1
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Schuknecht F, Kołątaj K, Steinberger M, Liedl T, Lohmueller T. Accessible hotspots for single-protein SERS in DNA-origami assembled gold nanorod dimers with tip-to-tip alignment. Nat Commun 2023; 14:7192. [PMID: 37938571 PMCID: PMC10632510 DOI: 10.1038/s41467-023-42943-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/27/2023] [Indexed: 11/09/2023] Open
Abstract
The label-free identification of individual proteins from liquid samples by surface-enhanced Raman scattering (SERS) spectroscopy is a highly desirable goal in biomedical diagnostics. However, the small Raman scattering cross-section of most (bio-)molecules requires a means to strongly amplify their Raman signal for successful measurement, especially for single molecules. This amplification can be achieved in a plasmonic hotspot that forms between two adjacent gold nanospheres. However, the small (≈1-2 nm) gaps typically required for single-molecule measurements are not accessible for most proteins. A useful strategy would thus involve dimer structures with gaps large enough to accommodate single proteins, whilst providing sufficient field enhancement for single-molecule SERS. Here, we report on using a DNA origami scaffold for tip-to-tip alignment of gold nanorods with an average gap size of 8 nm. The gaps are accessible to streptavidin and thrombin, which are captured at the plasmonic hotspot by specific anchoring sites on the origami template. The field enhancement achieved for the nanorod dimers is sufficient for single-protein SERS spectroscopy with sub-second integration times. This design for SERS probes composed of DNA origami with accessible hotspots promotes future use for single-molecule biodiagnostics in the near-infrared range.
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Affiliation(s)
- Francis Schuknecht
- Chair for Photonics and Optoelectronics, Nano-Institute Munich, Department of Physics, Ludwig-Maximilians-Universität (LMU), Königinstraße 10, 80539, Munich, Germany
| | - Karol Kołątaj
- Physics Department and CeNS, Ludwig-Maximilians-University Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
- Département de Physique, Université de Fribourg, Chemin du Musée 3, 1700, Fribourg, Switzerland
| | - Michael Steinberger
- Chair for Photonics and Optoelectronics, Nano-Institute Munich, Department of Physics, Ludwig-Maximilians-Universität (LMU), Königinstraße 10, 80539, Munich, Germany
| | - Tim Liedl
- Physics Department and CeNS, Ludwig-Maximilians-University Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany.
| | - Theobald Lohmueller
- Chair for Photonics and Optoelectronics, Nano-Institute Munich, Department of Physics, Ludwig-Maximilians-Universität (LMU), Königinstraße 10, 80539, Munich, Germany.
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2
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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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3
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Moreira G, Qian H, Datta SPA, Bliznyuk N, Carpenter J, Dean D, McLamore E, Vanegas D. A capacitive laser-induced graphene based aptasensor for SARS-CoV-2 detection in human saliva. PLoS One 2023; 18:e0290256. [PMID: 37590297 PMCID: PMC10434860 DOI: 10.1371/journal.pone.0290256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 08/03/2023] [Indexed: 08/19/2023] Open
Abstract
SARS-CoV-2 virus induced CoVID-19 pandemic has accelerated the development of diagnostic tools. Devices integrated with electrochemical biosensors may be an interesting alternative to respond to the high demand for testing, particularly in contexts where access to standard detection technologies is lacking. Aptamers as recognition elements are useful due to their stability, specificity, and sensitivity to binding target molecules. We have developed a non-invasive electrochemical aptamer-based biosensor targeting SARS-CoV-2 in human saliva. The aptamer is expected to detect the Spike protein of SARS-CoV-2 wildtype and its variants. Laser-induced graphene (LIG) electrodes coated with platinum nanoparticles were biofunctionalized with a biotin-tagged aptamer. Electrochemical Impedance Spectroscopy (EIS) for BA.1 sensing was conducted in sodium chloride/sodium bicarbonate solution supplemented with pooled saliva. To estimate sensing performance, the aptasensor was tested with contrived samples of UV-attenuated virions from 10 to 10,000 copies/ml. Selectivity was assessed by exposing the aptasensor to non-targeted viruses (hCoV-OC43, Influenza A, and RSV-A). EIS data outputs were further used to select a suitable response variable and cutoff frequency. Capacitance increases in response to the gradual loading of the attenuated BA.1. The aptasensor was sensitive and specific for BA.1 at a lower viral load (10-100 copies/ml) and was capable of discriminating between negative and positive contrived samples (with strain specificity against other viruses: OC43, Influenza A, and RSV-A). The aptasensor detected SARS-CoV-2 with an estimated LOD of 1790 copies/ml in contrived samples. In human clinical samples, the aptasensor presents an accuracy of 72%, with 75% of positive percent of agreement and 67% of negative percent of agreement. Our results show that the aptasensor is a promising candidate to detect SARS-CoV-2 during early stages of infection when virion concentrations are low, which may be useful for preventing the asymptomatic spread of CoVID-19.
