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Myres GJ, Kitt JP, Harris JM. Surface-Area Enhanced Raman Spectroscopy of DNA in Porous Silica: A Quantitative and Reproducible Alternative to Plasmonic-Based SERS. Anal Chem 2024; 96:7679-7686. [PMID: 38698534 DOI: 10.1021/acs.analchem.4c00600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Despite the success of surface-enhanced Raman spectroscopy (SERS) for detecting DNA immobilized on plasmonic metal surfaces, its quantitative response is limited by the rapid falloff of enhancement with distance from the metal surface and variations in sensitivity that depend on orientation and proximity to plasmonic "hot spots". In this work, we assess an alternative approach for enhancing detection by immobilizing DNA on the interior surfaces of porous silica particles. These substrates provide over a 1000-fold greater surface area for detection compared to a planar support. The porous silica substrate is a purely dielectric material with randomly oriented internal surfaces, where scattering is independent of proximity and orientation of oligonucleotides relative to the silica surface. We characterize the quantitative response of Raman scattering from DNA in porous silica particles with sequences used in previous SERS investigations of DNA for comparison. The results show that Raman scattering of DNA in porous silica is independent of distance of nucleotides from the silica surface, allowing detection of longer DNA strands with constant sensitivity. The surface area enhancement within particles is reproducible (<4% particle-to-particle variation) owing to the uniform internal pore structure and surface chemistry of the silica support. DNA immobilization with a bis-thiosuccinimide linker provides a Raman-active internal standard for quantitative interpretation of Raman scattering results. Despite the high (30 mM) concentrations of immobilized DNA within porous silica particles, they can be used to measure nanomolar binding affinities of target molecules to DNA by equilibrating a very small number of particles with a sufficiently large volume of low-concentration solution of target molecules.
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Affiliation(s)
- Grant J Myres
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Jay P Kitt
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Joel M Harris
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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Myres GJ, Kitt JP, Harris JM. Raman Scattering Reveals Ion-Dependent G-Quadruplex Formation in the 15-mer Thrombin-Binding Aptamer upon Association with α-Thrombin. Anal Chem 2023; 95:16160-16168. [PMID: 37870982 DOI: 10.1021/acs.analchem.3c02751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The discovery of DNA aptamers that bind biomolecular targets has enabled significant innovations in biosensing. Aptamers form secondary structures that exhibit selective high-affinity interactions with their binding partners. The binding of its target by an aptamer is often accompanied by conformational changes, and sensing by aptamers often relies on these changes to provide readout signals from extrinsic labels to detect target association. Many biosensing applications involve aptamers immobilized to surfaces, but methods to characterize conformations of immobilized aptamers and their in situ response have been lacking. To address this challenge, we have developed a structurally informative Raman spectroscopy method to determine conformations of the 15-mer thrombin-binding aptamer (TBA) immobilized on porous silica surfaces. The TBA is of interest because its binding of α-thrombin depends on the aptamer forming an antiparallel G-quadruplex, which is thought to drive signal changes that allow thrombin-binding to be detected. However, specific metal cations also stabilize the G-quadruplex conformation of the aptamer, even in the absence of its protein target. To develop a deeper understanding of the conformational response of the TBA, we utilize Raman spectroscopy to quantify the effects of the metal cations, K+ (stabilizing) and Li+ (nonstabilizing), on G-quadruplex versus unfolded populations of the TBA. In K+ or Li+ solutions, we then detect the association of α-thrombin with the immobilized aptamer, which can be observed in Raman scattering from the bound protein. The results show that the association of α-thrombin in K+ solutions produces no detectable change in aptamer conformation, which is found in the G-quadruplex form both before and after binding its target. In Li+ solutions, however, where the TBA is unfolded prior to α-thrombin association, protein binding occurs with the formation of a G-quadruplex by the aptamer.
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Affiliation(s)
- Grant J Myres
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Jay P Kitt
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Joel M Harris
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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Bekkouche I, Kuznetsova MN, Rejepov DT, Vetcher AA, Shishonin AY. Recent Advances in DNA Nanomaterials. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:2449. [PMID: 37686956 PMCID: PMC10490369 DOI: 10.3390/nano13172449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023]
Abstract
Applications of DNA-containing nanomaterials (DNA-NMs) in science and technology are currently attracting increasing attention in the fields of medicine, environment, engineering, etc. Such objects have become important for various branches of science and industries due to their outstanding characteristics such as small size, high controllability, clustering actions, and strong permeability. For these reasons, DNA-NMs deserve a review with respect to their recent advancements. On the other hand, precise cluster control, targeted drug distribution in vivo, and cellular micro-nano operation remain as problems. This review summarizes the recent progress in DNA-NMs and their crossover and integration into multiple disciplines (including in vivo/in vitro, microcircles excisions, and plasmid oligomers). We hope that this review will motivate relevant practitioners to generate new research perspectives and boost the advancement of nanomanipulation.
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Affiliation(s)
- Incherah Bekkouche
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia n.a. P. Lumumba (RUDN), Miklukho-Maklaya St. 6, Moscow 117198, Russia; (M.N.K.); (D.T.R.)
| | - Maria N. Kuznetsova
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia n.a. P. Lumumba (RUDN), Miklukho-Maklaya St. 6, Moscow 117198, Russia; (M.N.K.); (D.T.R.)
| | - Dovlet T. Rejepov
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia n.a. P. Lumumba (RUDN), Miklukho-Maklaya St. 6, Moscow 117198, Russia; (M.N.K.); (D.T.R.)
| | - Alexandre A. Vetcher
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia n.a. P. Lumumba (RUDN), Miklukho-Maklaya St. 6, Moscow 117198, Russia; (M.N.K.); (D.T.R.)
- Complementary and Integrative Health Clinic of Dr. Shishonin, 5, Yasnogorskaya Str., Moscow 117588, Russia;
| | - Alexander Y. Shishonin
- Complementary and Integrative Health Clinic of Dr. Shishonin, 5, Yasnogorskaya Str., Moscow 117588, Russia;
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Flatebo C, Conkright WR, Beckner ME, Batchelor RH, Kippin TE, Heikenfeld J, Plaxco KW. Efforts toward the continuous monitoring of molecular markers of performance. J Sci Med Sport 2023:S1440-2440(23)00028-2. [PMID: 36841706 DOI: 10.1016/j.jsams.2023.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 01/04/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023]
Abstract
OBJECTIVES Technologies supporting the continuous, real-time measurement of blood oxygen saturation and plasma glucose levels have improved our ability to monitor performance status. Our ability to monitor other molecular markers of performance, however, including the hormones known to indicate overtraining and general health, has lagged. That is, although a number of other molecular markers of performance status have been identified, we have struggled to develop viable technologies supporting their real-time monitoring in the body. Here we review biosensor approaches that may support such measurements, as well as the molecules potentially of greatest interest to monitor. DESIGN Narrative literature review. METHOD Literature review. RESULTS Significant effort has been made to harness the specificity, affinity, and generalizability of biomolecular recognition in a platform technology supporting continuous in vivo molecular measurements. Most biosensor approaches, however, are either not generalizable to most targets, or fail when challenged in the complex environments found in vivo. Electrochemical aptamer-based sensors, in contrast, are the first technology to simultaneously achieve both of these critical attributes. In an effort to illustrate the potential of this platform technology, we both critically review the literature describing it and briefly survey some of the molecular performance markers we believe will prove advantageous to monitor using it. CONCLUSIONS Electrochemical aptamer-based sensors may be the first truly generalizable technology for monitoring specific molecules in situ in the body and how adaptation of the platform to subcutaneous microneedles will enable the real-time monitoring of performance markers via a wearable, minimally invasive device.
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Affiliation(s)
- Charlotte Flatebo
- Institute for Collaborative Biotechnologies, University of California Santa Barbara, USA
| | | | | | | | - Tod E Kippin
- Neuroscience Research Institute, Department of Psychological and Brain Sciences, University of California Santa Barbara, USA
| | - Jason Heikenfeld
- Biomedical, Electrical, and Chemical Engineering, Director Novel Devices Laboratory, University of Cincinnati, USA
| | - Kevin W Plaxco
- Institute for Collaborative Biotechnologies, University of California Santa Barbara, USA; Department of Chemistry and Biochemistry, Biological Engineering Graduate Program, University of California Santa Barbara, USA.
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5
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Huang Z, Hu B, Wang H. Analytical methods for microplastics in the environment: a review. ENVIRONMENTAL CHEMISTRY LETTERS 2023; 21:383-401. [PMID: 36196263 PMCID: PMC9521859 DOI: 10.1007/s10311-022-01525-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 07/21/2022] [Indexed: 05/06/2023]
Abstract
Microplastic pollution is a recently discovered threat to ecosystems requiring the development of new analytical methods. Here, we review classical and advanced methods for microplastic analysis. Methods include visual analysis, laser diffraction particle, dynamic light scattering, scanning electron microscopy, Fourier-transform infrared spectroscopy, Raman spectroscopy, thermal analysis, mass spectrometry, aptamer and in vitro selection, and flow cytometry.
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Affiliation(s)
- Zike Huang
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083 China
| | - Bo Hu
- School of Engineering, The University of Edinburgh, Edinburgh, EH9 3JW UK
| | - Hui Wang
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083 China
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Karawdeniya BI, Damry AM, Murugappan K, Manjunath S, Bandara YMNDY, Jackson CJ, Tricoli A, Neshev D. Surface Functionalization and Texturing of Optical Metasurfaces for Sensing Applications. Chem Rev 2022; 122:14990-15030. [PMID: 35536016 DOI: 10.1021/acs.chemrev.1c00990] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Optical metasurfaces are planar metamaterials that can mediate highly precise light-matter interactions. Because of their unique optical properties, both plasmonic and dielectric metasurfaces have found common use in sensing applications, enabling label-free, nondestructive, and miniaturized sensors with ultralow limits of detection. However, because bare metasurfaces inherently lack target specificity, their applications have driven the development of surface modification techniques that provide selectivity. Both chemical functionalization and physical texturing methodologies can modify and enhance metasurface properties by selectively capturing analytes at the surface and altering the transduction of light-matter interactions into optical signals. This review summarizes recent advances in material-specific surface functionalization and texturing as applied to representative optical metasurfaces. We also present an overview of the underlying chemistry driving functionalization and texturing processes, including detailed directions for their broad implementation. Overall, this review provides a concise and centralized guide for the modification of metasurfaces with a focus toward sensing applications.
