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Hu C, Yang S, Li S, Liu X, Liu Y, Chen Z, Chen H, Li S, He N, Cui H, Deng Y. Viral aptamer screening and aptamer-based biosensors for virus detection: A review. Int J Biol Macromol 2024; 276:133935. [PMID: 39029851 DOI: 10.1016/j.ijbiomac.2024.133935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 07/14/2024] [Accepted: 07/15/2024] [Indexed: 07/21/2024]
Abstract
Virus-induced infectious diseases have a detrimental effect on public health and exert significant influence on the global economy. Therefore, the rapid and accurate detection of viruses is crucial for effectively preventing and diagnosing infections. Aptamer-based detection technologies have attracted researchers' attention as promising solutions. Aptamers, small single-stranded DNA or RNA screened via systematic evolution of ligands by exponential enrichment (SELEX), possess a high affinity towards their target molecules. Numerous aptamers targeting viral marker proteins or virions have been developed and widely employed in aptamer-based biosensors (aptasensor) for virus detection. This review introduces SELEX schemes for screening aptamers and discusses distinctive SELEX strategies designed explicitly for viral targets. Furthermore, recent advances in aptamer-based biosensing methods for detecting common viruses using different virus-specific aptamers are summarized. Finally, limitations and prospects associated with developing of aptamer-based biosensors are discussed.
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Affiliation(s)
- Changchun Hu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, Hunan 412007, China; School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Shuting Yang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, Hunan 412007, China
| | - Shuo Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, Hunan 412007, China
| | - Xueying Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, Hunan 412007, China
| | - Yuan Liu
- Institute for Future Sciences, University of South China, Changsha, Hunan 410000, China; Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, Hunan 412007, China
| | - Hui Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, Hunan 412007, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, Hunan 412007, China
| | - Nongyue He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, Hunan 412007, China
| | - Haipo Cui
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, Hunan 412007, China; Institute for Future Sciences, University of South China, Changsha, Hunan 410000, China; Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
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2
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Kouz S, Raouafi A, Ouhibi A, Lorrain N, Essafi M, Mejri M, Raouafi N, Moadhen A, Guendouz M. Detection of SARS-CoV-2 N protein using AgNPs-modified aligned silicon nanowires BioSERS chip. RSC Adv 2024; 14:12071-12080. [PMID: 38628480 PMCID: PMC11019291 DOI: 10.1039/d4ra00267a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/03/2024] [Indexed: 04/19/2024] Open
Abstract
The SARS-CoV-2 (COVID-19) pandemic had a strong impact on societies and economies worldwide and tests for high-performance detection of SARS-CoV-2 biomarkers are still needed for potential future outbreaks of the disease. In this paper, we present the different steps for the design of an aptamer-based surface-enhanced Raman scattering (BioSERS) sensing chip capable of detecting the coronavirus nucleocapsid protein (N protein) in spiked phosphate-buffered solutions and real samples of human blood serum. Optimization of the preparation steps in terms of the aptamer concentration used for the functionalization of the silver nanoparticles, time for affixing the aptamer, incubation time with target protein, and insulation of the silver active surface with cysteamine, led to a sensitive BioSERS chip, which was able to detect the N protein in the range from 1 to 75 ng mL-1 in spiked phosphate-buffered solutions with a detection limit of 1 ng mL-1 within 30 min. Furthermore, the BioSERS chip was used to detect the target protein in scarcely spiked human serum. This study demonstrates the possibility of a clinical application that can improve the detection limit and accuracy of the currently commercialized SARS-CoV-2 immunodiagnostic kit. Additionally, the system is modular and can be applied to detect other proteins by only changing the aptamer.
