1
|
Seymour E, Ekiz Kanik F, Diken Gür S, Bakhshpour-Yucel M, Araz A, Lortlar Ünlü N, Ünlü MS. Solid-Phase Optical Sensing Techniques for Sensitive Virus Detection. SENSORS (BASEL, SWITZERLAND) 2023; 23:5018. [PMID: 37299745 PMCID: PMC10255700 DOI: 10.3390/s23115018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 06/12/2023]
Abstract
Viral infections can pose a major threat to public health by causing serious illness, leading to pandemics, and burdening healthcare systems. The global spread of such infections causes disruptions to every aspect of life including business, education, and social life. Fast and accurate diagnosis of viral infections has significant implications for saving lives, preventing the spread of the diseases, and minimizing social and economic damages. Polymerase chain reaction (PCR)-based techniques are commonly used to detect viruses in the clinic. However, PCR has several drawbacks, as highlighted during the recent COVID-19 pandemic, such as long processing times and the requirement for sophisticated laboratory instruments. Therefore, there is an urgent need for fast and accurate techniques for virus detection. For this purpose, a variety of biosensor systems are being developed to provide rapid, sensitive, and high-throughput viral diagnostic platforms, enabling quick diagnosis and efficient control of the virus's spread. Optical devices, in particular, are of great interest due to their advantages such as high sensitivity and direct readout. The current review discusses solid-phase optical sensing techniques for virus detection, including fluorescence-based sensors, surface plasmon resonance (SPR), surface-enhanced Raman scattering (SERS), optical resonators, and interferometry-based platforms. Then, we focus on an interferometric biosensor developed by our group, the single-particle interferometric reflectance imaging sensor (SP-IRIS), which has the capability to visualize single nanoparticles, to demonstrate its application for digital virus detection.
Collapse
Affiliation(s)
- Elif Seymour
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M4P 1R2, Canada;
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA;
| | - Fulya Ekiz Kanik
- Department of Electrical Engineering, Boston University, Boston, MA 02215, USA; (F.E.K.); (M.B.-Y.)
| | - Sinem Diken Gür
- Department of Biology, Hacettepe University, Ankara 06800, Türkiye;
| | - Monireh Bakhshpour-Yucel
- Department of Electrical Engineering, Boston University, Boston, MA 02215, USA; (F.E.K.); (M.B.-Y.)
- Department of Chemistry, Bursa Uludag University, Bursa 16059, Türkiye
| | - Ali Araz
- Department of Chemistry, Dokuz Eylül University, Izmir 35390, Türkiye;
| | - Nese Lortlar Ünlü
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA;
| | - M. Selim Ünlü
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA;
- Department of Electrical Engineering, Boston University, Boston, MA 02215, USA; (F.E.K.); (M.B.-Y.)
| |
Collapse
|
2
|
Bakhshpour-Yucel M, Gür SD, Seymour E, Aslan M, Lortlar Ünlü N, Ünlü MS. Highly-Sensitive, Label-Free Detection of Microorganisms and Viruses via Interferometric Reflectance Imaging Sensor. MICROMACHINES 2023; 14:281. [PMID: 36837980 PMCID: PMC9960798 DOI: 10.3390/mi14020281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/08/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Pathogenic microorganisms and viruses can easily transfer from one host to another and cause disease in humans. The determination of these pathogens in a time- and cost-effective way is an extreme challenge for researchers. Rapid and label-free detection of pathogenic microorganisms and viruses is critical in ensuring rapid and appropriate treatment. Sensor technologies have shown considerable advancements in viral diagnostics, demonstrating their great potential for being fast and sensitive detection platforms. In this review, we present a summary of the use of an interferometric reflectance imaging sensor (IRIS) for the detection of microorganisms. We highlight low magnification modality of IRIS as an ensemble biomolecular mass measurement technique and high magnification modality for the digital detection of individual nanoparticles and viruses. We discuss the two different modalities of IRIS and their applications in the sensitive detection of microorganisms and viruses.
Collapse
Affiliation(s)
- Monireh Bakhshpour-Yucel
- Department of Electrical Engineering, Photonics Center, Boston University, Boston, MA 02215, USA
- Department of Chemistry, Faculty of Science and Art, Bursa Uludag University, Bursa 16059, Turkey
| | - Sinem Diken Gür
- Department of Biotechnology, Hacettepe University, Ankara 06800, Turkey
| | - Elif Seymour
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Mete Aslan
- Department of Electrical Engineering, Photonics Center, Boston University, Boston, MA 02215, USA
| | - Nese Lortlar Ünlü
- Department of Biomedical Engineering, Photonics Center, Boston University, Boston, MA 02215, USA
| | - M. Selim Ünlü
- Department of Electrical Engineering, Photonics Center, Boston University, Boston, MA 02215, USA
- Department of Biomedical Engineering, Photonics Center, Boston University, Boston, MA 02215, USA
| |
Collapse
|
3
|
Chee HY, Lam JY, Yaacob M. Tapered optical fiber DNA biosensor for detecting Leptospira DNA. ASIAN PAC J TROP MED 2023. [DOI: 10.4103/1995-7645.372293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
|
4
|
Through the looking-glass - Recent developments in reflectometry open new possibilities for biosensor applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
5
|
Yi Z, Zhou Y, Ren Y, Hu W, Long F, Zhu A. A novel sensitive DNAzyme-based optical fiber evanescent wave biosensor for rapid detection of Pb 2+ in human serum. Analyst 2022; 147:1467-1477. [PMID: 35266947 DOI: 10.1039/d2an00043a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe here a portable DNAzyme-based optical fiber evanescent wave biosensor (OFEWB) for the rapid and sensitive detection of Pb2+ in human serum. Unlike other biosensors, the OFEWB dispensed with the complicated process of attaching biometric elements to the optical fiber, and the optical fiber directly acted as a transducer to transmit the excitation light and simultaneously collected the fluorescence, which could simplify the detection process, avoid the susceptibility to interference from complex environments and strengthen the reusability of the biosensor. The fluorescence (Cy3) labelled substrate sequence (GR-5S-Cy3) could be cleaved under the catalysis of the GR-5 DNAzyme sequence (GR-5E-BHQ2) in the presence of Pb2+; then the released fluorescence labelled fragments could be directly excited and detected by the OFEWB due to the high transmission efficiency of the excitation light and fluorescence in the OFEWB. Several key factors affecting Pb2+ detection were investigated in detail and optimized. Under the optimal conditions, the LOD of Pb2+ in human serum was 9.34 nM (equivalent to 93.4 nM in whole serum) with a detection range of 0-120 nM. The possible matrix interference was evaluated with different spiked human serum samples, and the recovery of Pb2+ ranged from 74.4% to 112.5% with RSD < 14.8%, implying this method had excellent practicability and could be potentially used in analyzing some biomedical samples.