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Affiliation(s)
- Buddini I Karawdeniya
- ARC Centre of Excellence for Transformative Meta Optical Systems (TMOS), Department of Electronic Materials Engineering, Research School of Physics, The Australian National University, Canberra, ACT 2600, Australia
| | - Adam M Damry
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Krishnan Murugappan
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Shridhar Manjunath
- ARC Centre of Excellence for Transformative Meta Optical Systems (TMOS), Department of Electronic Materials Engineering, Research School of Physics, The Australian National University, Canberra, ACT 2600, Australia
| | - Y M Nuwan D Y Bandara
- ARC Centre of Excellence for Transformative Meta Optical Systems (TMOS), Department of Electronic Materials Engineering, Research School of Physics, The Australian National University, Canberra, ACT 2600, Australia
| | - Colin J Jackson
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Antonio Tricoli
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601, Australia
- School of Biomedical Engineering, Faculty of Engineering, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Dragomir Neshev
- ARC Centre of Excellence for Transformative Meta Optical Systems (TMOS), Department of Electronic Materials Engineering, Research School of Physics, The Australian National University, Canberra, ACT 2600, Australia
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Wang B, Zhao C, Wang Z, Yang KA, Cheng X, Liu W, Yu W, Lin S, Zhao Y, Cheung KM, Lin H, Hojaiji H, Weiss PS, Stojanović MN, Tomiyama AJ, Andrews AM, Emaminejad S. Wearable aptamer-field-effect transistor sensing system for noninvasive cortisol monitoring. SCIENCE ADVANCES 2022; 8:eabk0967. [PMID: 34985954 PMCID: PMC8730602 DOI: 10.1126/sciadv.abk0967] [Citation(s) in RCA: 94] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Wearable technologies for personalized monitoring require sensors that track biomarkers often present at low levels. Cortisol—a key stress biomarker—is present in sweat at low nanomolar concentrations. Previous wearable sensing systems are limited to analytes in the micromolar-millimolar ranges. To overcome this and other limitations, we developed a flexible field-effect transistor (FET) biosensor array that exploits a previously unreported cortisol aptamer coupled to nanometer-thin-film In2O3 FETs. Cortisol levels were determined via molecular recognition by aptamers where binding was transduced to electrical signals on FETs. The physiological relevance of cortisol as a stress biomarker was demonstrated by tracking salivary cortisol levels in participants in a Trier Social Stress Test and establishing correlations between cortisol in diurnal saliva and sweat samples. These correlations motivated the development and on-body validation of an aptamer-FET array–based smartwatch equipped with a custom, multichannel, self-referencing, and autonomous source measurement unit enabling seamless, real-time cortisol sweat sensing.
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Affiliation(s)
- Bo Wang
- Interconnected and Integrated Bioelectronics Lab (IBL), Department of Electrical and Computer Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Chuanzhen Zhao
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zhaoqing Wang
- Interconnected and Integrated Bioelectronics Lab (IBL), Department of Electrical and Computer Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kyung-Ae Yang
- Division of Experimental Therapeutics, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Xuanbing Cheng
- Interconnected and Integrated Bioelectronics Lab (IBL), Department of Electrical and Computer Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Wenfei Liu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Wenzhuo Yu
- Interconnected and Integrated Bioelectronics Lab (IBL), Department of Electrical and Computer Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Shuyu Lin
- Interconnected and Integrated Bioelectronics Lab (IBL), Department of Electrical and Computer Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yichao Zhao
- Interconnected and Integrated Bioelectronics Lab (IBL), Department of Electrical and Computer Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kevin M. Cheung
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Haisong Lin
- Interconnected and Integrated Bioelectronics Lab (IBL), Department of Electrical and Computer Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Hannaneh Hojaiji
- Interconnected and Integrated Bioelectronics Lab (IBL), Department of Electrical and Computer Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Paul S. Weiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Milan N. Stojanović
- Division of Experimental Therapeutics, Department of Medicine, Columbia University, New York, NY 10032, USA
- Department of Biomedical Engineering, Columbia University, New York, NY 10032, USA
| | - A. Janet Tomiyama
- Department of Psychology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Anne M. Andrews
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Hatos Center for Neuropharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Corresponding author. (A.M.A.); (S.E.)
| | - Sam Emaminejad
- Interconnected and Integrated Bioelectronics Lab (IBL), Department of Electrical and Computer Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Corresponding author. (A.M.A.); (S.E.)
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Daems E, Moro G, Campos R, De Wael K. Mapping the gaps in chemical analysis for the characterisation of aptamer-target interactions. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116311] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Cao X, Song Q, Sun Y, Mao Y, Lu W, Li L. A SERS-LFA biosensor combined with aptamer recognition for simultaneous detection of thrombin and PDGF-BB in prostate cancer plasma. NANOTECHNOLOGY 2021; 32:445101. [PMID: 34298537 DOI: 10.1088/1361-6528/ac1754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/23/2021] [Indexed: 06/13/2023]
Abstract
An innovative surface-enhanced Raman spectroscopy and lateral flow assay (SERS-LFA) biosensor combined with aptamer recognition had been developed for the convenient, rapid, sensitive and accurate detection of thrombin and platelet-derived growth factor-BB (PDGF-BB) associated with prostate cancer simultaneously. During the biosensor operation, thrombin and PDGF-BB in the sample were recognized and combined by thiol-modified aptamers immobilized on Au-Ag hollow nanoparticles (Au-Ag HNPs) surface and biotinylated aptamers immobilized on the test lines of the biosensor. Thus, thrombin and PDGF-BB were simultaneously captured between detection aptamers and capture aptamers in a sandwich structure. Finite difference time domain simulation confirmed that 'hot spots' appeared at the gaps of Au-Ag HNPs dimer in the enhanced electromagnetic field compared to that of a single Au-Ag HNP, indicating that the aggregated Au-Ag HNPs owned a good SERS signal amplification effect. The detection limits of thrombin and PDGF-BB in human plasma were as low as 4.837 pg ml-1and 3.802 pg ml-1, respectively. Moreover, the accuracy of the biosensor which was applied to detect thrombin and PDGF-BB in prostate cancer plasma had been verified. This designed biosensor had broad application prospects in the clinical diagnosis of prostate cancer.
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Affiliation(s)
- Xiaowei Cao
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, People's Republic of China
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, People's Republic of China
- Jiangsu Key Laboratory of Experimental & Translational Noncoding RNA Research, Medical College, Yangzhou University, Yangzhou, People's Republic of China
| | - Qilong Song
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, People's Republic of China
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, People's Republic of China
- Jiangsu Key Laboratory of Experimental & Translational Noncoding RNA Research, Medical College, Yangzhou University, Yangzhou, People's Republic of China
| | - Yue Sun
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, People's Republic of China
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, People's Republic of China
- Jiangsu Key Laboratory of Experimental & Translational Noncoding RNA Research, Medical College, Yangzhou University, Yangzhou, People's Republic of China
| | - Yu Mao
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, People's Republic of China
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, People's Republic of China
- Jiangsu Key Laboratory of Experimental & Translational Noncoding RNA Research, Medical College, Yangzhou University, Yangzhou, People's Republic of China
| | - Wenbo Lu
- Shanxi Normal University, College of Chemistry and Material Science, Linfen, 041004, People's Republic of China
| | - Li Li
- Children's Hospital of Nanjing Medical University, Nanjing, People's Republic of China
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10
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Nakatsuka N, Heard KJ, Faillétaz A, Momotenko D, Vörös J, Gage FH, Vadodaria KC. Sensing serotonin secreted from human serotonergic neurons using aptamer-modified nanopipettes. Mol Psychiatry 2021; 26:2753-2763. [PMID: 33767349 PMCID: PMC9997689 DOI: 10.1038/s41380-021-01066-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/17/2021] [Accepted: 03/11/2021] [Indexed: 02/01/2023]
Abstract
The serotonergic system in the human brain modulates several physiological processes, and altered serotonergic neurotransmission has been implicated in the neuropathology of several psychiatric disorders. The study of serotonergic neurotransmission in psychiatry has long been restricted to animal models, but advances in cell reprogramming technology have enabled the generation of serotonergic neurons from patient-induced pluripotent stem cells (iPSCs). While iPSC-derived human serotonergic neurons offer the possibility to study serotonin (5-HT) release and uptake, particularly by 5-HT-modulating drugs such as selective serotonin reuptake inhibitors (SSRIs), a major limitation is the inability to reliably quantify 5-HT secreted from neurons in vitro. Herein, we address this technical gap via a novel sensing technology that couples 5-HT-specific DNA aptamers into nanopores (glass nanopipettes) with orifices of ~10 nm to detect 5-HT in complex neuronal culture medium with higher selectivity, sensitivity, and stability than existing methods. The 5-HT aptamers undergo conformational rearrangement upon target capture and serve as gatekeepers of ionic flux through the nanopipette opening. We generated human serotonergic neurons in vitro and detected secreted 5-HT using aptamer-coated nanopipettes in a low nanomolar range, with the possibility of detecting significantly lower (picomolar) concentrations. Furthermore, as a proof of concept, we treated human serotonergic neurons in vitro with the SSRI citalopram and detected a significant increase in extracellular 5-HT using the aptamer-modified nanopipettes. We demonstrate the utility of such methods for 5-HT detection, raising the possibility of fast quantification of neurotransmitters secreted from patient-derived live neuronal cells.
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Affiliation(s)
- Nako Nakatsuka
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, Zurich, Switzerland
| | - Kelly J Heard
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Alix Faillétaz
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, Zurich, Switzerland
| | - Dmitry Momotenko
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, Zurich, Switzerland
| | - János Vörös
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, Zurich, Switzerland
| | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Krishna C Vadodaria
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA.
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11
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Myres GJ, Peterson EM, Harris JM. Confocal Raman Microscopy Enables Label-Free, Quantitative, and Structurally Informative Detection of DNA Hybridization at Porous Silica Surfaces. Anal Chem 2021; 93:7978-7986. [PMID: 34037395 DOI: 10.1021/acs.analchem.1c00885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Characterization of DNA at solid/liquid interfaces remains a challenge because most surface-sensitive techniques are unable to provide quantitative insight into the base content, length, or structure. Surface-enhanced Raman scattering measurements of DNA hybridization on plasmonic-metal substrates have been used to overcome small Raman-scattering cross-sections; however, surface-enhanced Raman spectroscopy measurements are not generally quantitative due to the fall-off in the scattering signal with the decay of the electric field enhancement from the surface, which also limits the length of oligonucleotides that can be investigated. In this work, we introduce an experimental methodology in which confocal Raman microscopy is used to characterize hybridization reactions of ssDNA immobilized at the solid/liquid interface of porous silica particles. By focusing the femtoliter confocal probe volume within a single porous particle, signal enhancement arises from the ∼1500-times greater surface area detected compared to a planar substrate. Because the porous support is a purely dielectric material, the scattering signal is independent of the proximity of the oligonucleotide to the silica surface. With this technique, we characterize a 19-mer capture strand and determine its hybridization efficiency with 9-mer and 16-mer target sequences from the scattering of a structurally insensitive phosphate-stretching mode. Changes in polarizability and frequency of scattering from DNA bases were observed, which are consistent with Watson-Crick base pairing. Quantification of base content from their duplex scattering intensities allows us to discriminate between hybridization of two target strands of equivalent length but with different recognition sequences. A duplex having a single-nucleotide polymorphism could be distinguished from hybridization of a fully complementary strand based on differences in base content and duplex conformation.
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Affiliation(s)
- Grant J Myres
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Eric M Peterson
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Joel M Harris
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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12
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Kumaravel S, Karthick K, Sankar SS, Karmakar A, Madhu R, Kundu S. Prospects in interfaces of biomolecule DNA and nanomaterials as an effective way for improvising surface enhanced Raman scattering: A review. Adv Colloid Interface Sci 2021; 291:102399. [PMID: 33774595 DOI: 10.1016/j.cis.2021.102399] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/27/2021] [Accepted: 03/01/2021] [Indexed: 01/20/2023]
Abstract
Surface Enhanced Raman Scattering (SERS) is a field of research that has shown promising application in the analysis of various substrate molecules by means of rough metallic surfaces. In directing the enhancement of substrate molecules in micro and nano-molar concentrations, plasmonic coupling of metal nanoparticles (NPs), morphology of metal NPs and the closely arrangement of rough metal surfaces that produces 'hot spots' can effectively increase the so-called enhancement factor (EF) that will be applicable in various fields. As the mechanistic aspects are still not clear, research has been triggered all over the world for the past two decades to have a clear understanding in chemical and electromagnetic effects. As the reproducibility of intensity of signals at low concentrations of probe molecules is of a big concern, metal NPs with various scaffolds were prepared and recently bio-molecule, DNA has been studied and showed promising advantages. This review first time highlights metal NPs with DNA interface as an effective rough metallic surface for SERS with high intensity and also with better reproducibility. Based on this review, similar kinds of scaffolds like DNA can be used to further analyze SERS activities of various metal NPs with different morphologies to have high intense signals at low concentrations of probe molecules.