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Affiliation(s)
- Geisianny Moreira
- Environmental Engineering and Earth Sciences, Clemson University, Clemson, South Carolina, United States of America
- Department of Agricultural Sciences, Clemson University, Clemson, South Carolina, United States of America
- Global Alliance for Rapid Diagnostics, Michigan State University, East Lancing, Michigan, United States of America
| | - Hanyu Qian
- Department of Agricultural and Biological Engineering, University of Florida, Gainesville, Florida, United States of America
| | - Shoumen Palit Austin Datta
- Department of Mechanical Engineering, MIT Auto-ID Labs, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Anesthesiology, Medical Device (MDPnP) Interoperability and Cybersecurity Labs, Biomedical Engineering Program, Massachusetts General Hospital, Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Nikolay Bliznyuk
- Department of Agricultural and Biological Engineering, University of Florida, Gainesville, Florida, United States of America
| | - Jeremiah Carpenter
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, South Carolina, United States of America
- Department of Bioengineering, Clemson University, Clemson, South Carolina, United States of America
| | - Delphine Dean
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, South Carolina, United States of America
- Department of Bioengineering, Clemson University, Clemson, South Carolina, United States of America
| | - Eric McLamore
- Environmental Engineering and Earth Sciences, Clemson University, Clemson, South Carolina, United States of America
- Department of Agricultural Sciences, Clemson University, Clemson, South Carolina, United States of America
- Global Alliance for Rapid Diagnostics, Michigan State University, East Lancing, Michigan, United States of America
| | - Diana Vanegas
- Environmental Engineering and Earth Sciences, Clemson University, Clemson, South Carolina, United States of America
- Global Alliance for Rapid Diagnostics, Michigan State University, East Lancing, Michigan, United States of America
- Interdisciplinary Group for Biotechnology Innovation and Ecosocial Change -BioNovo, Universidad del Valle, Cali, Colombia
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4
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Design and Prediction of Aptamers Assisted by In Silico Methods. Biomedicines 2023; 11:biomedicines11020356. [PMID: 36830893 PMCID: PMC9953197 DOI: 10.3390/biomedicines11020356] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
An aptamer is a single-stranded DNA or RNA that binds to a specific target with high binding affinity. Aptamers are developed through the process of systematic evolution of ligands by exponential enrichment (SELEX), which is repeated to increase the binding power and specificity. However, the SELEX process is time-consuming, and the characterization of aptamer candidates selected through it requires additional effort. Here, we describe in silico methods in order to suggest the most efficient way to develop aptamers and minimize the laborious effort required to screen and optimise aptamers. We investigated several methods for the estimation of aptamer-target molecule binding through conformational structure prediction, molecular docking, and molecular dynamic simulation. In addition, examples of machine learning and deep learning technologies used to predict the binding of targets and ligands in the development of new drugs are introduced. This review will be helpful in the development and application of in silico aptamer screening and characterization.
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5
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Hasanzadeh A, Hamblin MR, Kiani J, Noori H, Hardie JM, Karimi M, Shafiee H. Could artificial intelligence revolutionize the development of nanovectors for gene therapy and mRNA vaccines? NANO TODAY 2022; 47:101665. [PMID: 37034382 PMCID: PMC10081506 DOI: 10.1016/j.nantod.2022.101665] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Gene therapy enables the introduction of nucleic acids like DNA and RNA into host cells, and is expected to revolutionize the treatment of a wide range of diseases. This growth has been further accelerated by the discovery of CRISPR/Cas technology, which allows accurate genomic editing in a broad range of cells and organisms in vitro and in vivo. Despite many advances in gene delivery and the development of various viral and non-viral gene delivery vectors, the lack of highly efficient non-viral systems with low cellular toxicity remains a challenge. The application of cutting-edge technologies such as artificial intelligence (AI) has great potential to find new paradigms to solve this issue. Herein, we review AI and its major subfields including machine learning (ML), neural networks (NNs), expert systems, deep learning (DL), computer vision and robotics. We discuss the potential of AI-based models and algorithms in the design of targeted gene delivery vehicles capable of crossing extracellular and intracellular barriers by viral mimicry strategies. We finally discuss the role of AI in improving the function of CRISPR/Cas systems, developing novel nanobots, and mRNA vaccine carriers.
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Affiliation(s)
- Akbar Hasanzadeh
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein 2028, South Africa
- Radiation Biology Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Jafar Kiani
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hamid Noori
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Joseph M. Hardie
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02139 USA
| | - Mahdi Karimi
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Research Center for Science and Technology in Medicine, Tehran University of Medical Sciences, Tehran 141556559, Iran
- Applied Biotechnology Research Centre, Tehran Medical Science, Islamic Azad University, Tehran 1584743311, Iran
| | - Hadi Shafiee
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02139 USA
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6
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Tanwar S, Kaur V, Kaur G, Sen T. Broadband SERS Enhancement by DNA Origami Assembled Bimetallic Nanoantennas with Label-Free Single Protein Sensing. J Phys Chem Lett 2021; 12:8141-8150. [PMID: 34410129 DOI: 10.1021/acs.jpclett.1c02272] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Engineering hotspots in surface-enhanced Raman spectroscopy (SERS) through precisely controlled assembly of plasmonic nanostructures capable of expanding intense field enhancement are highly desirable to enhance the potentiality of SERS as a label-free optical tool for single molecule detection. Inspired by DNA origami technique, we constructed plasmonic dimer nanoantennas with a tunable gap decorated with Ag-coated Au nanostars on origami. Herein, we demonstrate the single-molecule SERS enhancements of three dyes with emission in different spectral regions after incorporation of single dye molecules in between two nanostars. The enhancement factors (EFs) achieved in the range of 109-1010 for all the single dye molecules, under both resonant and nonresonant excitation conditions, would enable enhanced photostability during time-series measurement. We further successfully explored the potential of our designed nanoantennas to accommodate and detect a single thrombin protein molecule after selective placement in the wide nanogap of 10 nm. Our results suggest that such nanoantennas can serve as a broadband SERS enhancer and enable specific detection of target biological molecules with single-molecule sensitivity.