Collapse
Affiliation(s)
- Zhihao Yi
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China.
| | - Yue Zhou
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China.
| | - Yashuang Ren
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China.
| | - Wei Hu
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China.
| | - Feng Long
- School of Environment and Natural Resource, Renmin University of China, Beijing, 100872, China.
| | - Anna Zhu
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China.
| |
Collapse
|
6
|
Vanjur L, Carzaniga T, Casiraghi L, Zanchetta G, Damin F, Sola L, Chiari M, Buscaglia M. Copolymer Coatings for DNA Biosensors: Effect of Charges and Immobilization Chemistries on Yield, Strength and Kinetics of Hybridization. Polymers (Basel) 2021; 13:polym13223897. [PMID: 34833198 PMCID: PMC8625010 DOI: 10.3390/polym13223897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 01/08/2023] Open
Abstract
The physical–chemical properties of the surface of DNA microarrays and biosensors play a fundamental role in their performance, affecting the signal’s amplitude and the strength and kinetics of binding. We studied how the interaction parameters vary for hybridization of complementary 23-mer DNA, when the probe strands are immobilized on different copolymers, which coat the surface of an optical, label-free biosensor. Copolymers of N, N-dimethylacrylamide bringing either a different type or density of sites for covalent immobilization of DNA probes, or different backbone charges, were used to functionalize the surface of a Reflective Phantom Interface multispot biosensor made of a glass prism with a silicon dioxide antireflective layer. By analyzing the kinetic hybridization curves at different probe surface densities and target concentrations in solution, we found that all the tested coatings displayed a common association kinetics of about 9 × 104 M−1·s−1 at small probe density, decreasing by one order of magnitude close to the surface saturation of probes. In contrast, both the yield of hybridization and the dissociation kinetics, and hence the equilibrium constant, depend on the type of copolymer coating. Nearly doubled signal amplitudes, although equilibrium dissociation constant was as large as 4 nM, were obtained by immobilizing the probe via click chemistry, whereas amine-based immobilization combined with passivation with diamine carrying positive charges granted much slower dissociation kinetics, yielding an equilibrium dissociation constant as low as 0.5 nM. These results offer quantitative criteria for an optimal selection of surface copolymer coatings, depending on the application.
Collapse
Affiliation(s)
- Luka Vanjur
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, 20054 Segrate, Italy; (L.V.); (T.C.); (L.C.); (G.Z.)
| | - Thomas Carzaniga
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, 20054 Segrate, Italy; (L.V.); (T.C.); (L.C.); (G.Z.)
| | - Luca Casiraghi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, 20054 Segrate, Italy; (L.V.); (T.C.); (L.C.); (G.Z.)
| | - Giuliano Zanchetta
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, 20054 Segrate, Italy; (L.V.); (T.C.); (L.C.); (G.Z.)
| | - Francesco Damin
- Istituto di Scienze e Tecnologie Chimiche, Consiglio Nazionale delle Ricerche (CNR-SCITEC), 20131 Milano, Italy; (F.D.); (L.S.); (M.C.)
| | - Laura Sola
- Istituto di Scienze e Tecnologie Chimiche, Consiglio Nazionale delle Ricerche (CNR-SCITEC), 20131 Milano, Italy; (F.D.); (L.S.); (M.C.)
| | - Marcella Chiari
- Istituto di Scienze e Tecnologie Chimiche, Consiglio Nazionale delle Ricerche (CNR-SCITEC), 20131 Milano, Italy; (F.D.); (L.S.); (M.C.)
| | - Marco Buscaglia
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, 20054 Segrate, Italy; (L.V.); (T.C.); (L.C.); (G.Z.)
- Correspondence: ; Tel.: +39-0250330352
| |
Collapse
|
7
|
Simple, rapid, and sensitive on-site detection of Hg 2+ in water samples through combining portable evanescent wave optofluidic biosensor and fluorescence resonance energy transfer principle. Anal Chim Acta 2021; 1155:338351. [PMID: 33766323 DOI: 10.1016/j.aca.2021.338351] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/17/2021] [Accepted: 02/23/2021] [Indexed: 12/28/2022]
Abstract
Rapid and sensitive detection of Hg2+ in the environment and drinking water is vital because of its non-degradability, bioaccumulation, and high toxicity. Herein, we report a portable evanescent wave optofluidic biosensor (EWOB) for simple sensitive detection of Hg2+ using fluorescence labeled poly-A DNA strand (CY-A14) and quencher labeled poly-T DNA strand (BQ-T14) as signal reporter and biorecognition element, respectively. Both CY-A14 and Hg2+ can competitively bind with BQ-T14 based on DNA hybridization and the specifical binding of Hg2+ and T bases of DNA to form T-Hg2+-T mismatch structure, respectively. Higher concentration of Hg2+ lead to less CY-A14 bound to BQ-T14 and thus a higher fluorescence intensity. The influence of several key environmental factors on Hg2+ biosensor, such as pH, temperature, and ionic strength, was investigated in details because they were essential for practical applications of Hg2+ biosensor. Under optimal conditions, a detection cycle for a single sample, including the measurement and regeneration, was less than 10 min with a Hg2+ detection limit of 8.5 nM. The high selectivity of the biosensor was showed by evaluating its response to various potentially interfering metal ions. Our results clearly demonstrated that the portable EWOB could serve as a powerful tool for rapid and sensitive on-site detection of Hg2+ in real water samples. The EWOB is also potentially applicable to detect other heavy metal ions or small molecule targets for which DNA/aptamers could be applied as specific biosensing probes.
Collapse
|
8
|
Gauglitz G. Critical assessment of relevant methods in the field of biosensors with direct optical detection based on fibers and waveguides using plasmonic, resonance, and interference effects. Anal Bioanal Chem 2020; 412:3317-3349. [PMID: 32313998 PMCID: PMC7214504 DOI: 10.1007/s00216-020-02581-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/28/2020] [Accepted: 03/04/2020] [Indexed: 12/16/2022]
Abstract
Direct optical detection has proven to be a highly interesting tool in biomolecular interaction analysis to be used in drug discovery, ligand/receptor interactions, environmental analysis, clinical diagnostics, screening of large data volumes in immunology, cancer therapy, or personalized medicine. In this review, the fundamental optical principles and applications are reviewed. Devices are based on concepts such as refractometry, evanescent field, waveguides modes, reflectometry, resonance and/or interference. They are realized in ring resonators; prism couplers; surface plasmon resonance; resonant mirror; Bragg grating; grating couplers; photonic crystals, Mach-Zehnder, Young, Hartman interferometers; backscattering; ellipsometry; or reflectance interferometry. The physical theories of various optical principles have already been reviewed in detail elsewhere and are therefore only cited. This review provides an overall survey on the application of these methods in direct optical biosensing. The "historical" development of the main principles is given to understand the various, and sometimes only slightly modified variations published as "new" methods or the use of a new acronym and commercialization by different companies. Improvement of optics is only one way to increase the quality of biosensors. Additional essential aspects are the surface modification of transducers, immobilization strategies, selection of recognition elements, the influence of non-specific interaction, selectivity, and sensitivity. Furthermore, papers use for reporting minimal amounts of detectable analyte terms such as value of mass, moles, grams, or mol/L which are difficult to compare. Both these essential aspects (i.e., biochemistry and the presentation of LOD values) can be discussed only in brief (but references are provided) in order to prevent the paper from becoming too long. The review will concentrate on a comparison of the optical methods, their application, and the resulting bioanalytical quality.