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Affiliation(s)
- Sangeetha Kumaravel
- Electrochemical Process Engineering (EPE) Division, CSIR-Central Electrochemical Research Institute (CECRI), Karaikudi 630003, Tamil Nadu, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Kannimuthu Karthick
- Electrochemical Process Engineering (EPE) Division, CSIR-Central Electrochemical Research Institute (CECRI), Karaikudi 630003, Tamil Nadu, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Selvasundarasekar Sam Sankar
- Electrochemical Process Engineering (EPE) Division, CSIR-Central Electrochemical Research Institute (CECRI), Karaikudi 630003, Tamil Nadu, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Arun Karmakar
- Electrochemical Process Engineering (EPE) Division, CSIR-Central Electrochemical Research Institute (CECRI), Karaikudi 630003, Tamil Nadu, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ragunath Madhu
- Electrochemical Process Engineering (EPE) Division, CSIR-Central Electrochemical Research Institute (CECRI), Karaikudi 630003, Tamil Nadu, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Subrata Kundu
- Electrochemical Process Engineering (EPE) Division, CSIR-Central Electrochemical Research Institute (CECRI), Karaikudi 630003, Tamil Nadu, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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13
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Nakatsuka N, Abendroth JM, Yang KA, Andrews AM. Divalent Cation Dependence Enhances Dopamine Aptamer Biosensing. ACS APPLIED MATERIALS & INTERFACES 2021; 13:9425-9435. [PMID: 33410656 PMCID: PMC7933093 DOI: 10.1021/acsami.0c17535] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Oligonucleotide receptors (aptamers), which change conformation upon target recognition, enable electronic biosensing under high ionic-strength conditions when coupled to field-effect transistors (FETs). Because highly negatively charged aptamer backbones are influenced by ion content and concentration, biosensor performance and target sensitivities were evaluated under application conditions. For a recently identified dopamine aptamer, physiological concentrations of Mg2+ and Ca2+ in artificial cerebrospinal fluid produced marked potentiation of dopamine FET-sensor responses. By comparison, divalent cation-associated signal amplification was not observed for FET sensors functionalized with a recently identified serotonin aptamer or a previously reported dopamine aptamer. Circular dichroism spectroscopy revealed Mg2+- and Ca2+-induced changes in target-associated secondary structure for the new dopamine aptamer, but not the serotonin aptamer nor the old dopamine aptamer. Thioflavin T displacement corroborated the Mg2+ dependence of the new dopamine aptamer for target detection. These findings imply allosteric binding interactions between divalent cations and dopamine for the new dopamine aptamer. Developing and testing sensors in ionic environments that reflect intended applications are best practices for identifying aptamer candidates with favorable attributes and elucidating sensing mechanisms.
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Affiliation(s)
- Nako Nakatsuka
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - John M. Abendroth
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Kyung-Ae Yang
- Division of Experimental Therapeutics, Department of Medicine, Columbia University, New York, New York 10032, United States
| | - Anne M. Andrews
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, United States
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, and Hatos Center for Neuropharmacology, University of California, Los Angeles, Los Angeles, CA 90095, United States
- Corresponding Author:
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14
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Caprara D, Ripanti F, Capocefalo A, Ceccarini M, Petrillo C, Postorino P. Exploiting SERS sensitivity to monitor DNA aggregation properties. Int J Biol Macromol 2020; 170:88-93. [PMID: 33358955 DOI: 10.1016/j.ijbiomac.2020.12.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/19/2020] [Accepted: 12/05/2020] [Indexed: 01/11/2023]
Abstract
In the last decades, DNA has been considered far more than the system carrying the essential genetic instructions. Indeed, because of the remarkable properties of the base-pairing specificity and thermoreversibility of the interactions, DNA plays a central role in the design of innovative architectures at the nanoscale. Here, combining complementary DNA strands with a custom-made solution of silver nanoparticles, we realize plasmonic aggregates to exploit the sensitivity of Surface Enhanced Raman Spectroscopy (SERS) for the identification/detection of the distinctive features of DNA hybridization, both in solution and on dried samples. Moreover, SERS allows monitoring the DNA aggregation process by following the temperature variation of a specific spectroscopic marker associated with the Watson-Crick hydrogen bond formation. This temperature-dependent behavior enables us to precisely reconstruct the melting profile of the selected DNA sequences by spectroscopic measurements only.
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Affiliation(s)
- Debora Caprara
- Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | | | - Angela Capocefalo
- Istituto dei Sistemi Complessi-CNR c/o Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Marina Ceccarini
- National Centre for Rare Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Caterina Petrillo
- Physics and Geology Department, University of Perugia, Via A. Pascoli, 06123 Perugia, Italy
| | - Paolo Postorino
- Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
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15
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Arshavsky-Graham S, Urmann K, Salama R, Massad-Ivanir N, Walter JG, Scheper T, Segal E. Aptamers vs. antibodies as capture probes in optical porous silicon biosensors. Analyst 2020; 145:4991-5003. [PMID: 32519701 DOI: 10.1039/d0an00178c] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Over the past decade aptamers have emerged as a promising class of bioreceptors for biosensing applications with significant advantages over conventional antibodies. However, experimental studies comparing aptasensors and immunosensors, under equivalent conditions, are limited and the results are inconclusive, in terms of benefits and limitations of each bioreceptor type. In the present work, the performance of aptamer and antibody bioreceptors for the detection of a his-tagged protein, used as a model target, is compared. The bioreceptors are immobilized onto a nanostructured porous silicon (PSi) thin film, used as the optical transducer, and the target protein is detected in a real-time and label-free format by reflective interferometric Fourier transform spectroscopy. For the antibodies, random-oriented immobilization onto the PSi nanostructure results in a poor biosensing performance. Contrary, Fc-oriented immobilization of the antibodies shows a similar biosensing performance to that exhibited by the aptamer-based biosensor, in terms of binding rate, dynamic detection range, limit of detection and selectivity. The aptasensor outperforms in terms of its reusability and storability, while the immunosensor could not be regenerated for subsequent experiments.
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Affiliation(s)
- Sofia Arshavsky-Graham
- Institute of Technical Chemistry, Leibniz University of Hannover, Callinstr. 5, 30167 Hannover, Germany.
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16
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Plasmonic biosensors relying on biomolecular conformational changes: Case of odorant binding proteins. Methods Enzymol 2020; 642:469-493. [PMID: 32828265 DOI: 10.1016/bs.mie.2020.04.068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Plasmonic nanostructures serve in a range of analytical techniques that were developed for the analysis of chemical and biological species. Among others, they have been pursued for the investigation of odorant binding proteins (OBP) and their interaction with odorant molecules. These compounds are low molecular weight agents, which makes their direct detection with conventional surface plasmon resonance (SPR) challenging. Therefore, other plasmonic sensor modalities need to be implemented for the detection and interaction analysis of OBPs. This chapter provides a guide for carrying out such experiments based on two techniques that take advantage of conformation changes of OBPs occurring upon specific interaction with their affinity partners. First, there is discussed SPR monitoring of conformation changes of biomolecules that are not accompanied by a strong increase in the surface mass density but rather with its re-distribution perpendicular to the surface. Second, the implementation of surface plasmon-enhanced fluorescence energy transfer is presented for the sensitive monitoring of conformational changes of biomolecules tagged with a fluorophore at its defined part. Examples from our and other laboratories illustrate the performance of these concepts and their applicability for the detection of low molecular weight odorant molecules by the use of OBPs attached to the sensor surface is discussed.
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17
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Cui X, Song M, Liu Y, Yuan Y, Huang Q, Cao Y, Lu F. Identifying conformational changes of aptamer binding to theophylline: A combined biolayer interferometry, surface-enhanced Raman spectroscopy, and molecular dynamics study. Talanta 2020; 217:121073. [PMID: 32498900 DOI: 10.1016/j.talanta.2020.121073] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/14/2020] [Accepted: 04/20/2020] [Indexed: 11/20/2022]
Abstract
Theophylline is a potent bronchodilator for the treatment of asthma, bronchitis, and emphysema. Its narrow therapeutic window (20-100 μM) demands that the blood concentration of theophylline be monitored carefully, which can be achieved by aptamer capture. Thus, an understanding of what occurs when aptamers bind to theophylline is critical for identifying a high-affinity and high-specificity aptamer, which improve the sensitivity and selectivity of theophylline detection. Consequently, there is an urgent need to develop a simple, convenient, and nondestructive method to monitor conformational changes during the binding process. Here, we report the determination of the affinity of a selected aptamer and theophylline via biolayer interferometry (BLI) experiments. Additionally, using surface-enhanced Raman spectroscopy (SERS), the conformational changes on theophylline-aptamer binding were identified from differences in the SER spectra. Finally, molecular dynamics (MD) simulations were used to identify the specific conformational changes of the aptamer during the binding process. Such a combined BLI-SERS-MD method provides an in-depth understanding of the theophylline-aptamer binding processes and a comprehensive explanation for conformational changes, which helps to select, design, and modify an aptamer with high affinity and specificity. It can also be used as a scheme for the study of other aptamer-ligand interactions, which can be applied to the detection, sensing, clinical diagnosis, and treatment of diseases.
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Affiliation(s)
- Xiaolin Cui
- School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Menghua Song
- State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yan Liu
- School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Yifan Yuan
- School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Qiang Huang
- State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yongbing Cao
- Institute of Vascular Disease, Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200082, China
| | - Feng Lu
- School of Pharmacy, Second Military Medical University, Shanghai, 200433, China; Shanghai Key Laboratory for Pharmaceutical Metabolite Research, Shanghai, 200433, China.