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Affiliation(s)
- Sadok Kouz
- Faculty of Sciences of Tunis, Laboratory of Nanomaterials Nanotechnology and Energy (L2NE), University of Tunis El Manar 2092 Tunis El Manar Tunisia
- UMR FOTON, CNRS, University of Rennes Enssat, BP 80518, 6 rue Kerampont F22305 Lannion France
| | - Amal Raouafi
- Faculty of Sciences of Tunis, Laboratory of Analytical Chemistry and Electrochemistry (LR99ES15), Sensor and Biosensors Group, University of Tunis El Manar 2092 Tunis El Manar Tunisia
| | - Awatef Ouhibi
- Faculty of Sciences of Tunis, Laboratory of Nanomaterials Nanotechnology and Energy (L2NE), University of Tunis El Manar 2092 Tunis El Manar Tunisia
| | - Nathalie Lorrain
- UMR FOTON, CNRS, University of Rennes Enssat, BP 80518, 6 rue Kerampont F22305 Lannion France
| | - Makram Essafi
- Pasteur Institute of Tunis, University of Tunis El Manar LTCII LR11 IPT02 Tunis Tunisia
| | - Manel Mejri
- Pasteur Institute of Tunis, University of Tunis El Manar LTCII LR11 IPT02 Tunis Tunisia
| | - Noureddine Raouafi
- Faculty of Sciences of Tunis, Laboratory of Analytical Chemistry and Electrochemistry (LR99ES15), Sensor and Biosensors Group, University of Tunis El Manar 2092 Tunis El Manar Tunisia
| | - Adel Moadhen
- Faculty of Sciences of Tunis, Laboratory of Nanomaterials Nanotechnology and Energy (L2NE), University of Tunis El Manar 2092 Tunis El Manar Tunisia
| | - Mohammed Guendouz
- UMR FOTON, CNRS, University of Rennes Enssat, BP 80518, 6 rue Kerampont F22305 Lannion France
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Zhao Y, Kumar A, Yang Y. Unveiling practical considerations for reliable and standardized SERS measurements: lessons from a comprehensive review of oblique angle deposition-fabricated silver nanorod array substrates. Chem Soc Rev 2024; 53:1004-1057. [PMID: 38116610 DOI: 10.1039/d3cs00540b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Recently, there has been an exponential growth in the number of publications focusing on surface-enhanced Raman scattering (SERS), primarily driven by advancements in nanotechnology and the increasing demand for chemical and biological detection. While many of these publications have focused on the development of new substrates and detection-based applications, there is a noticeable lack of attention given to various practical issues related to SERS measurements and detection. This review aims to fill this gap by utilizing silver nanorod (AgNR) SERS substrates fabricated through the oblique angle deposition method as an illustrative example. The review highlights and addresses a range of practical issues associated with SERS measurements and detection. These include the optimization of SERS substrates in terms of morphology and structural design, considerations for measurement configurations such as polarization and the incident angle of the excitation laser, and exploration of enhancement mechanisms encompassing both intrinsic properties induced by the structure and materials, as well as extrinsic factors arising from wetting/dewetting phenomena and analyte size. The manufacturing and storage aspects of SERS substrates, including scalable fabrication techniques, contamination control, cleaning procedures, and appropriate storage methods, are also discussed. Furthermore, the review delves into device design considerations, such as well arrays, flow cells, and fiber probes, and explores various sample preparation methods such as drop-cast and immersion. Measurement issues, including the effect of excitation laser wavelength and power, as well as the influence of buffer, are thoroughly examined. Additionally, the review discusses spectral analysis techniques, encompassing baseline removal, chemometric analysis, and machine learning approaches. The wide range of AgNR-based applications of SERS, across various fields, is also explored. Throughout the comprehensive review, key lessons learned from collective findings are outlined and analyzed, particularly in the context of detailed SERS measurements and standardization. The review also provides insights into future challenges and perspectives in the field of SERS. It is our hope that this comprehensive review will serve as a valuable reference for researchers seeking to embark on in-depth studies and applications involving their own SERS substrates.
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Affiliation(s)
- Yiping Zhao
- Department of Physics and Astronomy, The University of Georgia, Athens, GA 30602, USA.
| | - Amit Kumar
- Department of Physics and Astronomy, The University of Georgia, Athens, GA 30602, USA.
| | - Yanjun Yang
- School of Electrical and Computer Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA.
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4
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Lukose J, Barik AK, George SD, Murukeshan VM, Chidangil S. Raman spectroscopy for viral diagnostics. Biophys Rev 2023; 15:199-221. [PMID: 37113565 PMCID: PMC10088700 DOI: 10.1007/s12551-023-01059-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 03/24/2023] [Indexed: 04/29/2023] Open
Abstract
Raman spectroscopy offers the potential for fingerprinting biological molecules at ultra-low concentration and therefore has potential for the detection of viruses. Here we review various Raman techniques employed for the investigation of viruses. Different Raman techniques are discussed including conventional Raman spectroscopy, surface-enhanced Raman spectroscopy, Raman tweezer, tip-enhanced Raman Spectroscopy, and coherent anti-Stokes Raman scattering. Surface-enhanced Raman scattering can play an essential role in viral detection by multiplexing nanotechnology, microfluidics, and machine learning for ensuring spectral reproducibility and efficient workflow in sample processing and detection. The application of these techniques to diagnose the SARS-CoV-2 virus is also reviewed. Graphical abstract Supplementary Information The online version contains supplementary material available at 10.1007/s12551-023-01059-4.