Collapse
Affiliation(s)
- Günter Gauglitz
- Institute of Physical and Theoretical Chemistry, Eberhard Karls Universität, Auf der Morgenstelle 18, 72076, Tübingen, Germany.
| |
Collapse
|
9
|
Fu R, Su Y, Wang R, Lin X, Jiang K, Jin X, Yang H, Ma L, Luo X, Lu Y, Huang G. Label-free tomography of living cellular nanoarchitecture using hyperspectral self-interference microscopy. BIOMEDICAL OPTICS EXPRESS 2019; 10:2757-2767. [PMID: 31259049 PMCID: PMC6583342 DOI: 10.1364/boe.10.002757] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 04/11/2019] [Accepted: 04/24/2019] [Indexed: 06/09/2023]
Abstract
Quantitative phase imaging (QPI) is the most ideal method for achieving long-term cellular tomography because it is label free and quantitative. However, for current QPI instruments, interference signals from different layers overlay with each other and impede nanoscale optical sectioning. Integrated incubators and improved configurations also require further investigation for QPI instruments. In this work, hyperspectral self-reflectance microscopy is proposed to achieve label-free tomography of living cellular nanoarchitecture. The optical description and tomography reconstruction algorithm were proposed so that the quantitative morphological structure of the entire living cell can be acquired with 89.2 nm axial resolution and 1.91 nm optical path difference sensitivity. A cell incubator was integrated to culture living cells for in situ measurement and expensive precise optical components were not needed. The proposed system can reveal native and dynamic cellular nanoscale structure, providing an alternative approach for long-term monitoring and quantitative analysis of living cells.
Collapse
Affiliation(s)
- Rongxin Fu
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
- Contributed equally as co-authors
| | - Ya Su
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
- Contributed equally as co-authors
| | - Ruliang Wang
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xue Lin
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Kai Jiang
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiangyu Jin
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Han Yang
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Li Ma
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, China
| | - Xianbo Luo
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, China
| | - Ying Lu
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Guoliang Huang
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, China
| |
Collapse
|
10
|
Hlongwane GN, Dodoo-Arhin D, Wamwangi D, Daramola MO, Moothi K, Iyuke SE. DNA hybridisation sensors for product authentication and tracing: State of the art and challenges. SOUTH AFRICAN JOURNAL OF CHEMICAL ENGINEERING 2019. [DOI: 10.1016/j.sajce.2018.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
|
11
|
Needham JW, Ünlü NL, Yurdakul C, Ünlü MS. Interferometric Reflectance Imaging Sensor (IRIS) for Molecular Kinetics with a Low-Cost, Disposable Fluidic Cartridge. Methods Mol Biol 2019; 2027:15-28. [PMID: 31309469 DOI: 10.1007/978-1-4939-9616-2_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The determination of kinetic information and appropriate binding pairs is fundamental to the proper optimization and selection of ligands used in immunoassays, diagnostics, and therapeutics. However, the ability to estimate such parameters in a multiplexed and inexpensive format remains difficult and modification of the ligand is often necessary. Here, we detail the methods and materials necessary to evaluate hundreds of unlabeled ligands simultaneously using the interferometric reflectance imaging sensor (IRIS). The incorporation of a low-cost fluidic cartridge that integrates on the top of the sensor simplifies reagent handling considerably.
Collapse
Affiliation(s)
- James W Needham
- InBios International Inc., Seattle, WA, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
| | - Nese Lortlar Ünlü
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Celalettin Yurdakul
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| | - M Selim Ünlü
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| |
Collapse
|
12
|
Zainuddin NH, Chee HY, Ahmad MZ, Mahdi MA, Abu Bakar MH, Yaacob MH. Sensitive Leptospira DNA detection using tapered optical fiber sensor. JOURNAL OF BIOPHOTONICS 2018; 11:e201700363. [PMID: 29570957 DOI: 10.1002/jbio.201700363] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 03/16/2018] [Accepted: 03/19/2018] [Indexed: 06/08/2023]
Abstract
This paper presents the development of tapered optical fiber sensor to detect a specific Leptospira bacteria DNA. The bacteria causes Leptospirosis, a deadly disease but with common early flu-like symptoms. Optical single mode fiber (SMF) of 125 μm diameter is tapered to produce 12 μm waist diameter and 15 cm length. The novel DNA-based optical fiber sensor is functionalized by incubating the tapered region with sodium hydroxide (NaOH), (3-Aminopropyl) triethoxysilane and glutaraldehyde. Probe DNA is immobilized onto the tapered region and subsequently hybridized by its complementary DNA (cDNA). The transmission spectra of the DNA-based optical fiber sensor are measured in the 1500 to 1600 nm wavelength range. It is discovered that the shift of the wavelength in the SMF sensor is linearly proportional with the increase in the cDNA concentrations from 0.1 to 1.0 nM. The sensitivity of the sensor toward DNA is measured to be 1.2862 nm/nM and able to detect as low as 0.1 fM. The sensor indicates high specificity when only minimal shift is detected for non-cDNA testing. The developed sensor is able to distinguish between actual DNA of Leptospira serovars (Canicola and Copenhageni) against Clostridium difficile (control sample) at very low (femtomolar) target concentrations.
Collapse
Affiliation(s)
- Nurul H Zainuddin
- Department of Computer and Communication Systems, Faculty of Engineering, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Wireless and Photonic Networks Research Centre (WiPNET), Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Hui Y Chee
- Department of Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Muhammad Z Ahmad
- Biotechnology and Nanotechnology Research Center, Malaysian Agricultural Research and Development Institute (MARDI), Serdang, Selangor, Malaysia
| | - Mohd A Mahdi
- Department of Computer and Communication Systems, Faculty of Engineering, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Wireless and Photonic Networks Research Centre (WiPNET), Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Muhammad H Abu Bakar
- Department of Computer and Communication Systems, Faculty of Engineering, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Wireless and Photonic Networks Research Centre (WiPNET), Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Mohd H Yaacob
- Department of Computer and Communication Systems, Faculty of Engineering, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Wireless and Photonic Networks Research Centre (WiPNET), Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| |
Collapse
|
13
|
Su H, Cheng XR, Endo T, Kerman K. Photonic crystals on copolymer film for label-free detection of DNA hybridization. Biosens Bioelectron 2018; 103:158-162. [PMID: 29291596 DOI: 10.1016/j.bios.2017.12.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 11/09/2017] [Accepted: 12/07/2017] [Indexed: 11/28/2022]
Abstract
The presence of a single-nucleotide polymorphism in Apolipoprotein E4 gene is implicated with the increased risk of developing Alzheimer's disease (AD). In this study, detection of AD-related DNA oligonucleotide sequence associated with Apolipoprotein E4 gene sequence was achieved using localized-surface plasmon resonance (LSPR) on 2D-Photonic crystal (2D-PC) and Au-coated 2D-PC surfaces. 2D-PC surfaces were fabricated on a flexible copolymer film using nano-imprint lithography (NIL). The film surface was then coated with a dual-functionalized polymer to react with surface immobilized DNA probe. DNA hybridization was detected by monitoring the optical responses of either a Fresnel decrease in reflectance on 2D-PC surfaces or an increase in LSPR on Au-coated 2D-PC surfaces. The change in response due to DNA hybridization on the modified surfaces was also investigated using mismatched and non-complementary oligonucleotides sequences. The proof-of-concept results are promising towards the development of 2D-PC on copolymer film surfaces as miniaturized and wearable biosensors for various diagnostic and defense applications.