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18
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Solomon ML, Saleh AAE, Poulikakos LV, Abendroth JM, Tadesse LF, Dionne JA. Nanophotonic Platforms for Chiral Sensing and Separation. Acc Chem Res 2020; 53:588-598. [PMID: 31913015 DOI: 10.1021/acs.accounts.9b00460] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chirality in Nature can be found across all length scales, from the subatomic to the galactic. At the molecular scale, the spatial dissymmetry in the atomic arrangements of pairs of mirror-image molecules, known as enantiomers, gives rise to fascinating and often critical differences in chemical and physical properties. With increasing hierarchical complexity, protein function, cell communication, and organism health rely on enantioselective interactions between molecules with selective handedness. For example, neurodegenerative and neuropsychiatric disorders including Alzheimer's and Parkinson's diseases have been linked to distortion of chiral-molecular structure. Moreover, d-amino acids have become increasingly recognized as potential biomarkers, necessitating comprehensive analytical methods for diagnosis that are capable of distinguishing l- from d-forms and quantifying trace concentrations of d-amino acids. Correspondingly, many pharmaceuticals and agrochemicals consist of chiral molecules that target particular enantioselective pathways. Yet, despite the importance of molecular chirality, it remains challenging to sense and to separate chiral compounds. Chiral-optical spectroscopies are designed to analyze the purity of chiral samples, but they are often insensitive to the trace enantiomeric excess that might be present in a patient sample, such as blood, urine, or sputum, or pharmaceutical product. Similarly, existing separation schemes to enable enantiopure solutions of chiral products are inefficient or costly. Consequently, most pharmaceuticals or agrochemicals are sold as racemic mixtures, with reduced efficacy and potential deleterious impacts.Recent advances in nanophotonics lay the foundation toward highly sensitive and efficient chiral detection and separation methods. In this Account, we highlight our group's effort to leverage nanoscale chiral light-matter interactions to detect, characterize, and separate enantiomers, potentially down to the single molecule level. Notably, certain resonant nanostructures can significantly enhance circular dichroism for improved chiral sensing and spectroscopy as well as high-yield enantioselective photochemistry. We first describe how achiral metallic and dielectric nanostructures can be utilized to increase the local optical chirality density by engineering the coupling between electric and magnetic optical resonances. While plasmonic nanoparticles locally enhance the optical chirality density, high-index dielectric nanoparticles can enable large-volume and uniform-sign enhancements in the optical chirality density. By overlapping these electric and magnetic resonances, local chiral fields can be enhanced by several orders of magnitude. We show how these design rules can enable high-yield enantioselective photochemistry and project a 2000-fold improvement in the yield of a photoionization reaction. Next, we discuss how optical forces can enable selective manipulation and separation of enantiomers. We describe the design of low-power enantioselective optical tweezers with the ability to trap sub-10 nm dielectric particles. We also characterize their chiral-optical forces with high spatial and force resolution using combined optical and atomic force microscopy. These optical tweezers exhibit an enantioselective optical force contrast exceeding 10 pN, enabling selective attraction or repulsion of enantiomers based on the illumination polarization. Finally, we discuss future challenges and opportunities spanning fundamental research to technology translation. Disease detection in the clinic as well as pharmaceutical and agrochemical industrial applications requiring large-scale, high-throughput production will gain particular benefit from the simplicity and relative low cost that nanophotonic platforms promise.
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Affiliation(s)
- Michelle L. Solomon
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
| | - Amr A. E. Saleh
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
- Department of Engineering Mathematics and Physics, Faculty of Engineering, Cairo University, Giza 12613, Egypt
| | - Lisa V. Poulikakos
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
| | - John M. Abendroth
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
| | - Loza F. Tadesse
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Jennifer A. Dionne
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
- Department of Radiology, Stanford University, Stanford, California 94305, United States
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19
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Caprara D, Ripanti F, Capocefalo A, Sarra A, Brasili F, Petrillo C, Fasolato C, Postorino P. DNA-functionalized gold nanoparticle assemblies for Surface Enhanced Raman Scattering. Colloids Surf A Physicochem Eng Asp 2020. [DOI: 10.1016/j.colsurfa.2019.124399] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Cheung KM, Yang KA, Nakatsuka N, Zhao C, Ye M, Jung ME, Yang H, Weiss PS, Stojanović MN, Andrews AM. Phenylalanine Monitoring via Aptamer-Field-Effect Transistor Sensors. ACS Sens 2019; 4:3308-3317. [PMID: 31631652 PMCID: PMC6957227 DOI: 10.1021/acssensors.9b01963] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Determination of the amino acid phenylalanine is important for lifelong disease management in patients with phenylketonuria, a genetic disorder in which phenylalanine accumulates and persists at levels that alter brain development and cause permanent neurological damage and cognitive dysfunction. Recent approaches for treating phenylketonuria focus on injectable medications that efficiently break down phenylalanine but sometimes result in detrimentally low phenylalanine levels. We have identified new DNA aptamers for phenylalanine in two formats, initially as fluorescent sensors and then, incorporated with field-effect transistors (FETs). Aptamer-FET sensors detected phenylalanine over a wide range of concentrations (fM to mM). para-Chlorophenylalanine, which inhibits the enzyme that converts phenylalanine to tyrosine, was used to induce hyperphenylalaninemia during brain development in mice. Aptamer-FET sensors were specific for phenylalanine versus para-chlorophenylalanine and differentiated changes in mouse serum phenylalanine at levels expected in patients. Aptamer-FETs can be used to investigate models of hyperphenylalanemia in the presence of structurally related enzyme inhibitors, as well as naturally occurring amino acids. Nucleic acid-based receptors that discriminate phenylalanine analogs, some that differ by a single substituent, indicate a refined ability to identify aptamers with binding pockets tailored for high affinity and specificity. Aptamers of this type integrated into FETs enable rapid, electronic, label-free phenylalanine sensing.
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Affiliation(s)
- Kevin M. Cheung
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Kyung-Ae Yang
- Department of Medicine, Columbia University, New York, New York 10032, United States
| | - Nako Nakatsuka
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Chuanzhen Zhao
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Mao Ye
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Michael E. Jung
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Hongyan Yang
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience & Human Behavior, and Hatos Center for Neuropharmacology, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Paul S. Weiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Departments of Bioengineering and Materials Science and Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Milan N. Stojanović
- Department of Medicine, Columbia University, New York, New York 10032, United States
- Departments of Biomedical Engineering and Systems Biology, Columbia University, New York, New York 10032, United States
| | - Anne M Andrews
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience & Human Behavior, and Hatos Center for Neuropharmacology, University of California, Los Angeles, Los Angeles, California 90095, United States
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21
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Pyrak E, Krajczewski J, Kowalik A, Kudelski A, Jaworska A. Surface Enhanced Raman Spectroscopy for DNA Biosensors-How Far Are We? Molecules 2019; 24:E4423. [PMID: 31817059 PMCID: PMC6943648 DOI: 10.3390/molecules24244423] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 11/28/2019] [Accepted: 11/29/2019] [Indexed: 12/20/2022] Open
Abstract
A sensitive and accurate identification of specific DNA fragments (usually containing a mutation) can influence clinical decisions. Standard methods routinely used for this type of detection are PCR (Polymerase Chain Reaction, and its modifications), and, less commonly, NGS (Next Generation Sequencing). However, these methods are quite complicated, requiring time-consuming, multi-stage sample preparation, and specially trained staff. Usually, it takes weeks for patients to obtain their results. Therefore, different DNA sensors are being intensively developed by many groups. One technique often used to obtain an analytical signal from DNA sensors is Raman spectroscopy. Its modification, surface-enhanced Raman spectroscopy (SERS), is especially useful for practical analytical applications due to its extra low limit of detection. SERS takes advantage of the strong increase in the efficiency of Raman signal generation caused by a local electric field enhancement near plasmonic (typically gold and silver) nanostructures. In this condensed review, we describe the most important types of SERS-based nanosensors for genetic studies and comment on their potential for becoming diagnostic tools.
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Affiliation(s)
- Edyta Pyrak
- Faculty of Chemistry, University of Warsaw, 1 Pasteur St., 02-093 Warsaw, Poland; (E.P.); (J.K.)
- Nencki Institute of Experimental Biology of Polish Academy of Sciences, 3 Pasteur St., 02-093 Warsaw, Poland
| | - Jan Krajczewski
- Faculty of Chemistry, University of Warsaw, 1 Pasteur St., 02-093 Warsaw, Poland; (E.P.); (J.K.)
| | - Artur Kowalik
- Holy Cross Cancer Center, 3 Stefana Artwińskiego St., 25-734 Kielce, Poland
| | - Andrzej Kudelski
- Faculty of Chemistry, University of Warsaw, 1 Pasteur St., 02-093 Warsaw, Poland; (E.P.); (J.K.)
| | - Aleksandra Jaworska
- Faculty of Chemistry, University of Warsaw, 1 Pasteur St., 02-093 Warsaw, Poland; (E.P.); (J.K.)
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22
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Peltomaa R, Glahn-Martínez B, Benito-Peña E, Moreno-Bondi MC. Optical Biosensors for Label-Free Detection of Small Molecules. SENSORS (BASEL, SWITZERLAND) 2018; 18:E4126. [PMID: 30477248 PMCID: PMC6308632 DOI: 10.3390/s18124126] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/20/2018] [Accepted: 11/21/2018] [Indexed: 12/12/2022]
Abstract
Label-free optical biosensors are an intriguing option for the analyses of many analytes, as they offer several advantages such as high sensitivity, direct and real-time measurement in addition to multiplexing capabilities. However, development of label-free optical biosensors for small molecules can be challenging as most of them are not naturally chromogenic or fluorescent, and in some cases, the sensor response is related to the size of the analyte. To overcome some of the limitations associated with the analysis of biologically, pharmacologically, or environmentally relevant compounds of low molecular weight, recent advances in the field have improved the detection of these analytes using outstanding methodology, instrumentation, recognition elements, or immobilization strategies. In this review, we aim to introduce some of the latest developments in the field of label-free optical biosensors with the focus on applications with novel innovations to overcome the challenges related to small molecule detection. Optical label-free methods with different transduction schemes, including evanescent wave and optical fiber sensors, surface plasmon resonance, surface-enhanced Raman spectroscopy, and interferometry, using various biorecognition elements, such as antibodies, aptamers, enzymes, and bioinspired molecularly imprinted polymers, are reviewed.
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Affiliation(s)
- Riikka Peltomaa
- Departamento de Química Analítica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain.
| | - Bettina Glahn-Martínez
- Departamento de Química Analítica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain.
| | - Elena Benito-Peña
- Departamento de Química Analítica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain.
| | - María C Moreno-Bondi
- Departamento de Química Analítica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain.
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23
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Szlag VM, Rodriguez RS, He J, Hudson-Smith N, Kang H, Le N, Reineke TM, Haynes CL. Molecular Affinity Agents for Intrinsic Surface-Enhanced Raman Scattering (SERS) Sensors. ACS APPLIED MATERIALS & INTERFACES 2018; 10:31825-31844. [PMID: 30134102 DOI: 10.1021/acsami.8b10303] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Research at the interface of synthetic materials, biochemistry, and analytical techniques has enabled sensing platforms for applications across many research communities. Herein we review the materials used as affinity agents to create surface-enhanced Raman spectroscopy (SERS) sensors. Our scope includes those affinity agents (antibody, aptamer, small molecule, and polymer) that facilitate the intrinsic detection of targets relevant to biology, medicine, national security, environmental protection, and food safety. We begin with an overview of the analytical technique (SERS) and considerations for its application as a sensor. We subsequently describe four classes of affinity agents, giving a brief overview on affinity, production, attachment chemistry, and first uses with SERS. Additionally, we review the SERS features of the affinity agents, and the analytes detected by intrinsic SERS with that affinity agent class. We conclude with remarks on affinity agent selection for intrinsic SERS sensing platforms.