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Affiliation(s)
- Swati Tanwar
- Institute of Nano Science and Technology, Sector-81, Mohali, Punjab-140306, India
| | - Vishaldeep Kaur
- Institute of Nano Science and Technology, Sector-81, Mohali, Punjab-140306, India
| | - Gagandeep Kaur
- Institute of Nano Science and Technology, Sector-81, Mohali, Punjab-140306, India
| | - Tapasi Sen
- Institute of Nano Science and Technology, Sector-81, Mohali, Punjab-140306, India
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7
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Safar W, Tatar AS, Leray A, Potara M, Liu Q, Edely M, Djaker N, Spadavecchia J, Fu W, Derouich SG, Felidj N, Astilean S, Finot E, Lamy de la Chapelle M. New insight into the aptamer conformation and aptamer/protein interaction by surface-enhanced Raman scattering and multivariate statistical analysis. NANOSCALE 2021; 13:12443-12453. [PMID: 34251385 DOI: 10.1039/d1nr02180j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We study the interaction between one aptamer and its analyte (the MnSOD protein) by the combination of surface-enhanced Raman scattering and multivariate statistical analysis. We observe the aptamer structure and its evolution during the interaction under different experimental conditions (in air or in buffer). Through the spectral treatment by principal component analysis of a large set of SERS data, we were able to probe the aptamer conformations and orientations relative to the surface assuming that the in-plane nucleoside modes are selectively enhanced. We demonstrate that the aptamer orientation and thus its flexibility rely strongly on the presence of a spacer of 15 thymines and on the experimental conditions with the aptamer lying on the surface in air and standing in the buffer. We reveal for the first time that the interaction with MnSOD induces a large loss of flexibility and freezes the aptamer structure in a single conformation.
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Affiliation(s)
- Wafa Safar
- IMMM - UMR 6283 CNRS, Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, Cedex 9, France.
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8
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Chen Z, Hu L, Zhang BT, Lu A, Wang Y, Yu Y, Zhang G. Artificial Intelligence in Aptamer-Target Binding Prediction. Int J Mol Sci 2021; 22:3605. [PMID: 33808496 PMCID: PMC8038094 DOI: 10.3390/ijms22073605] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 12/18/2022] Open
Abstract
Aptamers are short single-stranded DNA, RNA, or synthetic Xeno nucleic acids (XNA) molecules that can interact with corresponding targets with high affinity. Owing to their unique features, including low cost of production, easy chemical modification, high thermal stability, reproducibility, as well as low levels of immunogenicity and toxicity, aptamers can be used as an alternative to antibodies in diagnostics and therapeutics. Systematic evolution of ligands by exponential enrichment (SELEX), an experimental approach for aptamer screening, allows the selection and identification of in vitro aptamers with high affinity and specificity. However, the SELEX process is time consuming and characterization of the representative aptamer candidates from SELEX is rather laborious. Artificial intelligence (AI) could help to rapidly identify the potential aptamer candidates from a vast number of sequences. This review discusses the advancements of AI pipelines/methods, including structure-based and machine/deep learning-based methods, for predicting the binding ability of aptamers to targets. Structure-based methods are the most used in computer-aided drug design. For this part, we review the secondary and tertiary structure prediction methods for aptamers, molecular docking, as well as molecular dynamic simulation methods for aptamer-target binding. We also performed analysis to compare the accuracy of different secondary and tertiary structure prediction methods for aptamers. On the other hand, advanced machine-/deep-learning models have witnessed successes in predicting the binding abilities between targets and ligands in drug discovery and thus potentially offer a robust and accurate approach to predict the binding between aptamers and targets. The research utilizing machine-/deep-learning techniques for prediction of aptamer-target binding is limited currently. Therefore, perspectives for models, algorithms, and implementation strategies of machine/deep learning-based methods are discussed. This review could facilitate the development and application of high-throughput and less laborious in silico methods in aptamer selection and characterization.
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Affiliation(s)
- Zihao Chen
- School of Chinese Medicine, The Chinese University of Hong Kong, Hong Kong, China; (Z.C.); (B.-T.Z.)
| | - Long Hu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China;
| | - Bao-Ting Zhang
- School of Chinese Medicine, The Chinese University of Hong Kong, Hong Kong, China; (Z.C.); (B.-T.Z.)
| | - Aiping Lu
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China;
- Guangdong-Hong Kong Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong, China
| | - Yaofeng Wang
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong, China
| | - Yuanyuan Yu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China;
- Guangdong-Hong Kong Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong, China
| | - Ge Zhang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China;
- Guangdong-Hong Kong Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery, Hong Kong, China
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9
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Dekhili R, Cherni K, Liu H, Li X, Djaker N, Spadavecchia J. Aptamer-Gold(III) Complex Nanoparticles: A New Way to Detect Cu, Zn SOD Glycoprotein. ACS OMEGA 2020; 5:13851-13859. [PMID: 32566851 PMCID: PMC7301578 DOI: 10.1021/acsomega.0c01192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 05/21/2020] [Indexed: 05/25/2023]
Abstract
Aptamers are small biomolecules composed of 20-100 nucleotides that recognize target molecules in three-dimensional structures. These natural targeting molecules have attracted interest in the biomedical field as biomarkers for cancer diagnostics. In this study, we investigated the interaction of a characteristic aptamer with its target protein, Cu, Zn superoxide dismutase (SOD 4), on a gold nanoparticle (AuNP) surface under experimental conditions. For this purpose, we applied two protocols to coat SOD 4 aptamer (APT) on the nanoparticle surface: carbodiimide chemistry (EDC/NHS) (Method ON) and a complexation methodology (Method IN). The nano-aptamer's interactions with SOD 4 were detected by UV-vis absorption and Raman spectroscopy in a range of protein concentrations (from 1 μM to 50 nM). We believe that the interaction is heavily dependent on the nature of the biomarker (SOD 4) and also on the steric arrangement of the aptamer on the gold nanoparticle surface. The lowest detectable concentration (limit of detection, LOD) was about 2 nM for APT IN PEG-AuNPs and 8 nM for APT ON PEG-AuNPs. For the first time, we demonstrated a very sensitive detection of SOD 4 in the nanomolar concentration range with new ways of biosensor synthesis (APT IN and ON), providing a very strong tool to understand the effect of aptamer conformation to detect SOD 4.