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Affiliation(s)
- Jijo Lukose
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, 576104 Manipal, India
| | - Ajaya Kumar Barik
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, 576104 Manipal, India
| | - Sajan D. George
- Centre for Applied Nanosciences, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, 576104 Manipal, India
| | - V. M. Murukeshan
- Centre for Optical and Laser Engineering, School of Mechanical and Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798 Singapore, Singapore
| | - Santhosh Chidangil
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, 576104 Manipal, India
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Villamil Giraldo AM, Mannsverk S, Kasson PM. Measuring single-virus fusion kinetics using an assay for nucleic acid exposure. Biophys J 2022; 121:4467-4475. [PMID: 36330566 PMCID: PMC9748363 DOI: 10.1016/j.bpj.2022.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 09/26/2022] [Accepted: 10/31/2022] [Indexed: 11/11/2022] Open
Abstract
The kinetics by which individual enveloped viruses fuse with membranes provide an important window into viral-entry mechanisms. We have developed a real-time assay using fluorescent probes for single-virus genome exposure than can report on stages of viral entry including or subsequent to fusion pore formation and prior to viral genome trafficking. We accomplish this using oxazole yellow nucleic-acid-binding dyes, which can be encapsulated in the lumen of target membranes to permit specific detection of fusion events. Since increased fluorescence of the dye occurs only when it encounters viral genome via a fusion pore and binds, this assay excludes content leakage without fusion. Using this assay, we show that influenza virus fuses with liposomes of different sizes with indistinguishable kinetics by both testing liposomes extruded through pores of different radii and showing that the fusion kinetics of individual liposomes are uncorrelated with the size of the liposome. These results suggest that the starting curvature of such liposomes does not control the rate-limiting steps in influenza entry.
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Affiliation(s)
- Ana M Villamil Giraldo
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Steinar Mannsverk
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Peter M Kasson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden; Departments of Molecular Physiology and Biomedical Engineering, University of Virginia, Charlottesville, Virginia.
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Lou B, Liu Y, Shi M, Chen J, Li K, Tan Y, Chen L, Wu Y, Wang T, Liu X, Jiang T, Peng D, Liu Z. Aptamer-based biosensors for virus protein detection. Trends Analyt Chem 2022; 157:116738. [PMID: 35874498 PMCID: PMC9293409 DOI: 10.1016/j.trac.2022.116738] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/23/2022] [Accepted: 07/13/2022] [Indexed: 02/07/2023]
Abstract
Virus threatens life health seriously. The accurate early diagnosis of the virus is vital for clinical control and treatment of virus infection. Aptamers are small single-stranded oligonucleotides (DNAs or RNAs). In this review, we summarized aptasensors for virus detection in recent years according to the classification of the viral target protein, and illustrated common detection mechanisms in the aptasensors (colorimetry, fluorescence assay, surface plasmon resonance (SPR), surface-enhanced raman spectroscopy (SERS), electrochemical detection, and field-effect transistor (FET)). Furthermore, aptamers against different target proteins of viruses were summarized. The relationships between the different biomarkers of the viruses and the detection methods, and their performances were revealed. In addition, the challenges and future directions of aptasensors were discussed. This review will provide valuable references for constructing on-site aptasensors for detecting viruses, especially the SARS-CoV-2.
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Affiliation(s)
- Beibei Lou
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Yanfei Liu
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, PR China
| | - Meilin Shi
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, PR China
| | - Jun Chen
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Ke Li
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Yifu Tan
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, PR China
| | - Liwei Chen
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, PR China
| | - Yuwei Wu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Ting Wang
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Xiaoqin Liu
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, PR China
| | - Ting Jiang
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, PR China
| | - Dongming Peng
- Department of Medicinal Chemistry, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, PR China
| | - Zhenbao Liu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, PR China.,Molecular Imaging Research Center of Central South University, Changsha, 410008, Hunan, PR China
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7
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Banu K, Mondal B, Rai B, Monica N, Hanumegowda R. Prospects for the application of aptamer based assay platforms in pathogen detection. Biocybern Biomed Eng 2022. [DOI: 10.1016/j.bbe.2022.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Bruno JG. Applications in Which Aptamers Are Needed or Wanted in Diagnostics and Therapeutics. Pharmaceuticals (Basel) 2022; 15:693. [PMID: 35745612 PMCID: PMC9228505 DOI: 10.3390/ph15060693] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 01/27/2023] Open
Abstract
One strategy for bringing aptamers more into the mainstream of biomedical diagnostics and therapeutics is to exploit niche applications where aptamers are truly needed or wanted for their innate differences versus antibodies. This brief review article highlights some of those relatively rare applications in which aptamers are necessary or better suited to the user requirements than antibodies with explanations for why the aptamer is a necessary or superior choice. These situations include when no commercial antibody exists, when antibodies are excessively difficult to develop against a particular target because the target is highly toxic to host animals, when antibodies fail to discriminate closely related targets, when a smaller size is preferable to penetrate a tissue, when humanized monoclonal antibodies are too expensive and when the target is rapidly evolving or mutating. Examples of each are provided to illustrate these points.