Collapse
Affiliation(s)
- Han Su
- Dept. of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON, Canada M1C 1A4
| | - Xin R Cheng
- Dept. of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON, Canada M1C 1A4
| | - Tatsuro Endo
- Dept. of Applied Chemistry, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai-shi, Osaka 599-8531, Japan
| | - Kagan Kerman
- Dept. of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON, Canada M1C 1A4.
| |
Collapse
|
14
|
Fu R, Li Q, Wang R, Xue N, Lin X, Su Y, Jiang K, Jin X, Lin R, Gan W, Lu Y, Huang G. An interferometric imaging biosensor using weighted spectrum analysis to confirm DNA monolayer films with attogram sensitivity. Talanta 2017; 181:224-231. [PMID: 29426505 DOI: 10.1016/j.talanta.2017.12.066] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 12/13/2017] [Accepted: 12/21/2017] [Indexed: 11/28/2022]
Abstract
Interferometric imaging biosensors are powerful and convenient tools for confirming the existence of DNA monolayer films on silicon microarray platforms. However, their accuracy and sensitivity need further improvement because DNA molecules contribute to an inconspicuous interferometric signal both in thickness and size. Such weaknesses result in poor performance of these biosensors for low DNA content analyses and point mutation tests. In this paper, an interferometric imaging biosensor with weighted spectrum analysis is presented to confirm DNA monolayer films. The interferometric signal of DNA molecules can be extracted and then quantitative detection results for DNA microarrays can be reconstructed. With the proposed strategy, the relative error of thickness detection was reduced from 88.94% to merely 4.15%. The mass sensitivity per unit area of the proposed biosensor reached 20 attograms (ag). Therefore, the sample consumption per unit area of the target DNA content was only 62.5 zeptomoles (zm), with the volume of 0.25 picolitres (pL). Compared with the fluorescence resonance energy transfer (FRET), the measurement veracity of the interferometric imaging biosensor with weighted spectrum analysis is free to the changes in spotting concentration and DNA length. The detection range was more than 1µm. Moreover, single nucleotide mismatch could be pointed out combined with specific DNA ligation. A mutation experiment for lung cancer detection proved the high selectivity and accurate analysis capability of the presented biosensor.
Collapse
Affiliation(s)
- Rongxin Fu
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Qi Li
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Ruliang Wang
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Ning Xue
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xue Lin
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Ya Su
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Kai Jiang
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiangyu Jin
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Rongzan Lin
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Wupeng Gan
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, China
| | - Ying Lu
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China
| | - Guoliang Huang
- Department of Biomedical Engineering, the School of Medicine, Tsinghua University, Beijing 100084, China; National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, China.
| |
Collapse
|
15
|
Peserico N, Castagna R, Bellieres L, Rodrigo M, Melloni A. Tip‐mould microcontact printing for functionalisation of optical microring resonator. IET Nanobiotechnol 2017; 12:87-91. [PMCID: PMC8676595 DOI: 10.1049/iet-nbt.2017.0031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 09/07/2017] [Accepted: 10/03/2017] [Indexed: 11/09/2023] Open
Abstract
We present an approach to functionalise optical microring resonators as hybridisation platforms, using tip‐mould reactive microcontact printing process. Derived from reactive microcontact printing using an ad hoc mould of polydimethylsiloxane (PDMS), the method functionalises single microring resonator with a target‐specific capture agent. The authors report the functionalisation of silicon nitride (SiN) 200 μ m diameter microring resonator with single‐strand DNA and the hybridisation detection of 100 nM target analyte, while concurrently monitoring not‐functionalised microring as a control sensor. Results show that the functionalisation approach permits to address single microring resonators with mutual distance lower than 100 μ m with high precision, enabling a better integration of multiple spotting zones on the chip concerning traditional functionalisation procedures.
Collapse
Affiliation(s)
- Nicola Peserico
- Dipartimento di Elettronica, Informazione e BioingegneriaPolitecnico di Milanovia G. Colombo 8120133MilanoItaly
| | - Rossella Castagna
- Dipartimento di Elettronica, Informazione e BioingegneriaPolitecnico di Milanovia G. Colombo 8120133MilanoItaly
| | | | - Manuel Rodrigo
- DAS Photonics SLCalle Islas Canarias, 6–846023ValenciaSpain
| | - Andrea Melloni
- Dipartimento di Elettronica, Informazione e BioingegneriaPolitecnico di Milanovia G. Colombo 8120133MilanoItaly
| |
Collapse
|
16
|
Rapisarda A, Giamblanco N, Marletta G. Kinetic discrimination of DNA single-base mutations by localized surface plasmon resonance. J Colloid Interface Sci 2017; 487:141-148. [DOI: 10.1016/j.jcis.2016.10.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/12/2016] [Accepted: 10/13/2016] [Indexed: 10/20/2022]
|
17
|
Liu YZ, Manivannan K, Lee AW, Huang YJ, Wei PL, Chen JK. Identification of DNA single-base mismatches by resistivity of poly(N-isopropylacrylamide)-block-ssDNA copolymer brush films at dual temperatures. RSC Adv 2017. [DOI: 10.1039/c6ra28270a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The resistivity of tethered PNIPAAm-b-ssDNA copolymer brushes can be exploited to detect a label-free target by homogeneous complexation and phase separation.
Collapse
Affiliation(s)
- Yi-Zu Liu
- Department of Materials Science and Engineering
- National Taiwan University of Science and Technology
- Taipei
- Republic of China
| | - Karthikeyan Manivannan
- Department of Materials Science and Engineering
- National Taiwan University of Science and Technology
- Taipei
- Republic of China
| | - Ai-Wei Lee
- Department of Anatomy and Cell Biology
- School of Medicine
- College of Medicine
- Taipei Medical University
- Taipei 110
| | - Yan-Jiun Huang
- Department of Surgery
- College of Medicine
- Division of Colorectal Surgery
- Taipei Medical University Hospital
- Taipei Medical University
| | - Po-Li Wei
- Cancer Center
- Division of General Surgery
- Department of Surgery
- Taipei Medical University Hospital
- College of Medicine
| | - Jem-Kun Chen
- Department of Materials Science and Engineering
- National Taiwan University of Science and Technology
- Taipei
- Republic of China
| |
Collapse
|
18
|
Jung YK, Kim J, Mathies RA. Microfluidic hydrogel arrays for direct genotyping of clinical samples. Biosens Bioelectron 2016; 79:371-8. [DOI: 10.1016/j.bios.2015.12.068] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 12/07/2015] [Accepted: 12/20/2015] [Indexed: 12/29/2022]
|
19
|
Nava G, Ceccarello E, Giavazzi F, Salina M, Damin F, Chiari M, Buscaglia M, Bellini T, Zanchetta G. Label-free detection of DNA single-base mismatches using a simple reflectance-based optical technique. Phys Chem Chem Phys 2016; 18:13395-402. [PMID: 27122358 DOI: 10.1039/c5cp08017g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Rapid and quantitative detection of the binding of nucleic acids to surface-immobilized probes remains a challenge in many biomedical applications. We investigated the hybridization of a set of fully complementary and defected 12-base long DNA oligomers by using the Reflective Phantom Interface (RPI), a recently developed multiplexed label-free detection technique. Based on the simple measurement of reflected light intensity, this technology enables to quantify the hybridization directly as it occurs on the surface with a sensitivity of 10 pg mm(-2). We found a strong effect of single-base mismatches and of their location on hybridization kinetics and equilibrium binding. In line with previous studies, we found that DNA-DNA binding is weaker on a surface than in the bulk. Our data indicate that this effect is a consequence of weak nonspecific binding of the probes to the surface.