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Affiliation(s)
- Rawdha Dekhili
- CNRS,
UMR 7244, NBD-CSPBAT, Laboratory of Chemistry, Structures and Properties
of Biomaterials and Therapeutic Agents University Paris13, Sorbonne Paris Nord, Bobigny 93000, France
| | - Khaoula Cherni
- CNRS,
UMR 7244, NBD-CSPBAT, Laboratory of Chemistry, Structures and Properties
of Biomaterials and Therapeutic Agents University Paris13, Sorbonne Paris Nord, Bobigny 93000, France
| | - Hui Liu
- Department
of Hepatobiliary Surgery, Shenzhen University General Hospital &
Guangdong Provincial Key Laboratory of Regional Immunity and Diseases
& Carson International Cancer Shenzhen University General Hospital
& Shenzhen University Clinical Medical Academy Center, Shenzhen University, Shenzhen 518000, China
| | - Xiaowu Li
- Department
of Hepatobiliary Surgery, Shenzhen University General Hospital &
Guangdong Provincial Key Laboratory of Regional Immunity and Diseases
& Carson International Cancer Shenzhen University General Hospital
& Shenzhen University Clinical Medical Academy Center, Shenzhen University, Shenzhen 518000, China
| | - Nadia Djaker
- CNRS,
UMR 7244, NBD-CSPBAT, Laboratory of Chemistry, Structures and Properties
of Biomaterials and Therapeutic Agents University Paris13, Sorbonne Paris Nord, Bobigny 93000, France
| | - Jolanda Spadavecchia
- CNRS,
UMR 7244, NBD-CSPBAT, Laboratory of Chemistry, Structures and Properties
of Biomaterials and Therapeutic Agents University Paris13, Sorbonne Paris Nord, Bobigny 93000, France
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10
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Sun Y, Zhu X, Liu H, Dai Y, Han R, Gao D, Luo C, Wang X, Wei Q. Novel Chemiluminescence Sensor for Thrombin Detection Based on Dual-Aptamer Biorecognition and Mesoporous Silica Encapsulated with Iron Porphyrin. ACS APPLIED MATERIALS & INTERFACES 2020; 12:5569-5577. [PMID: 31933352 DOI: 10.1021/acsami.9b20255] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Thrombin is a marker of blood-related diseases, and its detection is of great significance in the fields of medical and biological research. Herein, a novel chemiluminescence (CL) sensor for thrombin detection was prepared based on dual-aptamer biorecognition and mesoporous silica encapsulated with iron porphyrin. Mesoporous silica encapsulated with hematin by aptamer1 (Apt1/hematin/M-SiO2) and magnetic microspheres modified with aptamer2 (Apt2/NH2-MS) were successfully prepared, and the two materials were used to construct a CL sensor to detect thrombin. Primarily, Apt2/NH2-MS is used for pretreatment separation of thrombin samples by the biorecognition effect between the aptamer (Apt2) and target (thrombin). Then, thrombin/Apt2/NH2-MS is again recognized with Apt1 on the surface of Apt1/hematin/M-SiO2 and Apt1/thrombin/Apt2/NH2-MS is formed, so dual-aptamer biorecognition is realized. Meanwhile, the generated Apt1/thrombin/Apt2/NH2-MS makes Apt1 shed off the surface of M-SiO2 and release hematin. The released hematin can catalyze the luminol-H2O2 CL reaction. Therefore, a sandwich-type CL sensor was constructed based on dual-aptamer biorecognition and hematin catalysis for the detection of thrombin. The sensor has a linear range of 7.5 × 10-15 to 2.5 × 10-10 mol·L-1 and a detection limit of 2.2 × 10-15 mol·L-1 and also exhibits excellent selectivity, reproducibility, and stability. The sensor was successfully used for the detection of thrombin in serum samples, which makes it possible to apply the sensor in the detection of thrombin in actual samples.
