- ECEn Department, Brigham Young University, Provo, UT, 84602, USA
| | - Holger Schmidt
- School of Engineering, University of CA Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
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18
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Holmes M, Keeley J, Hurd K, Schmidt H, Hawkins A. Optimized piranha etching process for SU8-based MEMS and MOEMS construction. JOURNAL OF MICROMECHANICS AND MICROENGINEERING : STRUCTURES, DEVICES, AND SYSTEMS 2010; 20:1-8. [PMID: 21423840 PMCID: PMC3059272 DOI: 10.1088/0960-1317/20/11/115008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We demonstrate the optimization of the concentration, temperature and cycling of a piranha (H(2)O(2):H(2)SO(4)) mixture that produces high yields while quickly etching hollow structures made using a highly crosslinked SU8 polymer sacrificial core. The effects of the piranha mixture on the thickness, refractive index and roughness of common micro-electromechanical systems and micro-opto-electromechanical systems fabrication materials (SiN, SiO(2) and Si) were determined. The effectiveness of the optimal piranha mixture was demonstrated in the construction of hollow anti-resonant reflecting optical waveguides.
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Affiliation(s)
- Matthew Holmes
- ECE Department, Brigham Young University, 459 Clyde Building, Provo, UT 84602, USA
| | - Jared Keeley
- ECE Department, Brigham Young University, 459 Clyde Building, Provo, UT 84602, USA
| | - Katherine Hurd
- ECE Department, Brigham Young University, 459 Clyde Building, Provo, UT 84602, USA
| | - Holger Schmidt
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Aaron Hawkins
- ECE Department, Brigham Young University, 459 Clyde Building, Provo, UT 84602, USA
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Oita I, Halewyck H, Thys B, Rombaut B, Vander Heyden Y, Mangelings D. Microfluidics in macro-biomolecules analysis: macro inside in a nano world. Anal Bioanal Chem 2010; 398:239-64. [PMID: 20549494 PMCID: PMC7079953 DOI: 10.1007/s00216-010-3857-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2010] [Revised: 05/13/2010] [Accepted: 05/18/2010] [Indexed: 12/26/2022]
Abstract
Use of microfluidic devices in the life sciences and medicine has created the possibility of performing investigations at the molecular level. Moreover, microfluidic devices are also part of the technological framework that has enabled a new type of scientific information to be revealed, i.e. that based on intensive screening of complete sets of gene and protein sequences. A deeper bioanalytical perspective may provide quantitative and qualitative tools, enabling study of various diseases and, eventually, may offer support for the development of accurate and reliable methods for clinical assessment. This would open the way to molecule-based diagnostics, i.e. establish accurate diagnosis and disease prognosis based on identification and/or quantification of biomacromolecules, for example proteins or nucleic acids. Finally, the development of disposable and portable devices for molecule-based diagnosis would provide the perfect translation of the science behind life-science research into practical applications dedicated to patients and health practitioners. This review provides an analytical perspective of the impact of microfluidics on the detection and characterization of bio-macromolecules involved in pathological processes. The main features of molecule-based diagnostics and the specific requirements for the diagnostic devices are discussed. Further, the techniques currently used for testing bio-macromolecules for potential diagnostic purposes are identified, emphasizing the newest developments. Subsequently, the challenges of this type of application and the status of commercially available devices are highlighted, and future trends are noted.
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Affiliation(s)
- Iuliana Oita
- Department of Analytical Chemistry and Pharmaceutical Technology, Center for Pharmaceutical Research (CePhaR), Vrije Universiteit Brussel-VUB, Laarbeeklaan 103, Brussels, 1090 Belgium
| | - Hadewych Halewyck
- Department of Pharmaceutical Biotechnology & Molecular Biology, Center for Pharmaceutical Research (CePhaR), Vrije Universiteit Brussel-VUB, Laarbeeklaan 103, Brussels, 1090 Belgium
| | - Bert Thys
- Department of Pharmaceutical Biotechnology & Molecular Biology, Center for Pharmaceutical Research (CePhaR), Vrije Universiteit Brussel-VUB, Laarbeeklaan 103, Brussels, 1090 Belgium
| | - Bart Rombaut
- Department of Pharmaceutical Biotechnology & Molecular Biology, Center for Pharmaceutical Research (CePhaR), Vrije Universiteit Brussel-VUB, Laarbeeklaan 103, Brussels, 1090 Belgium
| | - Yvan Vander Heyden
- Department of Analytical Chemistry and Pharmaceutical Technology, Center for Pharmaceutical Research (CePhaR), Vrije Universiteit Brussel-VUB, Laarbeeklaan 103, Brussels, 1090 Belgium
| | - Debby Mangelings
- Department of Analytical Chemistry and Pharmaceutical Technology, Center for Pharmaceutical Research (CePhaR), Vrije Universiteit Brussel-VUB, Laarbeeklaan 103, Brussels, 1090 Belgium
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Lunt EJ, Wu B, Keeley JM, Measor P, Schmidt H, Hawkins AR. Hollow ARROW Waveguides on Self-Aligned Pedestals for Improved Geometry and Transmission. IEEE PHOTONICS TECHNOLOGY LETTERS : A PUBLICATION OF THE IEEE LASER AND ELECTRO-OPTICS SOCIETY 2010; 22:1147-1149. [PMID: 21423839 PMCID: PMC3059265 DOI: 10.1109/lpt.2010.2051145] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Micrometer-sized hollow antiresonant reflecting optical waveguides on silicon substrates have been previously demonstrated with liquid and gas-filled cores. Previous designs have nonideal geometries, with nonuniform lateral layers around the hollow core, resulting in higher loss than could potentially be achieved. A new design and fabrication process has been developed involving hollow waveguide fabrication on a self-aligned pedestal (SAP) using anisotropic plasma etching. With the SAP structure, the hollow core is surrounded by uniform layers and a terminal layer of air on three sides, resulting in air-core waveguide loss of 1.54 cm(-1) at 785 nm and high fabrication yield.