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Affiliation(s)
- John G Bruno
- Nanohmics Inc., 6201 E. Oltorf Street, Suite 400, Austin, TX 78640, USA
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Yap SHK, Pan J, Linh DV, Zhang X, Wang X, Teo WZ, Zamburg E, Tham CK, Yew WS, Poh CL, Thean AVY. Engineered Nucleotide Chemicapacitive Microsensor Array Augmented with Physics-Guided Machine Learning for High-Throughput Screening of Cannabidiol. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2107659. [PMID: 35521934 DOI: 10.1002/smll.202107659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 03/03/2022] [Indexed: 06/14/2023]
Abstract
The recent legalization of cannabidiol (CBD) to treat neurological conditions such as epilepsy has sparked rising interest across global pharmaceuticals and synthetic biology industries to engineer microbes for sustainable synthetic production of medicinal CBD. Since the process involves screening large amounts of samples, the main challenge is often associated with the conventional screening platform that is time consuming, and laborious with high operating costs. Here, a portable, high-throughput Aptamer-based BioSenSing System (ABS3 ) is introduced for label-free, low-cost, fully automated, and highly accurate CBD concentrations' classification in a complex biological environment. The ABS3 comprises an array of interdigitated microelectrode sensors, each functionalized with different engineered aptamers. To further empower the functionality of the ABS3 , unique electrochemical features from each sensor are synergized using physics-guided multidimensional analysis. The capabilities of this ABS3 are demonstrated by achieving excellent CBD concentrations' classification with a high prediction accuracy of 99.98% and a fast testing time of 22 µs per testing sample using the optimized random forest (RF) model. It is foreseen that this approach will be the key to the realistic transformation from fundamental research to system miniaturization for diagnostics of disease biomarkers and drug development in the field of chemical/bioanalytics.
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Affiliation(s)
- Stephanie Hui Kit Yap
- Department of Electrical and Computer Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore, 117583, Singapore
| | - Jieming Pan
- Department of Electrical and Computer Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore, 117583, Singapore
| | - Dao Viet Linh
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore, 117583, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
| | - Xiangyu Zhang
- Department of Electrical and Computer Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore, 117583, Singapore
| | - Xinghua Wang
- Department of Electrical and Computer Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore, 117583, Singapore
| | - Wei Zhe Teo
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore
| | - Evgeny Zamburg
- Department of Electrical and Computer Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore, 117583, Singapore
| | - Chen-Khong Tham
- Department of Electrical and Computer Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore, 117583, Singapore
| | - Wen Shan Yew
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore
| | - Chueh Loo Poh
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore, 117583, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
| | - Aaron Voon-Yew Thean
- Department of Electrical and Computer Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore, 117583, Singapore
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Liu Y, He L, Zhao Y, Cao Y, Yu Z, Lu F. Optimization of Surface-Enhanced Raman Spectroscopy Detection Conditions for Interaction between Gonyautoxin and Its Aptamer. Toxins (Basel) 2022; 14:toxins14010049. [PMID: 35051026 PMCID: PMC8779825 DOI: 10.3390/toxins14010049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/24/2021] [Accepted: 12/30/2021] [Indexed: 02/04/2023] Open
Abstract
This study aimed to optimize the detection conditions for surface-enhanced Raman spectroscopy (SERS) of single-stranded DNA (ssDNA) in four different buffers and explore the interaction between gonyautoxin (GTX1/4) and its aptamer, GO18. The influence of the silver colloid solution and MgSO4 concentration (0.01 M) added under four different buffered conditions on DNA SERS detection was studied to determine the optimum detection conditions. We explored the interaction between GTX1/4 and GO18 under the same conditions as those in the systematic evolution of ligands by exponential enrichment technique, using Tris-HCl as the buffer. The characteristic peaks of GO18 and its G-quadruplex were detected in four different buffer solutions. The change in peak intensity at 1656 cm−1 confirmed that the binding site between GTX1/4 and GO18 was in the G-quadruplex plane. The relative intensity of the peak at 1656 cm−1 was selected for the GTX1/4–GO18 complex (I1656/I1099) to plot the ratio of GTX1/4 in the Tris-HCl buffer condition (including 30 μL of silver colloid solution and 2 μL of MgSO4), and a linear relationship was obtained as follows: Y = 0.1867X + 1.2205 (R2 = 0.9239). This study provides a basis for subsequent application of SERS in the detection of ssDNA, as well as the binding of small toxins and aptamers.