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Affiliation(s)
- Yuanling Sun
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering , University of Jinan , Jinan 250022 , PR China
| | - Xiaodong Zhu
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering , University of Jinan , Jinan 250022 , PR China
| | - Hao Liu
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering , University of Jinan , Jinan 250022 , PR China
| | - Yuxue Dai
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering , University of Jinan , Jinan 250022 , PR China
| | - Rui Han
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering , University of Jinan , Jinan 250022 , PR China
| | - Dandan Gao
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering , University of Jinan , Jinan 250022 , PR China
| | - Chuannan Luo
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering , University of Jinan , Jinan 250022 , PR China
| | - Xueying Wang
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering , University of Jinan , Jinan 250022 , PR China
| | - Qin Wei
- Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering , University of Jinan , Jinan 250022 , PR China
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11
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Roxo C, Kotkowiak W, Pasternak A. G-Quadruplex-Forming Aptamers-Characteristics, Applications, and Perspectives. Molecules 2019; 24:E3781. [PMID: 31640176 PMCID: PMC6832456 DOI: 10.3390/molecules24203781] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/16/2019] [Accepted: 10/18/2019] [Indexed: 12/31/2022] Open
Abstract
G-quadruplexes constitute a unique class of nucleic acid structures formed by G-rich oligonucleotides of DNA- or RNA-type. Depending on their chemical nature, loops length, and localization in the sequence or structure molecularity, G-quadruplexes are highly polymorphic structures showing various folding topologies. They may be formed in the human genome where they are believed to play a pivotal role in the regulation of multiple biological processes such as replication, transcription, and translation. Thus, natural G-quadruplex structures became prospective targets for disease treatment. The fast development of systematic evolution of ligands by exponential enrichment (SELEX) technologies provided a number of G-rich aptamers revealing the potential of G-quadruplex structures as a promising molecular tool targeted toward various biologically important ligands. Because of their high stability, increased cellular uptake, ease of chemical modification, minor production costs, and convenient storage, G-rich aptamers became interesting therapeutic and diagnostic alternatives to antibodies. In this review, we describe the recent advances in the development of G-quadruplex based aptamers by focusing on the therapeutic and diagnostic potential of this exceptional class of nucleic acid structures.
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Affiliation(s)
- Carolina Roxo
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Weronika Kotkowiak
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Anna Pasternak
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
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12
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Raman Spectroscopy and Aptamers for a Label-Free Approach: Diagnostic and Application Tools. JOURNAL OF HEALTHCARE ENGINEERING 2019; 2019:2815789. [PMID: 31183028 PMCID: PMC6512054 DOI: 10.1155/2019/2815789] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 04/10/2019] [Indexed: 01/04/2023]
Abstract
Raman spectroscopy is a powerful optical technique based on the inelastic scattering of incident light to assess the chemical composition of a sample, including biological ones. Medical diagnostic applications of Raman spectroscopy are constantly increasing to provide biochemical and structural information on several specimens, being not affected by water interference, and potentially avoiding the constraint of additional labelling procedures. New strategies have been recently developed to overcome some Raman limitations related, for instance, to the need to deal with an adequate quantity of the sample to perform a reliable analysis. In this regard, the use of metallic nanoparticles, the optimization of fiber optic probes, and other approaches can actually enhance the signal intensity compared to spontaneous Raman scattering. Moreover, to further increase the potential of this investigation technique, aptamers can be considered as a valuable means, being synthetic, short, single, or double-stranded oligonucleotides (RNAs or DNAs) that fold up into unique 3D structures to specifically bind to selected molecules, even at very low concentrations, and thus allowing an early diagnosis of a possible disease. Due to the paramount relevance of the topic, this review focuses on the main Raman spectroscopy techniques combined with aptamer arrays in the label-free mode, providing an overview on different applications to support healthcare management.
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13
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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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14
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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: 422] [Impact Index Per Article: 70.3] [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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15
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Wu Y, Jiang Y, Zheng X, Jia S, Zhu Z, Ren B, Ma H. Facile fabrication of microfluidic surface-enhanced Raman scattering devices via lift-up lithography. ROYAL SOCIETY OPEN SCIENCE 2018; 5:172034. [PMID: 29765657 PMCID: PMC5936922 DOI: 10.1098/rsos.172034] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 03/09/2018] [Indexed: 05/22/2023]
Abstract
We describe a facile and low-cost approach for a flexibly integrated surface-enhanced Raman scattering (SERS) substrate in microfluidic chips. Briefly, a SERS substrate was fabricated by the electrostatic assembling of gold nanoparticles, and shaped into designed patterns by subsequent lift-up soft lithography. The SERS micro-pattern could be further integrated within microfluidic channels conveniently. The resulting microfluidic SERS chip allowed ultrasensitive in situ SERS monitoring from the transparent glass window. With its advantages in simplicity, functionality and cost-effectiveness, this method could be readily expanded into optical microfluidic fabrication for biochemical applications.
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Affiliation(s)
- Yuanzi Wu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350002, People's Republic of China
| | - Ye Jiang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350002, People's Republic of China
| | - Xiaoshan Zheng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, and Collaborative Innovation Center of Chemistry of Energy Materials, Xiamen University, Xiamen 361005, People's Republic of China
| | - Shasha Jia
- State Key Laboratory of Physical Chemistry of Solid Surfaces, the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, and Collaborative Innovation Center of Chemistry of Energy Materials, Xiamen University, Xiamen 361005, People's Republic of China
| | - Zhi Zhu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, and Collaborative Innovation Center of Chemistry of Energy Materials, Xiamen University, Xiamen 361005, People's Republic of China
| | - Bin Ren
- State Key Laboratory of Physical Chemistry of Solid Surfaces, the MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, and Collaborative Innovation Center of Chemistry of Energy Materials, Xiamen University, Xiamen 361005, People's Republic of China
- Authors for correspondence: Bin Ren e-mail:
| | - Hongwei Ma
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215125, People's Republic of China
- Authors for correspondence: Hongwei Ma e-mail:
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16
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Kumar N, Seminario JM. Molecular dynamics study of thrombin capture by aptamers TBA26 and TBA29 coupled to a DNA origami. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1448977] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Narendra Kumar
- Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Jorge M. Seminario
- Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
- Department of Materials Science and Engineering, Texas A&M University, College Station, TX, USA
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17
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Ma Q, Wang Y, Jia J, Xiang Y. Colorimetric aptasensors for determination of tobramycin in milk and chicken eggs based on DNA and gold nanoparticles. Food Chem 2018; 249:98-103. [PMID: 29407938 DOI: 10.1016/j.foodchem.2018.01.022] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 06/26/2017] [Accepted: 01/02/2018] [Indexed: 11/18/2022]
Abstract
Colorimetric aptasensors were designed for detection of tobramycin (TOB) based on unmodified gold nanoparticles (AuNPs) and single-strand DNA (ssDNA). In the absence of TOB, the DNA aptamer was coated on the surface of AuNPs to keep it against salt-induced aggregation. In the presence of TOB, aptamer will bind with TOB and detach from the surface of AuNPs because of higher affinities between aptamer and TOB. Then less protection of DNA may result in the aggregation of AuNPs by salt and an apparent color change from red to purple-blue. The developed aptasensors showed a high selectivity and sensitivity for TOB detection. The linearity range and the detection limit were 40-200 nM and 23.3 nM respectively. The validity of the procedure and applicability of aptasensors were successfully used to detect TOB in milk and chicken eggs, and the results were excellent in accord with the values obtained by spectrofluorimetric detection.