Collapse
Affiliation(s)
- G Nava
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, via Fratelli Cervi 93, 20090 Segrate, Milano, Italy.
| | | | | | | | | | | | | | | | | |
Collapse
|
20
|
An ultrasensitive scanning electrochemical microscopy (SECM)-based DNA biosensing platform amplified with the long self-assembled DNA concatemers. Electrochim Acta 2016. [DOI: 10.1016/j.electacta.2015.12.102] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
|
21
|
Abstract
The DNA microarray technology is currently a useful biomedical tool which has been developed for a variety of diagnostic applications. However, the development pathway has not been smooth and the technology has faced some challenges. The reliability of the microarray data and also the clinical utility of the results in the early days were criticized. These criticisms added to the severe competition from other techniques, such as next-generation sequencing (NGS), impacting the growth of microarray-based tests in the molecular diagnostic market.Thanks to the advances in the underlying technologies as well as the tremendous effort offered by the research community and commercial vendors, these challenges have mostly been addressed. Nowadays, the microarray platform has achieved sufficient standardization and method validation as well as efficient probe printing, liquid handling and signal visualization. Integration of various steps of the microarray assay into a harmonized and miniaturized handheld lab-on-a-chip (LOC) device has been a goal for the microarray community. In this respect, notable progress has been achieved in coupling the DNA microarray with the liquid manipulation microsystem as well as the supporting subsystem that will generate the stand-alone LOC device.In this chapter, we discuss the major challenges that microarray technology has faced in its almost two decades of development and also describe the solutions to overcome the challenges. In addition, we review the advancements of the technology, especially the progress toward developing the LOC devices for DNA diagnostic applications.
Collapse
Affiliation(s)
| | - Abootaleb Sedighi
- Department of Chemistry, Simon Fraser University, Burnaby, BC, Canada, V5A 1S6
| | - Paul C H Li
- Department of Chemistry, Simon Fraser University, Burnaby, BC, Canada, V5A 1S6.
| |
Collapse
|
22
|
Electrical sensing of DNA-hybridization using two-port network based on suspended carbon nanotube membrane. Biomed Microdevices 2015; 17:103. [DOI: 10.1007/s10544-015-0009-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
23
|
Interferometric Reflectance Imaging Sensor (IRIS)--A Platform Technology for Multiplexed Diagnostics and Digital Detection. SENSORS 2015. [PMID: 26205273 PMCID: PMC4541952 DOI: 10.3390/s150717649] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Over the last decade, the growing need in disease diagnostics has stimulated rapid development of new technologies with unprecedented capabilities. Recent emerging infectious diseases and epidemics have revealed the shortcomings of existing diagnostics tools, and the necessity for further improvements. Optical biosensors can lay the foundations for future generation diagnostics by providing means to detect biomarkers in a highly sensitive, specific, quantitative and multiplexed fashion. Here, we review an optical sensing technology, Interferometric Reflectance Imaging Sensor (IRIS), and the relevant features of this multifunctional platform for quantitative, label-free and dynamic detection. We discuss two distinct modalities for IRIS: (i) low-magnification (ensemble biomolecular mass measurements) and (ii) high-magnification (digital detection of individual nanoparticles) along with their applications, including label-free detection of multiplexed protein chips, measurement of single nucleotide polymorphism, quantification of transcription factor DNA binding, and high sensitivity digital sensing and characterization of nanoparticles and viruses.
Collapse
|
24
|
McLeod E, Wei Q, Ozcan A. Democratization of Nanoscale Imaging and Sensing Tools Using Photonics. Anal Chem 2015; 87:6434-45. [PMID: 26068279 PMCID: PMC4497296 DOI: 10.1021/acs.analchem.5b01381] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 06/12/2015] [Indexed: 01/28/2023]
Abstract
Providing means for researchers and citizen scientists in the developing world to perform advanced measurements with nanoscale precision can help to accelerate the rate of discovery and invention as well as improve higher education and the training of the next generation of scientists and engineers worldwide. Here, we review some of the recent progress toward making optical nanoscale measurement tools more cost-effective, field-portable, and accessible to a significantly larger group of researchers and educators. We divide our review into two main sections: label-based nanoscale imaging and sensing tools, which primarily involve fluorescent approaches, and label-free nanoscale measurement tools, which include light scattering sensors, interferometric methods, photonic crystal sensors, and plasmonic sensors. For each of these areas, we have primarily focused on approaches that have either demonstrated operation outside of a traditional laboratory setting, including for example integration with mobile phones, or exhibited the potential for such operation in the near future.
Collapse
Affiliation(s)
- Euan McLeod
- Department
of Electrical Engineering, University of
California Los Angeles (UCLA), Los Angeles, California 90095, United States
- Department
of Bioengineering, University of California
Los Angeles (UCLA), Los Angeles, California 90095, United States
| | - Qingshan Wei
- Department
of Electrical Engineering, University of
California Los Angeles (UCLA), Los Angeles, California 90095, United States
- Department
of Bioengineering, University of California
Los Angeles (UCLA), Los Angeles, California 90095, United States
| | - Aydogan Ozcan
- Department
of Electrical Engineering, University of
California Los Angeles (UCLA), Los Angeles, California 90095, United States
- Department
of Bioengineering, University of California
Los Angeles (UCLA), Los Angeles, California 90095, United States
- California
NanoSystems Institute (CNSI), University
of California Los Angeles (UCLA), Los Angeles, California 90095, United States
| |
Collapse
|
25
|
Jung YK, Kim J, Mathies RA. Microfluidic Linear Hydrogel Array for Multiplexed Single Nucleotide Polymorphism (SNP) Detection. Anal Chem 2015; 87:3165-70. [DOI: 10.1021/ac5048696] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Yun Kyung Jung
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- School
of Natural
Science, Ulsan National Institute of Science and Technology, Ulsan 689-798, Republic of Korea
| | - Jungkyu Kim
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Mechanical Engineering, Texas Tech University, Lubbock, Texas 79409, United States
| | - Richard A. Mathies
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| |
Collapse
|
26
|
|
27
|
Abstract
AbstractIn addition to its role as a carrier of genetic information, DNA has been recognized as a construction material for the assembly of different objects and structural arrangements with nanoscale features. As a result of DNA’s self-recognition properties (based on the specific base-pairing of G-C and T-A), monolayer films of nucleic acids on solid supports have attracted an escalating attentions. Recently, numerous novel materials based on two-dimensional (2D) and three-dimensional (3D) DNA structures have been reported, which extends their utility to a large number of appliations. This review paper intends to be a new and comprehensive overview of recent strategies to site-specifically immobilized DNA on various materials, including carbonaceous substances, gold, and silica substrate, emphasizing the applications of site-specific DNA nanostructure-based devices for diagnostic, bioanalytical, food safety and environmental monitoring. Additionally, an up-to-date perspective is proposed at the end of this review.