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Affiliation(s)
- Evan J. Lunt
- Department of Electrical and Computer Engineering, Brigham Young University, Provo, UT 84602 USA
| | - Bin Wu
- School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064 USA
| | - Jared M. Keeley
- Department of Electrical and Computer Engineering, Brigham Young University, Provo, UT 84602 USA
| | - Philip Measor
- School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064 USA
| | - Holger Schmidt
- School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064 USA
| | - Aaron R. Hawkins
- Department of Electrical and Computer Engineering, Brigham Young University, Provo, UT 84602 USA
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Phillips BS, Measor P, Zhao Y, Schmidt H, Hawkins AR. Optofluidic notch filter integration by lift-off of thin films. OPTICS EXPRESS 2010; 18:4790-5. [PMID: 20389492 PMCID: PMC3378351 DOI: 10.1364/oe.18.004790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Optofluidic platforms used for biomolecular detection require spectral filtering for distinguishing analyte signals from unwanted background. Towards a fully integrated platform, an on-chip filter is required. Selective deposition of dielectric thin films on an optofluidic sensor based on antiresonant reflecting optical waveguide (ARROW) technology provides the means for localized, on-chip optical filtering. We present a lift-off technique, compatible with thin-film processing including plasma-enhanced chemical vapor and sputtering deposition. The resulting optofluidic notch filters exhibited a 20 dB rejection with linewidths as low as 20 nm for approximately 1 cm long chips consisting of liquid-core and solid-core waveguides.
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Affiliation(s)
- Brian S. Phillips
- ECEn Department, Brigham Young University, 459 Clyde Building, Provo, UT 84602,
USA
| | - Philip Measor
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95604,
USA
| | - Yue Zhao
- ECEn Department, Brigham Young University, 459 Clyde Building, Provo, UT 84602,
USA
| | - Holger Schmidt
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95604,
USA
| | - Aaron R. Hawkins
- ECEn Department, Brigham Young University, 459 Clyde Building, Provo, UT 84602,
USA
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Holmes MR, Shang T, Hawkins AR, Rudenko M, Measor P, Schmidt H. Micropore and nanopore fabrication in hollow antiresonant reflecting optical waveguides. JOURNAL OF MICRO/NANOLITHOGRAPHY, MEMS, AND MOEMS : JM3 2010; 9:23004. [PMID: 21922035 PMCID: PMC3171701 DOI: 10.1117/1.3378152] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We demonstrate the fabrication of micropore and nanopore features in hollow antiresonant reflecting optical waveguides to create an electrical and optical analysis platform that can size select and detect a single nanoparticle. Micropores (4 μm diameter) are reactive-ion etched through the top SiO(2) and SiN layers of the waveguides, leaving a thin SiN membrane above the hollow core. Nanopores are formed in the SiN membranes using a focused ion-beam etch process that provides control over the pore size. Openings as small as 20 nm in diameter are created. Optical loss measurements indicate that micropores did not significantly alter the loss along the waveguide.
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Affiliation(s)
- Matthew R. Holmes
- Brigham Young University, Electrical and Computer Engineering Department, 459 Clyde Building, Provo, Utah 84602
| | - Tao Shang
- Brigham Young University, Electrical and Computer Engineering Department, 459 Clyde Building, Provo, Utah 84602
| | - Aaron R. Hawkins
- Brigham Young University, Electrical and Computer Engineering Department, 459 Clyde Building, Provo, Utah 84602
| | - Mikhail Rudenko
- University of California Santa Cruz, School of Engineering, 1156 High Street, Santa Cruz, California 95064
| | - Philip Measor
- University of California Santa Cruz, School of Engineering, 1156 High Street, Santa Cruz, California 95064
| | - Holger Schmidt
- University of California Santa Cruz, School of Engineering, 1156 High Street, Santa Cruz, California 95064
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Measor P, Kühn S, Lunt EJ, Phillips BS, Hawkins AR, Schmidt H. Multi-mode mitigation in an optofluidic chip for particle manipulation and sensing. OPTICS EXPRESS 2009; 17:24342-8. [PMID: 20052144 PMCID: PMC2860178 DOI: 10.1364/oe.17.024342] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
A new waveguide design for an optofluidic chip is presented. It mitigates multi-mode behavior in solid and liquid-core waveguides by increasing fundamental mode coupling to 82% and 95%, respectively. Additionally, we demonstrate a six-fold improvement in lateral confinement of optically guided dielectric microparticles and double the detection efficiency of fluorescent particles.
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Affiliation(s)
- Philip Measor
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
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