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Affiliation(s)
- Qiang Ma
- Department of Chemistry, Capital Normal University, Beijing 100048, China
| | - Yuxian Wang
- Department of Chemistry, Capital Normal University, Beijing 100048, China
| | - Jie Jia
- Department of Chemistry, Capital Normal University, Beijing 100048, China
| | - Yuhong Xiang
- Department of Chemistry, Capital Normal University, Beijing 100048, China.
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18
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Han Y, Qian J, Zhang J, Hu C, Wang C. Structure-toxicity relationship of cefoperazone and its impurities to developing zebrafish by transcriptome and Raman analysis. Toxicol Appl Pharmacol 2017; 327:39-51. [DOI: 10.1016/j.taap.2017.04.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/20/2017] [Accepted: 04/28/2017] [Indexed: 11/30/2022]
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19
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Agoston R, Izake EL, Sivanesan A, Lott WB, Sillence M, Steel R. Rapid isolation and detection of erythropoietin in blood plasma by magnetic core gold nanoparticles and portable Raman spectroscopy. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2015; 12:633-641. [PMID: 26656628 DOI: 10.1016/j.nano.2015.11.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/24/2015] [Accepted: 11/07/2015] [Indexed: 11/29/2022]
Abstract
UNLABELLED Isolating, purifying, and identifying proteins in complex biological matrices are often difficult, time consuming, and unreliable. Herein we describe a rapid screening technique for proteins in biological matrices that combines selective protein isolation with direct surface enhanced Raman spectroscopy (SERS) detection. Magnetic core gold nanoparticles were synthesized, characterized, and subsequently functionalized with recombinant human erythropoietin (rHuEPO)-specific antibody. The functionalized nanoparticles were used to capture rHuEPO from horse blood plasma within 15 min. The selective binding between the protein and the functionalized nanoparticles was monitored by SERS. The purified protein was then released from the nanoparticles' surface and directly spectroscopically identified on a commercial nanopillar SERS substrate. ELISA independently confirmed the SERS identification and quantified the released rHuEPO. Finally, the direct SERS detection of the extracted protein was successfully demonstrated for in-field screening by a handheld Raman spectrometer within 1 min sample measurement time. FROM THE CLINICAL EDITOR The rapid detection of recombinant human erythropoietin (rHuEPO) is important in competitive sports to screen for doping offences. In this article, the authors reported their technique of direct surface enhanced Raman spectroscopy (SERS) detection using magnetic core gold nanoparticles functionalized with recombinant human erythropoietin-specific antibody. The findings should open a new way for future detection of other proteins.
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Affiliation(s)
- Roland Agoston
- Nanotechnology and Molecular Sciences Discipline, Faculty of Science and Engineering, Queensland University of Technology, Brisbane, Australia
| | - Emad L Izake
- Nanotechnology and Molecular Sciences Discipline, Faculty of Science and Engineering, Queensland University of Technology, Brisbane, Australia.
| | - Arumugam Sivanesan
- Nanotechnology and Molecular Sciences Discipline, Faculty of Science and Engineering, Queensland University of Technology, Brisbane, Australia.
| | - William B Lott
- Nanotechnology and Molecular Sciences Discipline, Faculty of Science and Engineering, Queensland University of Technology, Brisbane, Australia
| | - Martin Sillence
- Nanotechnology and Molecular Sciences Discipline, Faculty of Science and Engineering, Queensland University of Technology, Brisbane, Australia
| | - Rohan Steel
- Biological Research Unit, Racing Analytical Services Ltd., Melbourne, VIC, Australia
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20
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Kahraman M, Wachsmann-Hogiu S. Label-free and direct protein detection on 3D plasmonic nanovoid structures using surface-enhanced Raman scattering. Anal Chim Acta 2014; 856:74-81. [PMID: 25542360 DOI: 10.1016/j.aca.2014.11.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 11/15/2014] [Indexed: 11/18/2022]
Abstract
In this paper we use surface-enhanced Raman spectroscopy (SERS) on 3D metallic structures for label-free detection and characterization of proteins of interest at low concentrations. The substrates are prepared via nanopatterning with latex nano/microparticles and Cr and Ag sputtering, yielding stable, tunable, and mechanically flexible plasmonic structures. The nanovoids generate a SERS signal of the proteins of interest that is background free and independent of the protein charge. Concentrations as low as 0.05 μg mL(-1) could be detected for 4 different proteins. The proteins also exhibit significantly different SERS spectra on these substrates, which is an important feature for future label-free direct detection schemes.