Collapse
|
28
|
Yu C, Lopez CA, Hu H, Xia Y, Freedman DS, Reddington AP, Daaboul GG, Ünlü MS, Genco CA. A high-throughput method to examine protein-nucleotide interactions identifies targets of the bacterial transcriptional regulatory protein fur. PLoS One 2014; 9:e96832. [PMID: 24811061 PMCID: PMC4014563 DOI: 10.1371/journal.pone.0096832] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 04/13/2014] [Indexed: 11/19/2022] Open
Abstract
The Ferric uptake regulatory protein (Fur) is a transcriptional regulatory protein that functions to control gene transcription in response to iron in a number of pathogenic bacteria. In this study, we applied a label-free, quantitative and high-throughput analysis method, Interferometric Reflectance Imaging Sensor (IRIS), to rapidly characterize Fur-DNA interactions in vitro with predicted Fur binding sequences in the genome of Neisseria gonorrhoeae, the causative agent of the sexually transmitted disease gonorrhea. IRIS can easily be applied to examine multiple protein-protein, protein-nucleotide and nucleotide-nucleotide complexes simultaneously and demonstrated here that seventy percent of the predicted Fur boxes in promoter regions of iron-induced genes bound to Fur in vitro with a range of affinities as observed using this microarray screening technology. Combining binding data with mRNA expression levels in a gonococcal fur mutant strain allowed us to identify five new gonococcal genes under Fur-mediated direct regulation.
Collapse
Affiliation(s)
- Chunxiao Yu
- Department of Medicine, Section of Infectious Diseases, Boston University School of Medicine, Boston University, Boston, Massachusetts, United States of America
| | - Carlos A. Lopez
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Han Hu
- Bioinformatics Graduate Program, Boston University, Boston, Massachusetts, United States of America
| | - Yu Xia
- Bioinformatics Graduate Program, Boston University, Boston, Massachusetts, United States of America
| | - David S. Freedman
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Alexander P. Reddington
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, United States of America
| | - George G. Daaboul
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - M. Selim Ünlü
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, United States of America
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
- Physics Department, Boston University, Boston, Massachusetts, United States of America
| | - Caroline Attardo Genco
- Department of Medicine, Section of Infectious Diseases, Boston University School of Medicine, Boston University, Boston, Massachusetts, United States of America
- Department of Microbiology, Boston University School of Medicine, Boston University, Boston, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
29
|
Sedighi A, Li PC. Challenges and Future Trends in DNA Microarray Analysis. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/b978-0-444-62651-6.00002-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
|
30
|
Cheng XR, Daaboul GG, Ünlü MS, Kerman K. LED-based interferometric reflectance imaging sensor for the detection of amyloid-β aggregation. Analyst 2014; 139:59-65. [DOI: 10.1039/c3an01307c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
31
|
|
32
|
Wu NY, Gao W, He XL, Chang Z, Xu MT. Direct electrochemical sensor for label-free DNA detection based on zero current potentiometry. Biosens Bioelectron 2013; 39:210-4. [DOI: 10.1016/j.bios.2012.07.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 07/16/2012] [Accepted: 07/21/2012] [Indexed: 11/29/2022]
|
33
|
Ahn S, Freedman DS, Zhang X, Unlü MS. High-throughput label-free detection of DNA hybridization and mismatch discrimination using interferometric reflectance imaging sensor. Methods Mol Biol 2013; 1039:181-200. [PMID: 24026697 DOI: 10.1007/978-1-62703-535-4_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Optical label-free biosensors have demonstrated advantages over fluorescent-based detection methods by allowing accurate quantification while also being capable of measuring dynamic bimolecular interactions. A simple, high-throughput, solid-phase, and label-free technique, interferometric reflectance imaging sensor (IRIS), can quantify the mass density of DNA with pg/mm(2) sensitivity by measuring the optical path difference. We present the design of the IRIS instrument and complementary microarrays that can be used to perform a quantitative analysis of DNA microarrays. Finally, we present methods to accurately calculate the hybridization efficiency and identify SNPs from dynamic measurements, as well as supporting software algorithms needed for robust data processing.
Collapse
Affiliation(s)
- Sunmin Ahn
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | | | | | | |
Collapse
|
34
|
TATA binding proteins can recognize nontraditional DNA sequences. Biophys J 2012; 103:1510-7. [PMID: 23062343 DOI: 10.1016/j.bpj.2012.08.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 08/10/2012] [Accepted: 08/14/2012] [Indexed: 11/21/2022] Open
Abstract
We demonstrate an accurate, quantitative, and label-free optical technology for high-throughput studies of receptor-ligand interactions, and apply it to TATA binding protein (TBP) interactions with oligonucleotides. We present a simple method to prepare single-stranded and double-stranded DNA microarrays with comparable surface density, ensuring an accurate comparison of TBP activity with both types of DNA. In particular, we find that TBP binds tightly to single-stranded DNA, especially to stretches of polythymine (poly-T), as well as to the traditional TATA box. We further investigate the correlation of TBP activity with various lengths of DNA and find that the number of TBPs bound to DNA increases >7-fold as the oligomer length increases from 9 to 40. Finally, we perform a full human genome analysis and discover that 35.5% of human promoters have poly-T stretches. In summary, we report, for the first time to our knowledge, the activity of TBP with poly-T stretches by presenting an elegant stepwise analysis of multiple techniques: discovery by a novel quantitative detection of microarrays, confirmation by a traditional gel electrophoresis, and a full genome prediction with computational analyses.
Collapse
|
35
|
Serdiuk T, Zakharko Y, Nychyporuk T, Geloen A, Lemiti M, Lysenko V. Nanostructured silicon nitride thin films for label-free multicolor luminescent cell imaging. NANOSCALE 2012; 4:5860-5863. [PMID: 22945418 DOI: 10.1039/c2nr31376f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The application of nanostructured luminescent silicon nitride (SiN(X)) thin films for label-free cell imaging is reported for the first time. Different strong local fields ensured by various molecules concentrated in various cell compartments can lead to the creation of preferential electronic conditions for radiative recombination of photogenerated charge carriers via a given electronic channel. Thus, highly contrasted multicolor luminescent cell imaging under one photon excitation becomes possible. The described label-free bio-imaging approach has good compatibility with fluorescence optical microscopy, and allows rapid and efficient cell imaging and cell line recognition.
Collapse
Affiliation(s)
- T Serdiuk
- University of Lyon, CarMeN Laboratory, INSA de Lyon, UMR INSERM 1060, France.
| | | | | | | | | | | |
Collapse
|
36
|
Cretich M, Monroe MR, Reddington A, Zhang X, Daaboul GG, Damin F, Sola L, Unlu MS, Chiari M. Interferometric silicon biochips for label and label-free DNA and protein microarrays. Proteomics 2012; 12:2963-77. [PMID: 22930463 DOI: 10.1002/pmic.201200202] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 08/16/2012] [Accepted: 08/20/2012] [Indexed: 11/12/2022]
Abstract
Protein and DNA microarrays hold the promise to revolutionize the field of molecular diagnostics. Traditional microarray applications employ labeled detection strategies based on the use of fluorescent and chemiluminescent secondary antibodies. However, the development of high throughput, sensitive, label-free detection techniques is attracting attention as they do not require labeled reactants and provide quantitative information on binding kinetics. In this article, we will provide an overview of the recent author's work in label and label-free sensing platforms employing silicon/silicon oxide (Si/SiO(2)) substrates for interferometric and/or fluorescence detection of microarrays. The review will focus on applications of Si/SiO(2) with controlled oxide layers to (i) enhance the fluorescence intensity by optical interferences, (ii) quantify with sub-nanometer accuracy the axial locations of fluorophore-labeled probes tethered to the surface, and (iii) detect protein-protein interactions label free. Different methods of biofunctionalization of the sensing surface will be discussed. In particular, organosilanization reactions for monodimensional coatings and polymeric coatings will be extensively reviewed. Finally, the importance of calibration of protein microarrays through the dual use of labeled and label-free detection schemes on the same chip will be illustrated.