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Affiliation(s)
- Victoria M Szlag
- Department of Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Rebeca S Rodriguez
- Department of Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Jiayi He
- Department of Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Natalie Hudson-Smith
- Department of Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Hyunho Kang
- Department of Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Ngoc Le
- Department of Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Theresa M Reineke
- Department of Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Christy L Haynes
- Department of Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
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Nakatsuka N, Yang KA, Abendroth JM, Cheung KM, Xu X, Yang H, Zhao C, Zhu B, Rim YS, Yang Y, Weiss PS, Stojanović MN, Andrews AM. Aptamer-field-effect transistors overcome Debye length limitations for small-molecule sensing. Science 2018; 362:319-324. [PMID: 30190311 DOI: 10.1126/science.aao6750] [Citation(s) in RCA: 447] [Impact Index Per Article: 74.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 04/30/2018] [Accepted: 08/06/2018] [Indexed: 12/17/2022]
Abstract
Detection of analytes by means of field-effect transistors bearing ligand-specific receptors is fundamentally limited by the shielding created by the electrical double layer (the "Debye length" limitation). We detected small molecules under physiological high-ionic strength conditions by modifying printed ultrathin metal-oxide field-effect transistor arrays with deoxyribonucleotide aptamers selected to bind their targets adaptively. Target-induced conformational changes of negatively charged aptamer phosphodiester backbones in close proximity to semiconductor channels gated conductance in physiological buffers, resulting in highly sensitive detection. Sensing of charged and electroneutral targets (serotonin, dopamine, glucose, and sphingosine-1-phosphate) was enabled by specifically isolated aptameric stem-loop receptors.
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Affiliation(s)
- Nako Nakatsuka
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA.,Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Kyung-Ae Yang
- Center for Innovative Diagnostic and Therapeutic Approaches, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - John M Abendroth
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA.,Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Kevin M Cheung
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA.,Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Xiaobin Xu
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA.,Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Hongyan Yang
- Department of Psychiatry and Biobehavioral Science, Semel Institute for Neuroscience and Human Behavior, and Hatos Center for Neuropharmacology, University of California, Los Angeles, CA 90095, USA
| | - Chuanzhen Zhao
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA.,Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Bowen Zhu
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA.,Department of Materials Science and Engineering, University of California, Los Angeles, CA 90095, USA
| | - You Seung Rim
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA.,Department of Materials Science and Engineering, University of California, Los Angeles, CA 90095, USA
| | - Yang Yang
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA.,Department of Materials Science and Engineering, University of California, Los Angeles, CA 90095, USA
| | - Paul S Weiss
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA. .,Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA.,Department of Materials Science and Engineering, University of California, Los Angeles, CA 90095, USA
| | - Milan N Stojanović
- Center for Innovative Diagnostic and Therapeutic Approaches, Department of Medicine, Columbia University, New York, NY 10032, USA. .,Departments of Biomedical Engineering and Systems Biology, Columbia University, New York, NY 10032, USA
| | - Anne M Andrews
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA. .,Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA.,Department of Psychiatry and Biobehavioral Science, Semel Institute for Neuroscience and Human Behavior, and Hatos Center for Neuropharmacology, University of California, Los Angeles, CA 90095, USA
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Zhou Q, Yan H, Ran F, Cao J, Chen L, Shang B, Chen H, Wei J, Chen Q. Ultrasensitive enzyme-free fluorescent detection of VEGF 165 based on target-triggered hybridization chain reaction amplification. RSC Adv 2018; 8:25955-25960. [PMID: 35548700 PMCID: PMC9086580 DOI: 10.1039/c8ra04721a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 07/03/2018] [Indexed: 12/28/2022] Open
Abstract
Sensitive detection of vascular endothelial growth factor (VEGF165) is important for early cancer disease diagnosis in the clinic. A sensitive fluorescent sensing platform for VEGF165 detection is developed in this work. It is based on a target-triggered hybridization chain reaction (HCR) and graphene oxide (GO) selective fluorescence quenching. In this assay, in the presence of the VEGF165, the hairpin structure of Hp opens up and the initiation sequence will be exposed to Hp1 to open its hairpin structure. Then the opened Hp1 hybridizes with Hp2 to expose the complementary sequence of Hp1 which hybridizes with Hp1 again by HCR. Thus HCR would be initiated, generating super-long dsDNA. After the HCR, the double strands of the HCR product cannot be adsorbed on the GO surface. As a result, the HCR product gives a strong fluorescence signal which is dependent on the concentration of VEGF165. By using VEGF165 as a model analyte, the assay provides a highly sensitive fluorescence detection method for VEGF165 with a detection limit down to 20 pg mL-1. The proposed aptasensing strategy based on target-triggered HCR amplification can thus be realized. It was successfully applied to the determination of VEGF165 in spiked human serum, urine and saliva. Therefore, it can easily have wide applications in the diagnosis of vital diseases.
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Affiliation(s)
- Qingzhen Zhou
- Affiliated Dongfeng Hospital, Hubei University of Medicine Hubei Shiyan 442008 China +86 0719-8272283
| | - Hongxia Yan
- Department of Radiotherapy, Hubei Cancer Hospital 116 South Zuodaoquan Road Wuhan 430074 China
| | - Fengying Ran
- Affiliated Dongfeng Hospital, Hubei University of Medicine Hubei Shiyan 442008 China +86 0719-8272283
| | - Jianjun Cao
- Affiliated Dongfeng Hospital, Hubei University of Medicine Hubei Shiyan 442008 China +86 0719-8272283
| | - Long Chen
- Affiliated Dongfeng Hospital, Hubei University of Medicine Hubei Shiyan 442008 China +86 0719-8272283
| | - Bing Shang
- Affiliated Dongfeng Hospital, Hubei University of Medicine Hubei Shiyan 442008 China +86 0719-8272283
| | - Hao Chen
- Affiliated Dongfeng Hospital, Hubei University of Medicine Hubei Shiyan 442008 China +86 0719-8272283
| | - Jian Wei
- Affiliated Dongfeng Hospital, Hubei University of Medicine Hubei Shiyan 442008 China +86 0719-8272283
| | - Qinhua Chen
- Affiliated Dongfeng Hospital, Hubei University of Medicine Hubei Shiyan 442008 China +86 0719-8272283
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Zong C, Xu M, Xu LJ, Wei T, Ma X, Zheng XS, Hu R, Ren B. Surface-Enhanced Raman Spectroscopy for Bioanalysis: Reliability and Challenges. Chem Rev 2018; 118:4946-4980. [PMID: 29638112 DOI: 10.1021/acs.chemrev.7b00668] [Citation(s) in RCA: 876] [Impact Index Per Article: 146.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Surface-enhanced Raman spectroscopy (SERS) inherits the rich chemical fingerprint information on Raman spectroscopy and gains sensitivity by plasmon-enhanced excitation and scattering. In particular, most Raman peaks have a narrow width suitable for multiplex analysis, and the measurements can be conveniently made under ambient and aqueous conditions. These merits make SERS a very promising technique for studying complex biological systems, and SERS has attracted increasing interest in biorelated analysis. However, there are still great challenges that need to be addressed until it can be widely accepted by the biorelated communities, answer interesting biological questions, and solve fatal clinical problems. SERS applications in bioanalysis involve the complex interactions of plasmonic nanomaterials with biological systems and their environments. The reliability becomes the key issue of bioanalytical SERS in order to extract meaningful information from SERS data. This review provides a comprehensive overview of bioanalytical SERS with the main focus on the reliability issue. We first introduce the mechanism of SERS to guide the design of reliable SERS experiments with high detection sensitivity. We then introduce the current understanding of the interaction of nanomaterials with biological systems, mainly living cells, to guide the design of functionalized SERS nanoparticles for target detection. We further introduce the current status of label-free (direct) and labeled (indirect) SERS detections, for systems from biomolecules, to pathogens, to living cells, and we discuss the potential interferences from experimental design, measurement conditions, and data analysis. In the end, we give an outlook of the key challenges in bioanalytical SERS, including reproducibility, sensitivity, and spatial and time resolution.
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Affiliation(s)
- Cheng Zong
- State Key Laboratory of Physical Chemistry of Solid Surfaces, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China
| | - Mengxi Xu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China
| | - Li-Jia Xu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China
| | - Ting Wei
- State Key Laboratory of Physical Chemistry of Solid Surfaces, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China
| | - Xin Ma
- State Key Laboratory of Physical Chemistry of Solid Surfaces, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China
| | - Xiao-Shan Zheng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China
| | - Ren Hu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China
| | - Bin Ren
- State Key Laboratory of Physical Chemistry of Solid Surfaces, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China
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Pang X, Cui C, Su M, Wang Y, Wei Q, Tan W. Construction of self-powered cytosensing device based on ZnO nanodisks@g-C 3N 4 quantum dots and application in the detection of CCRF-CEM cells. NANO ENERGY 2018; 46:101-109. [PMID: 30271703 PMCID: PMC6157620 DOI: 10.1016/j.nanoen.2018.01.018] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We herein report a self-powered and renewable cytosensing device based on ZnO nanodisks(NDs)@g-C3N4 quantum dots. The device features enhanced photoelectrochemical (PEC) activity compared to ZnO NDs or g-C3N4 QDs alone. The enhanced PEC ability is attributed to the synergistic effect of the high visible light sensitivity of g-C3N4 QDs and the staggered band alignment heterojunction structure with suitable band offset, which affords higher photoelectron transfer and separation efficiency. In addition, the hybridization of g-C3N4 QDs further accelerates interfacial electron transfer and blocks recombination between electron donors and photo-generated holes. The device was applied to the detection of CCRF-CEM cells. By conjugation to Sgc8c aptamer, which preferentially interacts with membrane-bound PTK7 on CCRF-CEM membranes, capture of target CCRF-CEM cells resulted in a decrease in apparent power output, which was then exploited for the ultrasensitive detection of the target cells. This decrease in power output can be recovered by simply increasing the temperature to release the cells, thus recycling the cytosensing performance. The device displayed a linear relationship between the change of power output and the logarithm of the cell concentration from 20 to 20,000 cell/mL (R2 = 0.9837) and a detection limit down to 20 cell/mL, as well as excellent selectivity and reproducibility. Thus, this ZnO NDs@g-C3N4 QDs-based device exhibits high potential for the detection of CCRF-CEM cells.
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Affiliation(s)
- Xuehui Pang
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong 250022, People’s Republic of China
- Center for Research at the Bio/nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, UF Genetics Institute and McKnight Brain Institute, Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200, United States
| | - Cheng Cui
- Center for Research at the Bio/nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, UF Genetics Institute and McKnight Brain Institute, Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200, United States
| | - Minhui Su
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong 250022, People’s Republic of China
| | - Yaoguang Wang
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong 250022, People’s Republic of China
| | - Qin Wei
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong 250022, People’s Republic of China
| | - Weihong Tan
- Center for Research at the Bio/nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, UF Genetics Institute and McKnight Brain Institute, Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200, United States
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, People’s Republic of China
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Optical Aggregation of Gold Nanoparticles for SERS Detection of Proteins and Toxins in Liquid Environment: Towards Ultrasensitive and Selective Detection. MATERIALS 2018; 11:ma11030440. [PMID: 29562606 PMCID: PMC5873019 DOI: 10.3390/ma11030440] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/12/2018] [Accepted: 03/15/2018] [Indexed: 01/16/2023]
Abstract
Optical forces are used to aggregate plasmonic nanoparticles and create SERS-active hot spots in liquid. When biomolecules are added to the nanoparticles, high sensitivity SERS detection can be accomplished. Here, we pursue studies on Bovine Serum Albumin (BSA) detection, investigating the BSA-nanorod aggregations in a range from 100 µM to 50 nM by combining light scattering, plasmon resonance and SERS, and correlating the SERS signal with the concentration. Experimental data are fitted with a simple model describing the optical aggregation process. We show that BSA-nanorod complexes can be optically printed on non-functionalized glass surfaces, designing custom patterns stable with time. Furthermore, we demonstrate that this methodology can be used to detect catalase and hemoglobin, two Raman resonant biomolecules, at concentrations of 10 nM and 1 pM, respectively, i.e., well beyond the limit of detection of BSA. Finally, we show that nanorods functionalized with specific aptamers can be used to capture and detect Ochratoxin A, a fungal toxin found in food commodities and wine. This experiment represents the first step towards the addition of molecular specificity to this novel biosensor strategy.