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Affiliation(s)
- Mehmet Kahraman
- Department of Chemistry, Faculty of Arts and Sciences, University of Gaziantep, 27310 Sehitkamil, Gaziantep, Turkey.
| | - Sebastian Wachsmann-Hogiu
- Center for Biophotonics, University of California Davis, Sacramento, CA 95817, USA; Department of Pathology and Laboratory Medicine, University of California Davis, Sacramento, CA 95817, USA.
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21
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Marks HL, Pishko MV, Jackson GW, Coté GL. Rational design of a bisphenol A aptamer selective surface-enhanced Raman scattering nanoprobe. Anal Chem 2014; 86:11614-9. [PMID: 25329684 PMCID: PMC4255672 DOI: 10.1021/ac502541v] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Surface-enhanced
Raman scattering (SERS) optical nanoprobes offer
a number of advantages for ultrasensitive analyte detection. These
functionalized colloidal nanoparticles are a multifunctional assay
component. providing a platform for conjugation to spectral tags,
stabilizing polymers, and biorecognition elements such as aptamers
or antibodies. We demonstrate the design and characterization of a
SERS-active nanoprobe and investigate the nanoparticles’ biorecognition
capabilities for use in a competitive binding assay. Specifically,
the nanoprobe is designed for the quantification of bisphenol A (BPA)
levels in the blood after human exposure to the toxin in food and
beverage plastic packaging. The nanoprobes demonstrated specific affinity
to a BPA aptamer with a dissociation constant Kd of 54 nM, and provided a dose-dependent SERS spectra with
a limit of detection of 3 nM. Our conjugation approach shows the versatility
of colloidal nanoparticles in assay development, acting as detectable
spectral tagging elements and biologically active ligands concurrently.
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Affiliation(s)
- Haley L Marks
- Department of Biomedical Engineering, Texas A&M University , College Station, Texas 77843, United States
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22
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Development of aptamer-conjugated magnetic graphene/gold nanoparticle hybrid nanocomposites for specific enrichment and rapid analysis of thrombin by MALDI-TOF MS. Talanta 2014; 129:282-9. [DOI: 10.1016/j.talanta.2014.05.045] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 05/18/2014] [Accepted: 05/21/2014] [Indexed: 11/20/2022]
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23
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Kobeissy FH, Gulbakan B, Alawieh A, Karam P, Zhang Z, Guingab-Cagmat JD, Mondello S, Tan W, Anagli J, Wang K. Post-genomics nanotechnology is gaining momentum: nanoproteomics and applications in life sciences. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014; 18:111-31. [PMID: 24410486 DOI: 10.1089/omi.2013.0074] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The post-genomics era has brought about new Omics biotechnologies, such as proteomics and metabolomics, as well as their novel applications to personal genomics and the quantified self. These advances are now also catalyzing other and newer post-genomics innovations, leading to convergences between Omics and nanotechnology. In this work, we systematically contextualize and exemplify an emerging strand of post-genomics life sciences, namely, nanoproteomics and its applications in health and integrative biological systems. Nanotechnology has been utilized as a complementary component to revolutionize proteomics through different kinds of nanotechnology applications, including nanoporous structures, functionalized nanoparticles, quantum dots, and polymeric nanostructures. Those applications, though still in their infancy, have led to several highly sensitive diagnostics and new methods of drug delivery and targeted therapy for clinical use. The present article differs from previous analyses of nanoproteomics in that it offers an in-depth and comparative evaluation of the attendant biotechnology portfolio and their applications as seen through the lens of post-genomics life sciences and biomedicine. These include: (1) immunosensors for inflammatory, pathogenic, and autoimmune markers for infectious and autoimmune diseases, (2) amplified immunoassays for detection of cancer biomarkers, and (3) methods for targeted therapy and automatically adjusted drug delivery such as in experimental stroke and brain injury studies. As nanoproteomics becomes available both to the clinician at the bedside and the citizens who are increasingly interested in access to novel post-genomics diagnostics through initiatives such as the quantified self, we anticipate further breakthroughs in personalized and targeted medicine.
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Affiliation(s)
- Firas H Kobeissy
- 1 Center for Neuroproteomics and Biomarkers Research, Department of Psychiatry, McKnight Brain Institute, University of Florida , Gainesville, Florida
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Synergizing nucleic acid aptamers with 1-dimensional nanostructures as label-free field-effect transistor biosensors. Biosens Bioelectron 2013; 50:278-93. [PMID: 23872609 DOI: 10.1016/j.bios.2013.06.033] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 06/06/2013] [Accepted: 06/17/2013] [Indexed: 01/04/2023]
Abstract
Since the introduction by Gold et al. in 1990, nucleic acid aptamers had evolved to become a true contender in biosensors for protein and cell detections. Aptamers are short strands of synthetically designed DNA or RNA oligonucleotides that can be self-assembled into unique 3-dimensional structures and can bind to different proteins, cells or even small molecules at a high level of specificity and affinity. In recent years, there had been many reports in literature in using aptamers in place of conventional antibodies as capture biomolecules on the surface. This is mainly due to the better thermal stability properties and ease in production. Consequently, also these characteristics allowed the aptamers to find use in field effect transistors (FETs) based upon 1D nanostructured (1D-NS) as label-free biosensing. In terms of designing label-free platforms for biosensors applications, 1D-NS FET had been an attractive option due to reported high sensitivities toward protein targets arising from the large surface area for detection as well as to their label-free nature. Since the first aptamer-based 1D-NS FET biosensor had surfaced in 2005, there had been many more improvements in the overall design and sensitivity in recent years. In this review, the latest developments in synergizing these two interesting areas of research (aptamers and 1D-NS FET) will be discussed for a range of different nanowire types as well as for the detection results.