Collapse
Affiliation(s)
- Marina Cretich
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare, Milano, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Ahn S, Spuhler PS, Chiari M, Cabodi M, Ünlü MS. Quantification of surface etching by common buffers and implications on the accuracy of label-free biological assays. Biosens Bioelectron 2012; 36:222-9. [PMID: 22560160 DOI: 10.1016/j.bios.2012.04.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 04/11/2012] [Indexed: 11/29/2022]
Abstract
High throughput analyses in biochemical assays are gaining popularity in the post-genomic era. Multiple label-free detection methods are especially of interest, as they allow quantitative monitoring of biomolecular interactions. It is assumed that the sensor surface is stable to the surrounding medium while the biochemical processes are taking place. Using the Interferometric Reflectance Imaging Sensor (IRIS), we found that buffers commonly used in biochemical reactions can remove silicon dioxide, a material frequently used as the solid support in the microarray industry. Here, we report 53 pm to 731 pm etching of the surface silicon oxide over a 12-h period for several different buffers, including various concentrations of SSC, SSPE, PBS, TRIS, MES, sodium phosphate, and potassium phosphate buffers, and found that PBS and MES buffers are much more benign than the others. We observe a linear dependence of the etch depth over time, and we find the etch rate of silicon dioxide in different buffers that ranges from 2.73±0.76 pm/h in 1M NaCl to 43.54±2.95 pm/h in 6×SSC. The protective effects by chemical modifications of the surface are explored. We demonstrate unaccounted glass etching leading to erroneous results with label-free detection of DNA microarrays, and offer remedies to increase the accuracy of quantitative analysis.
Collapse
Affiliation(s)
- Sunmin Ahn
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | | | | | | | | |
Collapse
|
38
|
Hu L, Wang Y, Wang W, Gao Q, Qi H, Zhang C. Recognition of a C-C mismatch in a DNA duplex using a fluorescent small molecule with application for "off-on" discrimination of C/G mutation. APPLIED SPECTROSCOPY 2012; 66:170-174. [PMID: 22449280 DOI: 10.1366/11-06410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The fluorescent small molecule 2-amino-7-methyl-1,8-naphthyridine (AMND) can selectively bind to a cytosine (C) at a C-C mismatch in double-stranded DNA (dsDNA). The interactions between AMND and C-C mismatch-containing dsDNA were investigated by measuring ultraviolet (UV) absorption as a function of temperature to obtain melting curves as well as circular dichroism and fluorescence spectra. Results show that AMND strongly stabilizes C-C mismatch-containing dsDNA, whereas fully matched duplexes are not stabilized under the same conditions. The fluorescence of AMND was efficiently quenched when it was bound to a C-C mismatch in dsDNA. Binding constants (K(11)), obtained by fluorescence titration, were 1.2 × 10(5) M(-1). Although sensing functions depend on the sequences flanking the mismatch site, the change in AMND fluorescence intensity can be utilized to detect the C-C mismatch-containing dsDNA. Accordingly, discrimination of the C/G mutation in the model sequence (PGR gene rs1255998) was achieved by visualizing fluorescence of AMND. A probe DNA molecule was designed to contain a C opposite the C/G base in the target DNA, and this probe was used to hybridize the target DNA. The fluorescence of AMND was "on" for a C-G match, while the fluorescence was "off" for a C-C mismatch. This assay is simple and does not require DNA labeling.
Collapse
Affiliation(s)
- Liangliang Hu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Materials Science, Shaanxi Normal University, Xi'an 710062, China
| | | | | | | | | | | |
Collapse
|
39
|
Kussrow A, Enders CS, Bornhop DJ. Interferometric methods for label-free molecular interaction studies. Anal Chem 2012; 84:779-92. [PMID: 22060037 PMCID: PMC4317347 DOI: 10.1021/ac202812h] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amanda Kussrow
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, 7330 Stevenson Center, Nashville, Tennessee 37235, United States
| | - Carolyn S. Enders
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, 7330 Stevenson Center, Nashville, Tennessee 37235, United States
| | - Darryl J. Bornhop
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, 7330 Stevenson Center, Nashville, Tennessee 37235, United States
| |
Collapse
|
40
|
Pereira C, Yalçın A, Cretich M, Chiari M, Unlü MS, Nunes D, Bergstein DA. Synergetic chemiluminescence and label-free dual detection for developing a hepatitis protein array. J Immunol Methods 2011; 371:159-64. [PMID: 21718699 DOI: 10.1016/j.jim.2011.06.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Revised: 05/27/2011] [Accepted: 06/03/2011] [Indexed: 12/01/2022]
Abstract
A dual detection system for protein arrays is presented that combines label-free detection by optical interference with chemiluminescence. A planar protein array that targets hepatitis B surface antigen is developed. Surface densities for individual antibody spots are quantitated using optical interference prior to use. Target binding (10 ng/ml) is detected label-free. Target binding (1 ng/ml) is detected by both optical interference and chemiluminescence with the inclusion of secondary antibodies. Binding results using both methods are found to be directly proportion to the capture probe density measured initially. The dual detection system provides the analytical utility of optical interference detection with the established clinical utility of chemiluminescence detection.
Collapse
Affiliation(s)
- C Pereira
- Zoiray Technologies Inc., Boston, MA, USA
| | | | | | | | | | | | | |
Collapse
|
41
|
van Grinsven B, Vanden Bon N, Grieten L, Murib M, Janssens SD, Haenen K, Schneider E, Ingebrandt S, Schöning MJ, Vermeeren V, Ameloot M, Michiels L, Thoelen R, De Ceuninck W, Wagner P. Rapid assessment of the stability of DNA duplexes by impedimetric real-time monitoring of chemically induced denaturation. LAB ON A CHIP 2011; 11:1656-1663. [PMID: 21448492 DOI: 10.1039/c1lc20027e] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In this article, we report on the electronic monitoring of DNA denaturation by NaOH using electrochemical impedance spectroscopy in combination with fluorescence imaging as a reference technique. The probe DNA consisting of a 36-mer fragment was covalently immobilized on nanocrystalline-diamond electrodes and hybridized with different types of 29-mer target DNA (complementary, single-nucleotide defects at two different positions, and a non-complementary random sequence). The mathematical separation of the impedimetric signals into the time constant for NaOH exposure and the intrinsic denaturation-time constants gives clear evidence that the denaturation times reflect the intrinsic stability of the DNA duplexes. The intrinsic time constants correlate with calculated DNA-melting temperatures. The impedimetric method requires minimal instrumentation, is label-free and fast with a typical time scale of minutes and is highly reproducible. The sensor electrodes can be used repetitively. These elements suggest that the monitoring of chemically induced denaturation at room temperature is an interesting approach to measure DNA duplex stability as an alternative to thermal denaturation at elevated temperatures, used in DNA-melting experiments and single nucleotide polymorphism (SNP) analysis.