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Label-free SERS detection of Salmonella Typhimurium on DNA aptamer modified AgNR substrates. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2017. [DOI: 10.1007/s11694-017-9558-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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30
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Du X, Dai L, Jiang D, Li H, Hao N, You T, Mao H, Wang K. Gold nanrods plasmon-enhanced photoelectrochemical aptasensing based on hematite/N-doped graphene films for ultrasensitive analysis of 17β-estradiol. Biosens Bioelectron 2017; 91:706-713. [PMID: 28126660 DOI: 10.1016/j.bios.2017.01.034] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/09/2017] [Accepted: 01/17/2017] [Indexed: 12/14/2022]
Abstract
It remains a vital task to establish ultrasensitive sensing interfaces for detection of target analytes to meet the demands of modern analysis. Herein, a highly sensitive turn-on photoelectrochemical (PEC) platform for trace 17β-estradiol (E2) assay was developed based on Au nanrods (AuNRs) with surface plasmon resonance (SPR) properties induced signal amplification. Specifically, a ternary hybrid was prepared by integrating hematite (α-Fe2O3) nanocrystals and N-doped graphene (NG) with AuNRs, which further served as highly efficient photoactive species. Subsequently, a PEC sensing platform was fabricated based on the specific binding of E2 and its aptamer. On such a sensor, the capture of E2 molecules by aptamers led to increased photocurrent. This was attributed to that the specific recognition reaction between E2 and aptamer resulted in the conformational change of the aptamers and complete dissociation of some aptamers on the PEC sensing interface. It can be confirmed by the electrochemical impedance spectroscopy (EIS) results. This process decreased the steric hindrances between the electrode surface and solution and thus increased the photocurrent response. Under the optimal conditions, the as-prepared PEC aptasensor exhibited superb analytical performances for detection of E2 in the range from 1×10-15M to 1×10-9M with a detection limit of 3.3×10-16M. The aptasensor manifested outstanding selectivity towards E2 when other endocrine disrupting compounds with similar structure coexisted. Furthermore, the aptasensor was successfully applied for the determination of E2 in milk powder. The present strategy provides a potential way to boost the activity of photoactive materials and improve the sensitivity of PEC biosensor.
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Affiliation(s)
- Xiaojiao Du
- Key Laboratory of Modern Agriculture Equipment and Technology, School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Liming Dai
- Key Laboratory of Modern Agriculture Equipment and Technology, School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Ding Jiang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Henan Li
- Key Laboratory of Modern Agriculture Equipment and Technology, School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Nan Hao
- Key Laboratory of Modern Agriculture Equipment and Technology, School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Tianyan You
- Key Laboratory of Modern Agriculture Equipment and Technology, School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Hanping Mao
- Key Laboratory of Modern Agriculture Equipment and Technology, School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Kun Wang
- Key Laboratory of Modern Agriculture Equipment and Technology, School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013, PR China.
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Rhouati A, Catanante G, Nunes G, Hayat A, Marty JL. Label-Free Aptasensors for the Detection of Mycotoxins. SENSORS 2016; 16:s16122178. [PMID: 27999353 PMCID: PMC5191157 DOI: 10.3390/s16122178] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/08/2016] [Accepted: 12/14/2016] [Indexed: 01/13/2023]
Abstract
Various methodologies have been reported in the literature for the qualitative and quantitative monitoring of mycotoxins in food and feed samples. Based on their enhanced specificity, selectivity and versatility, bio-affinity assays have inspired many researchers to develop sensors by exploring bio-recognition phenomena. However, a significant problem in the fabrication of these devices is that most of the biomolecules do not generate an easily measurable signal upon binding to the target analytes, and signal-generating labels are required to perform the measurements. In this context, aptamers have been emerged as a potential and attractive bio-recognition element to design label-free aptasensors for various target analytes. Contrary to other bioreceptor-based approaches, the aptamer-based assays rely on antigen binding-induced conformational changes or oligomerization states rather than binding-assisted changes in adsorbed mass or charge. This review will focus on current designs in label-free conformational switchable design strategies, with a particular focus on applications in the detection of mycotoxins.
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Affiliation(s)
- Amina Rhouati
- BAE Laboratory, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, Perpignan 66860, France.
- Ecole Nationale Supérieure de Biotechnologie, Constantine 25100, Algeria.
| | - Gaelle Catanante
- BAE Laboratory, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, Perpignan 66860, France.
| | - Gilvanda Nunes
- Technological Chemistry Department, Federal University of Maranhão, CCET/UFMA, Av. Portugueses, Cidade Universitária do Canga, 65080-040 São Luis, Brazil.
| | - Akhtar Hayat
- BAE Laboratory, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, Perpignan 66860, France.
- Interdisciplinary Research Centre in Biomedical Materials (IRCBM) COMSATS Institute of Information Technology (CIIT), Lahore 54000, Pakistan.
| | - Jean-Louis Marty
- BAE Laboratory, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, Perpignan 66860, France.
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Karaballi RA, Nel A, Krishnan S, Blackburn J, Brosseau CL. Development of an electrochemical surface-enhanced Raman spectroscopy (EC-SERS) aptasensor for direct detection of DNA hybridization. Phys Chem Chem Phys 2016; 17:21356-63. [PMID: 25780805 DOI: 10.1039/c4cp05077k] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Rapid detection of disease biomarkers at the patient point-of-care is essential to timely and effective treatment. The research described herein focuses on the development of an electrochemical surface-enhanced Raman spectroscopy (EC-SERS) DNA aptasensor capable of direct detection of tuberculosis (TB) DNA. Specifically, a plausible DNA biomarker present in TB patient urine was chosen as the model target for detection. Cost-effective screen printed electrodes (SPEs) modified with silver nanoparticles (AgNP) were used as the aptasensor platform, onto which the aptamer specific for the target DNA was immobilized. Direct detection of the target DNA was demonstrated through the appearance of SERS peaks characteristic for adenine, present only in the target strand. Modulation of the applied potential allowed for a sizeable increase in the observed SERS response and the use of thiol back-filling prevented non-specific adsorption of non-target DNA. To our knowledge, this work represents the first EC-SERS study of an aptasensor for the direct, label-free detection of DNA hybridization. Such a technology paves the way for rapid detection of disease biomarkers at the patient point-of-care.
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Affiliation(s)
- R A Karaballi
- Department of Chemistry, Saint Mary's University, Halifax, Nova Scotia B3H 3C3, Canada.
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Chen YJ, Tsai CY, Hu WP, Chang LS. DNA Aptamers against Taiwan Banded Krait α-Bungarotoxin Recognize Taiwan Cobra Cardiotoxins. Toxins (Basel) 2016; 8:toxins8030066. [PMID: 26959062 PMCID: PMC4810211 DOI: 10.3390/toxins8030066] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 02/29/2016] [Accepted: 02/29/2016] [Indexed: 02/07/2023] Open
Abstract
Bungarus multicinctus α-bungarotoxin (α-Bgt) and Naja atra cardiotoxins (CTXs) share a common structural scaffold, and their tertiary structures adopt three-fingered loop motifs. Four DNA aptamers against α-Bgt have been reported previously. Given that the binding of aptamers with targeted proteins depends on structural complementarity, in this study, we investigated whether DNA aptamers against α-Bgt could also recognize CTXs. It was found that N.atra cardiotoxin 3 (CTX3) reduced the electrophoretic mobility of aptamers against α-Bgt. Analysis of the changes in the fluorescence intensity of carboxyfluorescein-labeled aptamers upon binding toxin molecules revealed that CTX3 and α-Bgt could bind the tested aptamers. Moreover, the aptamers inhibited the membrane-damaging activity and cytotoxicity of CTX3. In addition to CTX3, other N. atra CTX isotoxins also bound to the aptamer against α-Bgt. Taken together, our data indicate that aptamers against α-Bgt show cross-reactivity with CTXs. The findings that aptamers against α-Bgt also suppress the biological activities of CTX3 highlight the potential utility of aptamers in regard to the broad inhibition of snake venom three-fingered proteins.
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Affiliation(s)
- Ying-Jung Chen
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung 804, Taiwan.
| | - Chia-Yu Tsai
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung 804, Taiwan.
| | - Wan-Ping Hu
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
| | - Long-Sen Chang
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung 804, Taiwan.
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
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Zhang Y, Ren W, Luo HQ, Li NB. Label-free cascade amplification strategy for sensitive visual detection of thrombin based on target-triggered hybridization chain reaction-mediated in situ generation of DNAzymes and Pt nanochains. Biosens Bioelectron 2016; 80:463-470. [PMID: 26878483 DOI: 10.1016/j.bios.2016.02.016] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 02/05/2016] [Accepted: 02/06/2016] [Indexed: 12/19/2022]
Abstract
A new magnetic bead-based cascade amplification strategy for highly sensitive visual detection of proteins (thrombin as a model analyte) was developed by coupling target-triggered hybridization chain reaction (HCR) with the synergistic catalysis of DNA concatemer-mediated hemin/G-quadruplex DNAzymes and Pt nanozymes. Initially, the biotinylated primer DNA (P-DNA) was complementary with aptamer to form dsDNA which was further linked to streptavidin-coated magnetic bead (MB), thereby fabricating the expected MB-based aptasensor. In the presence of target TB, the aptamer was taken away from the aptasensor, and the free P-DNA immediately triggered HCR to spontaneously form DNA concatemer-directed nanochains with numerous DNAzymes and Pt nanoclusters (PtNCs) to achieve cascades signal amplification. The dual peroxidase mimetics catalyzed the H2O2-mediated oxidation of colorless 3,3',5,5'-tetramethylbenzidine (TMB) into the colored TMB oxides (oxTMB), causing intensified color change of the chromogenic solution for the highly sensitive naked-eye detection of as low as 100.0 pM TB. In this strategy, the employment of magnetic separation and exonuclease III (Exo III)-assisted digestion of residual dsDNA minimized the background noise and avoided the false positive results, greatly improving the detection accuracy and sensitivity with a low limit of detection (LOD=15.0 pM). The proposed visual platform has promise for detecting various types of proteins with careful DNA sequence designs.
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Affiliation(s)
- Ying Zhang
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China; College of Chemistry and Pharmaceutical Engineering, Key Laboratory of Green Catalysis of Higher Education Institutes of Sichuan, Sichuan University of Science and Engineering, Zigong 643000, PR China
| | - Wang Ren
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China; College of Chemistry and Pharmaceutical Engineering, Key Laboratory of Green Catalysis of Higher Education Institutes of Sichuan, Sichuan University of Science and Engineering, Zigong 643000, PR China
| | - Hong Qun Luo
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
| | - Nian Bing Li
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
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Zeinabad HA, Kachooei E, Saboury AA, Kostova I, Attar F, Vaezzadeh M, Falahati M. Thermodynamic and conformational changes of protein toward interaction with nanoparticles: a spectroscopic overview. RSC Adv 2016. [DOI: 10.1039/c6ra16422f] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Nanoparticles (NPs) in different forms have been widely used in medicine and pharmaceutics for diagnosis and drug delivery.