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25
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Muntean CM, Stefan R, Bindea M, Cozma V. Fourier transform infrared spectroscopy of DNA from Borrelia burgdorferi sensu lato and Ixodes ricinus ticks. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 110:185-192. [PMID: 23563637 DOI: 10.1016/j.saa.2013.03.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 02/15/2013] [Accepted: 03/03/2013] [Indexed: 06/02/2023]
Abstract
In this work we present a method for detection of motile and immotile Borrelia burgdorferi genomic DNA, in relation with infectious and noninfectious spirochetes. An FT-IR study of DNA isolated from B. burgdorferi sensu lato strains and from positive and negative Ixodes ricinus ticks, respectively, is reported. Motile bacterial cells from the species B. burgdorferi sensu stricto, Borrelia garinii and Borrelia afzelii were of interest. Also, FT-IR absorbance spectra of DNA from immotile spirochetes of B. burgdorferi sensu stricto, in the absence and presence of different antibiotics (doxycycline, erythromycin, gentamicin, penicillin V or phenoxymethylpenicillin, tetracycline, respectively) were investigated. FT-IR spectra, providing a high molecular structural information, have been analyzed in the wavenumber range 400-1800 cm(-1). FT-IR signatures, spectroscopic band assignments and structural interpretations of these DNAs are reported. Spectral differences between FT-IR absorbances of DNAs from motile bacterial cells and immotile spirochetes, respectively, have been found. Particularly, alterations of the sugar-phosphate B-form chain in the case of DNA from Borrelia immotile cells, as compared with DNA from B. burgdorferi sensu lato motile cells have been observed. Based on this work, specific B. burgdorferi sensu lato and I. ricinus DNA-ligand interactions, respectively, might be further investigated using Fourier transform infrared spectroscopy.
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Affiliation(s)
- Cristina M Muntean
- National Institute for Research & Development of Isotopic and Molecular Technologies, 65-103 Donath St., 400293 Cluj-Napoca, Romania
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26
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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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Citartan M, Gopinath SCB, Tominaga J, Tang TH. Label-free methods of reporting biomolecular interactions by optical biosensors. Analyst 2013; 138:3576-92. [DOI: 10.1039/c3an36828a] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Negri P, Dluhy RA. Ag nanorod based surface-enhanced Raman spectroscopy applied to bioanalytical sensing. JOURNAL OF BIOPHOTONICS 2013; 6:20-35. [PMID: 23175392 PMCID: PMC3767285 DOI: 10.1002/jbio.201200133] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 09/25/2012] [Accepted: 09/26/2012] [Indexed: 06/01/2023]
Abstract
Recent progress in substrate nanofabrication has led to the development of Ag nanorod arrays as uniform, reproducible, large area SERS-active substrates with high signal enhancement. These novel nanostructures fabricated by oblique angle vapor deposition (OAD) offer a robust platform for the rapid detection of biological agents and open new perspectives for the development and integration of biomedical diagnostic for clinical and therapeutic applications. Ag nanorod arrays have been investigated as SERS-active substrates for the detection and identification of pathogens, including bacteria and viruses, as well as to evaluate the potential of this biosensing platform for bio-recognition of high affinity events using oligonucleotide-modified substrates. This review summarizes the various nanostructured substrates designed for SERS-based applications, highlights the nanofabrication methodology used to produce Ag nanorod arrays, outlines their morphological and physical properties, and provides a summary of the most recent uses of these substrates for clinical diagnostic and biomedical applications.
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Affiliation(s)
- Pierre Negri
- Department of Chemistry, University of Georgia, Athens, GA 30602
| | - Richard A. Dluhy
- Department of Chemistry, University of Georgia, Athens, GA 30602
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29
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Kahraman M, Balz BN, Wachsmann-Hogiu S. Hydrophobicity-driven self-assembly of protein and silver nanoparticles for protein detection using surface-enhanced Raman scattering. Analyst 2013; 138:2906-13. [DOI: 10.1039/c3an00025g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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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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31
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Rusciano G, De Luca AC, Pesce G, Sasso A, Oliviero G, Amato J, Borbone N, D'Errico S, Piccialli V, Piccialli G, Mayol L. Label-free probing of G-quadruplex formation by surface-enhanced Raman scattering. Anal Chem 2011; 83:6849-55. [PMID: 21780762 DOI: 10.1021/ac201783h] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In this work, we establish the use of surface-enhanced Raman scattering (SERS) as a label-free analytical technique for the direct detection of G-quadruplex formation. In particular, we demonstrate that SERS analysis allows the evaluation of the relative stability of G quadruplexes that differ for the number of G tetrads and investigate several structural features of quadruplexes, such as the orientation of glycosidic bonds, the identification of distortions in the sugar-phosphate backbone, and the degree of hydrogen-bond solvation. Herein, the fluctuation of the SERS spectra, due to the specific interaction of vibrational modes with the SERS-active substrate, is quantitatively analyzed before and after quadruplex formation. The results of this study suggest a perpendicular orientation of the quadruplexes (with or without the 3'-tetra end linker) with respect to the silver colloidal surface, which opens new perspectives for the use of SERS as a label-free analytical tool for the study of the binding mode between quadruplexes and their ligands.
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Affiliation(s)
- Giulia Rusciano
- Dipartimento di Scienze Fisiche, Complesso Universitario, Universitá di Napoli Federico II, Monte S. Angelo, Via Cinthia, I-80126 Napoli, Italy.
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