Collapse
Affiliation(s)
- B van Grinsven
- Hasselt University, Institute for Materials Research, Wetenschapspark 1, B-3590, Diepenbeek, Belgium.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Lopez CA, Daaboul GG, Ahn S, Reddington AP, Monroe MR, Zhang X, Irani RJ, Yu C, Genco CA, Cretich M, Chiari M, Goldberg BB, Connor JH, Ünlü MS. Biomolecular detection employing the Interferometric Reflectance Imaging Sensor (IRIS). J Vis Exp 2011:2694. [PMID: 21587155 PMCID: PMC3197112 DOI: 10.3791/2694] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
The sensitive measurement of biomolecular interactions has use in many fields and industries such as basic biology and microbiology, environmental/agricultural/biodefense monitoring, nanobiotechnology, and more. For diagnostic applications, monitoring (detecting) the presence, absence, or abnormal expression of targeted proteomic or genomic biomarkers found in patient samples can be used to determine treatment approaches or therapy efficacy. In the research arena, information on molecular affinities and specificities are useful for fully characterizing the systems under investigation. Many of the current systems employed to determine molecular concentrations or affinities rely on the use of labels. Examples of these systems include immunoassays such as the enzyme-linked immunosorbent assay (ELISA), polymerase chain reaction (PCR) techniques, gel electrophoresis assays, and mass spectrometry (MS). Generally, these labels are fluorescent, radiological, or colorimetric in nature and are directly or indirectly attached to the molecular target of interest. Though the use of labels is widely accepted and has some benefits, there are drawbacks which are stimulating the development of new label-free methods for measuring these interactions. These drawbacks include practical facets such as increased assay cost, reagent lifespan and usability, storage and safety concerns, wasted time and effort in labelling, and variability among the different reagents due to the labelling processes or labels themselves. On a scientific research basis, the use of these labels can also introduce difficulties such as concerns with effects on protein functionality/structure due to the presence of the attached labels and the inability to directly measure the interactions in real time. Presented here is the use of a new label-free optical biosensor that is amenable to microarray studies, termed the Interferometric Reflectance Imaging Sensor (IRIS), for detecting proteins, DNA, antigenic material, whole pathogens (virions) and other biological material. The IRIS system has been demonstrated to have high sensitivity, precision, and reproducibility for different biomolecular interactions [1-3]. Benefits include multiplex imaging capacity, real time and endpoint measurement capabilities, and other high-throughput attributes such as reduced reagent consumption and a reduction in assay times. Additionally, the IRIS platform is simple to use, requires inexpensive equipment, and utilizes silicon-based solid phase assay components making it compatible with many contemporary surface chemistry approaches. Here, we present the use of the IRIS system from preparation of probe arrays to incubation and measurement of target binding to analysis of the results in an endpoint format. The model system will be the capture of target antibodies which are specific for human serum albumin (HSA) on HSA-spotted substrates.
Collapse
Affiliation(s)
- Carlos A Lopez
- Department of Electrical and Computer Engineering, Boston University, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Lopez CA, Daaboul GG, Vedula RS, Ozkumur E, Bergstein DA, Geisbert TW, Fawcett HE, Goldberg BB, Connor JH, Unlü MS. Label-free multiplexed virus detection using spectral reflectance imaging. Biosens Bioelectron 2011; 26:3432-7. [PMID: 21342761 DOI: 10.1016/j.bios.2011.01.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2010] [Revised: 12/21/2010] [Accepted: 01/14/2011] [Indexed: 10/18/2022]
Abstract
We demonstrate detection of whole viruses and viral proteins with a new label-free platform based on spectral reflectance imaging. The Interferometric Reflectance Imaging Sensor (IRIS) has been shown to be capable of sensitive protein and DNA detection in a real time and high-throughput format. Vesicular stomatitis virus (VSV) was used as the target for detection as it is well-characterized for protein composition and can be modified to express viral coat proteins from other dangerous, highly pathogenic agents for surrogate detection while remaining a biosafety level 2 agent. We demonstrate specific detection of intact VSV virions achieved with surface-immobilized antibodies acting as capture probes which is confirmed using fluorescence imaging. The limit of detection is confirmed down to 3.5 × 10(5)plaque-forming units/mL (PFUs/mL). To increase specificity in a clinical scenario, both the external glycoprotein and internal viral proteins were simultaneously detected with the same antibody arrays with detergent-disrupted purified VSV and infected cell lysate solutions. Our results show sensitive and specific virus detection with a simple surface chemistry and minimal sample preparation on a quantitative label-free interferometric platform.
Collapse
Affiliation(s)
- Carlos A Lopez
- Department of Electrical & Computer Engineering, Boston University, Boston, MA 02215, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Monroe MR, Reddington AP, Cretich M, Chiari M, Little F, Ünlü MS. Multiplexed, rapid point of care platform to quantify allergen-specific IgE. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2011; 2011:478-481. [PMID: 22254352 PMCID: PMC3640299 DOI: 10.1109/iembs.2011.6090069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Variation of probe immobilization on microarrays hinders the ability to make high quality, assertive and statistically relevant conclusions needed in the healthcare setting. To address this problem, we have developed a calibrated, compact, inexpensive, multiplexed, dual modality point-of-care detection platform that calibrates and correlates surface probe density measured label-free to captured labeled secondary antibody, is independent of chip-to-chip variability, and improves upon existing diagnostic technology. We have identified four major technological advantages of our proposed platform: the capability to perform single spot analysis based on the fluorophore used for detection, a 10-fold gain in fluorescence signal due to optimized substrate, a calibrated, quantitative method that uses the combined fluorescent and label-free modalities to accurately measure the density of probe and bound target for a variety of systems, and a compact measurement platform offering reliable and rapid results at the doctor's office. Already, we have formulated over a 90% linear correlation between the amount of probe bound to surface and the resulting fluorescence of captured target for IgG, β-lactoglobulin, Ara h 1 peanut allergen, and Phl 5a Timothy grass allergen.
Collapse
Affiliation(s)
- M. R. Monroe
- Biomedical Engineering Department Boston University, Boston, Ma, 02446 USA (386-490-2636)
| | - A. P. Reddington
- Electrical Engineering Department, Boston University, Boston, Ma 02446 USA
| | - M. Cretich
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Milano, Italy
| | - M. Chiari
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Milano, Italy
| | - F. Little
- Pulmony Center at Boston University School of Medicine, Boston, Ma 02118 USA
| | - M. S. Ünlü
- Biomedical Engineering, Electrical Engineering, and Physics Departments, Boston University, Boston, Ma 02446 USA
| |
Collapse
|
45
|
Zhang Z, Wang X, Wang Y, Yang X. Distinction of single base mismatches in duplex DNA using methylene blue as optical indicator. Analyst 2010; 135:2960-4. [DOI: 10.1039/c0an00359j] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
|