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Affiliation(s)
- Hojjat Alizadeh Zeinabad
- Department of Nanotechnology
- Faculty of Advance Science and Technology
- Pharmaceutical Sciences Branch
- Islamic Azad University (IAUPS)
- Tehran
| | - Ehsan Kachooei
- Institute of Biochemistry and Biophysics
- University of Tehran
- Tehran
- Iran
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics
- University of Tehran
- Tehran
- Iran
| | - Irena Kostova
- Department of Chemistry
- Faculty of Pharmacy
- Medical University
- Sofia 1000
- Bulgaria
| | - Farnoosh Attar
- Department of Biology
- Faculty of Food Industry & Agriculture
- Standard Research Institute (SRI)
- Karaj
- Iran
| | - Mahsa Vaezzadeh
- Department of Biology
- Research and Science Branch
- Islamic Azad University
- Tehran
- Iran
| | - Mojtaba Falahati
- Department of Nanotechnology
- Faculty of Advance Science and Technology
- Pharmaceutical Sciences Branch
- Islamic Azad University (IAUPS)
- Tehran
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36
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Wang X, Jiang A, Hou T, Li H, Li F. Enzyme-free and label-free fluorescence aptasensing strategy for highly sensitive detection of protein based on target-triggered hybridization chain reaction amplification. Biosens Bioelectron 2015; 70:324-9. [PMID: 25840018 DOI: 10.1016/j.bios.2015.03.053] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 03/19/2015] [Accepted: 03/23/2015] [Indexed: 11/24/2022]
Abstract
Proteins are of great importance in medical and biological fields. In this paper, a novel fluorescent aptasensing strategy for protein assay has been developed based on target-triggered hybridization chain reaction (HCR) and graphene oxide (GO)-based selective fluorescence quenching. Three DNA probes, a helper DNA probe (HP), hairpin probe 1 (H1) and hairpin probe 2 (H2) are ingeniously designed. In the presence of the target, the aptamer sequences in HP recognize the target to form a target-aptamer complex, which causes the HP conformation change, and then triggers the chain-like assembly of H1 and H2 through the hybridization chain reaction, generating a long chain of HP leading complex of H1 and H2. At last the fluorescence indicator SYBR Green I (SG) binds with the long double strands of the HCR product through both intercalation and minor groove binding. When GO was added into the solutions after HCR, the free H1, H2 and SG would be closely adsorbed onto GO surface via π-π stacking. However, the HCR product cannot be adsorbed on GO surface, thereby the SG bound to HCR product gives a strong fluorescence signal dependent on the concentration of the target. With the use of platelet-derived growth factor BB (PDGF-BB) as the model analyte, this newly designed protocol provides a highly sensitive fluorescence detection of PDGF-BB with a limit of detection down to 1.25 pM, and also exhibit good selectivity and applicability in complex matrixes. Therefore, the proposed aptasensing strategy based on target-triggered hybridization chain reaction amplification should have wide applications in the diagnosis of genetic diseases due to its simplicity, low cost, and high sensitivity at extremely low target concentrations.
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Affiliation(s)
- Xiuzhong Wang
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Aiwen Jiang
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Ting Hou
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Haiyin Li
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Feng Li
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, China.
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Lin JS, Kauff A, Diao Y, Yang H, Lawrence S, Juengel JL. Creation of DNA aptamers against recombinant bone morphogenetic protein 15. Reprod Fertil Dev 2015; 28:RD14409. [PMID: 25557239 DOI: 10.1071/rd14409] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 12/01/2014] [Indexed: 12/12/2022] Open
Abstract
The oocyte-derived growth factor bone morphogenetic protein (BMP) 15 plays important roles in fertility, but its mechanism of action differs between species. Generation of BMP15-binding molecules, as an essential investigation tool, would be helpful to provide valuable insight into the underlying biological features of BMP15. The BMP15-binding molecules could be antibodies or aptamers. Aptamers have many advantages over antibodies as macromolecular ligands for target proteins. DNA aptamers can be obtained by a method of Systematic Evolution of Ligands by EXponential enrichment (SELEX) beginning with a pool of random sequences. However, the success of this technique cannot be guaranteed if the initial pool lacks candidate sequences. Herein, we report on the creation of DNA aptamers by means of modified SELEX. The modification included enhanced mutation and progressive selection during an in vitro evolutionary process. As a proof-of-principle, we started from a single sequence instead of a multiple-sequence pool. Functional aptamers against the recombinant BMP15 were successfully created and identified.
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Roushani M, Shahdost-Fard F. A highly selective and sensitive cocaine aptasensor based on covalent attachment of the aptamer-functionalized AuNPs onto nanocomposite as the support platform. Anal Chim Acta 2014; 853:214-221. [PMID: 25467461 DOI: 10.1016/j.aca.2014.09.031] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Revised: 09/11/2014] [Accepted: 09/19/2014] [Indexed: 12/12/2022]
Abstract
Based on the conformational changes of the aptamer-functionalized gold nanoparticles (AuNPs) onto MWCNTs/IL/Chit nanocomposite as the support platform, we have developed a sensitive and selective electrochemical aptasensor for the detection of cocaine. The 5'-amine-3'-AuNP terminated aptamer is covalently attached to a MWCNTs/IL/Chit nanocomposite. The interaction of cocaine with the aptamer functionalized AuNP caused the aptamer to be folded and the AuNPs with negative charge at the end of the aptamer came to the near of electrode surface therefore, the electron transfer between ferricyanide (K3Fe(CN)6) as redox probe and electrode surface was inhibited. A decreased current of (K3Fe(CN)6) was monitored by differential pulse voltammetry technique. In an optimized condition the calibration curve for cocaine concentration was linear up to 11 μM with detection limit (signal-to-noise ratio of 3) of 100 pM. To test the selectivity of the prepared aptasensor sensing platform applicability, some analgesic drugs as the interferes were examined. The potential of the aptasensor was successfully applied for measuring cocaine concentration in human blood serum. Based on our experiments it can be said that the present method is absolutely beneficial in developing other electrochemical aptasensor.
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39
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Kim D, Campos AR, Datt A, Gao Z, Rycenga M, Burrows ND, Greeneltch NG, Mirkin CA, Murphy CJ, Van Duyne RP, Haynes CL. Microfluidic-SERS devices for one shot limit-of-detection. Analyst 2014; 139:3227-3234. [PMID: 24756225 PMCID: PMC4067008 DOI: 10.1039/c4an00357h] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Microfluidic sensing platforms facilitate parallel, low sample volume detection using various optical signal transduction mechanisms. Herein, we introduce a simple mixing microfluidic device, enabling serial dilution of introduced analyte solution that terminates in five discrete sensing elements. We demonstrate the utility of this device with on-chip fluorescence and surface-enhanced Raman scattering (SERS) detection of analytes, and we demonstrate device use both when combined with a traditional inflexible SERS substrate and with SERS-active nanoparticles that are directly incorporated into microfluidic channels to create a flexible SERS platform. The results indicate, with varying sensitivities, that either flexible or inflexible devices can be easily used to create a calibration curve and perform a limit of detection study with a single experiment.
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Affiliation(s)
- Donghyuk Kim
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota, 55455 U.S.A
| | - Antonio R Campos
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota, 55455 U.S.A
| | - Ashish Datt
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota, 55455 U.S.A
| | - Zhe Gao
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota, 55455 U.S.A
| | - Matthew Rycenga
- Department of Chemistry, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208 U.S.A
| | - Nathan D Burrows
- Department of Chemistry, University of Illinois at Urbana-Champaign, 505 S Mathews Avenue, Urbana, Illinois 61801 U.S.A
| | - Nathan G Greeneltch
- Department of Chemistry, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208 U.S.A
| | - Chad A Mirkin
- Department of Chemistry, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208 U.S.A
| | - Catherine J Murphy
- Department of Chemistry, University of Illinois at Urbana-Champaign, 505 S Mathews Avenue, Urbana, Illinois 61801 U.S.A
| | - Richard P Van Duyne
- Department of Chemistry, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208 U.S.A
| | - Christy L Haynes
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota, 55455 U.S.A
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Tokel O, Inci F, Demirci U. Advances in plasmonic technologies for point of care applications. Chem Rev 2014; 114:5728-52. [PMID: 24745365 PMCID: PMC4086846 DOI: 10.1021/cr4000623] [Citation(s) in RCA: 221] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Indexed: 12/12/2022]
Affiliation(s)
- Onur Tokel
- Demirci
Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical
School, Cambridge, Massachusetts 02139, United States
| | - Fatih Inci
- Demirci
Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical
School, Cambridge, Massachusetts 02139, United States
- Demirci
Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Stanford University School of Medicine, Canary Center at Stanford
for Cancer Early Detection, Palo
Alto, California 94304, United States
| | - Utkan Demirci
- Demirci
Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical
School, Cambridge, Massachusetts 02139, United States
- Division of Infectious Diseases, Brigham
and Women’s Hospital, Harvard Medical
School, Boston, Massachusetts 02115, United States
- Harvard-MIT
Health Sciences and Technology, Cambridge, Massachusetts 02139, United States
- Demirci
Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Stanford University School of Medicine, Canary Center at Stanford
for Cancer Early Detection, Palo
Alto, California 94304, United States
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Song W, Li H, Liang H, Qiang W, Xu D. Disposable electrochemical aptasensor array by using in situ DNA hybridization inducing silver nanoparticles aggregate for signal amplification. Anal Chem 2014; 86:2775-83. [PMID: 24490908 DOI: 10.1021/ac500011k] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Nanomaterials as tracing tags have been widely used in biosensors with high sensitivity and selectivity. In this work, a signal amplification electrochemical aptamer sensing strategy for the detection of protein was designed by combining the hybridization-inducing aggregate of DNA-functionalized silver nanoparticles (AgNPs) and differential pulse stripping voltammetry (DPSV) detection. The multiprobes containing hybridization DNA and aptamers were anchored onto the silver nanoparticles. The protein assay was prepared through the immobilization of capture aptamer that specifically recognizes platelet-derived growth factor (PDGF-BB) on gold nanoparticles modified screen-printed electrode (SPE) array. After a sandwich-type reaction, two kinds of DNA-modified AgNPs were simultaneously added on the electrode surface for specifically recognizing PDGF-BB and forming the AgNPs aggregate caused by in situ hybridization of DNA. Compared to the signal-labeled tag, the tracing aggregate tags showed a strong electroactivity for signal amplification through stripping detection of silver after preoxidation. By using the hybridization-inducing aggregate as electrochemical readouts, the sensor showed wide linear range and low detection limit. The hybridization-inducing AgNPs aggregate were further used as tracing tags in multiplied proteins assays for PDGF-BB and thrombin by using the SPE array chip as sensing platform. The cross-talk between different aptamer-modified electrodes on the same array was avoided because of the advantage of labeled AgNPs. The array detection was also applied in the logic gate operation. The proposed method described here is ideal for multianalytes determination in clinical diagnostics with good analytical performance.
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Affiliation(s)
- Wei Song
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University , 22 Hankou Road, Nanjing, Jiangsu 210093, People's Republic of China
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Hayat A, Yang C, Rhouati A, Marty JL. Recent advances and achievements in nanomaterial-based, and structure switchable aptasensing platforms for ochratoxin A detection. SENSORS (BASEL, SWITZERLAND) 2013; 13:15187-208. [PMID: 24201319 PMCID: PMC3871093 DOI: 10.3390/s131115187] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 10/28/2013] [Accepted: 11/04/2013] [Indexed: 02/07/2023]
Abstract
Aptamer-based bioreceptors that can easily adopt their surroundings have captured the attention of scientists from a wide spectrum of domains in designing highly sensitive, selective and structure switchable sensing assays. Through elaborate design and chemical functionalization, numerous aptamer-based assays have been developed that can switch their conformation upon incubation with target analyte, resulting in an enhanced output signal. To further lower the detection limits to picomolar levels, nanomaterials have attracted great interest in the design of aptamer-based sensing platforms. Associated to their unique properties, nanomaterials offer great promise for numerous aptasensing applications. This review will discuss current research activities in the aptasensing with typical example of detection of ochratoxin A (OTA). OTA, a secondary fungal metabolite, contaminates a variety of food commodities, and has several toxicological effects such as nephrotoxic, hepatotoxic, neurotoxic, teratogenic and immunotoxic activities. The review will introduce advances made in the methods of integrating nanomaterials in aptasensing, and will discuss current conformational switchable design strategies in aptasensor fabrication methodologies.
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Affiliation(s)
- Akhtar Hayat
- BIOMEM, Université de Perpignan, 52 Avenue Paul Alduy, Perpignan Cedex 66860, France; E-Mails: (A.H.); (C.Y.); (A.R.)
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Cheng Yang
- BIOMEM, Université de Perpignan, 52 Avenue Paul Alduy, Perpignan Cedex 66860, France; E-Mails: (A.H.); (C.Y.); (A.R.)
| | - Amina Rhouati
- BIOMEM, Université de Perpignan, 52 Avenue Paul Alduy, Perpignan Cedex 66860, France; E-Mails: (A.H.); (C.Y.); (A.R.)
| | - Jean Louis Marty
- BIOMEM, Université de Perpignan, 52 Avenue Paul Alduy, Perpignan Cedex 66860, France; E-Mails: (A.H.); (C.Y.); (A.R.)
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Wu TC, Vasudev M, Dutta M, Stroscio MA. Raman and surface-enhanced Raman scattering (SERS) studies of the thrombin-binding aptamer. IEEE Trans Nanobioscience 2013; 12:93-7. [PMID: 23694695 DOI: 10.1109/tnb.2013.2242484] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Surface-enhanced Raman scattering is used to study the Raman spectra and peak shifts the thrombin-binding aptamer (TBA) on substrates having two different geometries; one with a single stranded sequence and one with double stranded sequence. The Raman signals of the deoxyribonucleic acids on both substrates are enhanced and specific peaks of bases are identified. These results are highly reproducible and have promising applications in low cost nucleic acid detection.
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Affiliation(s)
- Tsai-Chin Wu
- Bioengineering Department, University of Illinois, Chicago, IL 60607, USA.
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Barahona F, Bardliving CL, Phifer A, Bruno JG, Batt CA. An Aptasensor Based on Polymer-Gold Nanoparticle Composite Microspheres for the Detection of Malathion Using Surface-Enhanced Raman Spectroscopy. Ind Biotechnol (New Rochelle N Y) 2013. [DOI: 10.1089/ind.2012.0029] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | | | | | - John G. Bruno
- Operational Technologies Corporation, San Antonio, TX
| | - Carl A. Batt
- Department of Food Science, Cornell University, Ithaca, NY
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45
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Marotta NE, Beavers KR, Bottomley LA. Limitations of surface enhanced Raman scattering in sensing DNA hybridization demonstrated by label-free DNA oligos as molecular rulers of distance-dependent enhancement. Anal Chem 2013; 85:1440-6. [PMID: 23259584 DOI: 10.1021/ac302454j] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
This article presents a critical evaluation of silver nanorod arrays as substrates for assaying nucleic acid hybridization by surface enhanced Raman scattering (SERS). SERS spectra acquired on complementary oligos, alone or in combination, contain the known spectral signatures of the nucleotides that comprise the oligo; however, no signature bands characteristic of the hybrid were observed. Spectra acquired on an oligo with a 5'- or 3'-thiol were distinctly different from that acquired on the identical oligo without a thiol pendant group suggesting a degree of control over the orientation of the oligo on the nanorod surface. A set of oligos consisting of adenine tracts in a polycytosine chain served as molecular rulers to probe the distance dependence of the SERS enhancement. Using these, we have identified the point at which the characteristic bands for the nucleotides that comprise the oligo disappear from the spectrum. These findings suggest that the applicability of SERS for label-free detection of nucleic acid hybridization is limited to short oligos of less than nine nucleotides.
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Affiliation(s)
- Nicole E Marotta
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
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Galarreta BC, Tabatabaei M, Guieu V, Peyrin E, Lagugné-Labarthet F. Microfluidic channel with embedded SERS 2D platform for the aptamer detection of ochratoxin A. Anal Bioanal Chem 2012. [PMID: 23187825 DOI: 10.1007/s00216-012-6557-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A selective aptameric sequence is adsorbed on a two-dimensional nanostructured metallic platform optimized for surface-enhanced Raman spectroscopy (SERS) measurements. Using nanofabrication methods, a metallic nanostructure was prepared by electron-beam lithography onto a glass coverslip surface and embedded within a microfluidic channel made of polydimethylsiloxane, allowing one to monitor in situ SERS fingerprint spectra from the adsorbed molecules on the metallic nanostructures. The gold structure was designed so that its localized surface plasmon resonance matches the excitation wavelength used for the Raman measurement. This optofluidic device is then used to detect the presence of a toxin, namely ochratoxin-A (OTA), in a confined environment, using very small amounts of chemicals, and short data acquisition times, by taking advantage of the optical properties of a SERS platform to magnify the Raman signals of the aptameric monolayer system and avoiding chemical labeling of the aptamer or the OTA target.
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Affiliation(s)
- Betty C Galarreta
- Department of Chemistry, University of Western Ontario, London, ON, Canada
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Chang CC, Wei SC, Wu TH, Lee CH, Lin CW. Aptamer-based colorimetric detection of platelet-derived growth factor using unmodified gold nanoparticles. Biosens Bioelectron 2012. [PMID: 23202340 DOI: 10.1016/j.bios.2012.10.072] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We developed a simple method for the detection of platelet-derived growth factors (PDGFs) based on base stacking effect coupled with an unmodified gold nanoparticle (AuNP) indicator. In the absence of a target, an aptamer probe and a capture probe stably co-exist in a solution, as it is difficult to sustain an interaction between both these probes due to the short 8bp duplex. However, when a target protein binds to the aptamer probe, the strong base stacking effect can lead to a favorable and stable interaction between the aptamer and capture probes. Hence, the capture probe dissociates from the AuNP surfaces, inducing AuNP aggregation. Compared with other AuNP-based aptasensors for PDGFs, using this base stacking effect can overcome a structured-aptamer method's limitation of requiring thiolated-aptamer-modified AuNPs. Under optimal detection conditions, this label-free colorimetric sensor could detect PDGFs down to 6nM with high selectivity in the presence of other interferring proteins. This simple detection approach provides viable methods for a structured-aptamer sensing protocol.
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Affiliation(s)
- Chia-Chen Chang
- Institute of Biomedical Engineering, National Taiwan University, Taipei 10617, Taiwan
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Multiplex optical sensing with surface-enhanced Raman scattering: a critical review. Anal Chim Acta 2012; 745:10-23. [PMID: 22938601 DOI: 10.1016/j.aca.2012.08.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 08/01/2012] [Accepted: 08/02/2012] [Indexed: 01/25/2023]
Abstract
Multiplex analysis permits the detection of several analytical targets at the same time. This approach may permit to draw a rapid and accurate diagnostic about the health of an individual or an environment. Among the analytical techniques with potential for multiplexing surface-enhanced Raman scattering (SERS) offer unique advantages such as ultrasensitive detection down low the deconvolution times, a unique signature containing all the vibrational information of the target molecules, and the possibility of performing the experiments even in very demanding environments such as natural or biological fluids. Here we review the late advances in multiplex SERS including the direct methods, those aided by the surface functionalization of the plasmonic nanoparticles and the use of SERS encoded particles.
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Negri P, Chen G, Kage A, Nitsche A, Naumann D, Xu B, Dluhy RA. Direct optical detection of viral nucleoprotein binding to an anti-influenza aptamer. Anal Chem 2012; 84:5501-8. [PMID: 22687054 DOI: 10.1021/ac202427e] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We have demonstrated label-free optical detection of viral nucleoprotein binding to a polyvalent anti-influenza aptamer by monitoring the surface-enhanced Raman (SERS) spectra of the aptamer-nucleoprotein complex. The SERS spectra demonstrated that selective binding of the aptamer-nucleoprotein complex could be differentiated from that of the aptamer alone based solely on the direct spectral signature for the aptamer-nucleoprotein complex. Multivariate statistical methods, including principal components analysis, hierarchical clustering, and partial least squares, were used to confirm statistically significant differences between the spectra of the aptamer-nucleoprotein complex and the spectra of the unbound aptamer. Two separate negative controls were used to evaluate the specificity of binding of the viral nucleoproteins to this aptamer. In both cases, no spectral changes were observed that showed protein binding to the control surfaces, indicating a high degree of specificity for the binding of influenza viral nucleoproteins only to the influenza-specific aptamer. Statistical analysis of the spectra supports this interpretation. AFM images demonstrate morphological changes consistent with formation of the influenza aptamer-nucleoprotein complex. These results provide the first evidence for the use of aptamer-modified SERS substrates as diagnostic tools for influenza virus detection in a complex biological matrix.
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Affiliation(s)
- Pierre Negri
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
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50
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Ye J, Wen F, Sobhani H, Lassiter JB, Van Dorpe P, Nordlander P, Halas NJ. Plasmonic nanoclusters: near field properties of the Fano resonance interrogated with SERS. NANO LETTERS 2012; 12:1660-1667. [PMID: 22339688 DOI: 10.1021/nl3000453] [Citation(s) in RCA: 221] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
While the far field properties of Fano resonances are well-known, clusters of plasmonic nanoparticles also possess Fano resonances with unique and spatially complex near field properties. Here we examine the near field properties of individual Fano resonant plasmonic clusters using surface-enhanced Raman scattering (SERS) both from molecules distributed randomly on the structure and from dielectric nanoparticles deposited at specific locations within the cluster. Cluster size, geometry, and interparticle spacing all modify the near field properties of the Fano resonance. For molecules, the spatially dependent SERS response obtained from near field calculations correlates well with the relative SERS intensities observed for individual clusters and for specific Stokes modes of a para-mercaptoaniline adsorbate. In all cases, the largest SERS enhancement is found when both the excitation and the Stokes shifted wavelengths overlap the Fano resonances. In contrast, for SERS from carbon nanoparticles we find that the dielectric screening introduced by the nanoparticle can drastically redistribute the field enhancement associated with the Fano resonance and lead to a significantly modified SERS response compared to what would be anticipated from the bare nanocluster.
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Affiliation(s)
- Jian Ye
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas 77005, USA.
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