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Affiliation(s)
- Yan Liu
- Department of Pharmaceutical Analysis, College of Pharmacy, Naval Medical University, Shanghai 200433, China;
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, Naval Medical University, Shanghai 200433, China
| | - Lijuan He
- Department of Pharmaceutical Analysis, School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China; (L.H.); (Y.Z.)
| | - Yunli Zhao
- Department of Pharmaceutical Analysis, School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China; (L.H.); (Y.Z.)
| | - Yongbing Cao
- Institute of Vascular Disease, Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200082, China
- Correspondence: (Y.C.); (Z.Y.); (F.L.)
| | - Zhiguo Yu
- Department of Pharmaceutical Analysis, School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China; (L.H.); (Y.Z.)
- Correspondence: (Y.C.); (Z.Y.); (F.L.)
| | - Feng Lu
- Department of Pharmaceutical Analysis, College of Pharmacy, Naval Medical University, Shanghai 200433, China;
- Shanghai Key Laboratory for Pharmaceutical Metabolite Research, Naval Medical University, Shanghai 200433, China
- Correspondence: (Y.C.); (Z.Y.); (F.L.)
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Aptamers in Virology-A Consolidated Review of the Most Recent Advancements in Diagnosis and Therapy. Pharmaceutics 2021; 13:pharmaceutics13101646. [PMID: 34683938 PMCID: PMC8540715 DOI: 10.3390/pharmaceutics13101646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/28/2021] [Accepted: 10/01/2021] [Indexed: 01/05/2023] Open
Abstract
The use of short oligonucleotide or peptide molecules as target-specific aptamers has recently garnered substantial attention in the field of the detection and treatment of viral infections. Based on their high affinity and high specificity to desired targets, their use is on the rise to replace antibodies for the detection of viruses and viral antigens. Furthermore, aptamers inhibit intracellular viral transcription and translation, in addition to restricting viral entry into host cells. This has opened up a plethora of new targets for the research and development of novel vaccines against viruses. Here, we discuss the advances made in aptamer technology for viral diagnosis and therapy in the past decade.
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Payne TD, Klawa SJ, Jian T, Kim S, Papanikolas MJ, Freeman R, Schultz ZD. Catching COVID: Engineering Peptide-Modified Surface-Enhanced Raman Spectroscopy Sensors for SARS-CoV-2. ACS Sens 2021; 6:3436-3444. [PMID: 34491043 PMCID: PMC8442610 DOI: 10.1021/acssensors.1c01344] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/24/2021] [Indexed: 12/11/2022]
Abstract
COVID-19 remains an ongoing issue across the globe, highlighting the need for a rapid, selective, and accurate sensor for SARS-CoV-2 and its emerging variants. The chemical specificity and signal amplification of surface-enhanced Raman spectroscopy (SERS) could be advantageous for developing a quantitative assay for SARS-CoV-2 with improved speed and accuracy over current testing methods. Here, we have tackled the challenges associated with SERS detection of viruses. As viruses are large, multicomponent species, they can yield different SERS signals, but also other abundant biomolecules present in the sample can generate undesired signals. To improve selectivity in complex biological environments, we have employed peptides as capture probes for viral proteins and developed an angiotensin-converting enzyme 2 (ACE2) mimetic peptide-based SERS sensor for SARS-CoV-2. The unique vibrational signature of the spike protein bound to the peptide-modified surface is identified and used to construct a multivariate calibration model for quantification. The sensor demonstrates a 300 nM limit of detection and high selectivity in the presence of excess bovine serum albumin. This work provides the basis for designing a SERS-based assay for the detection of SARS-CoV-2 as well as engineering SERS biosensors for other viruses in the future.
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Affiliation(s)
- Taylor D. Payne
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Stephen J. Klawa
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Tengyue Jian
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Sanghoon Kim
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Micah J. Papanikolas
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Ronit Freeman
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Zachary D. Schultz
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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13
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Payne TD, Klawa SJ, Jian T, Kim SH, Papanikolas MJ, Freeman R, Schultz ZD. Catching COVID: Engineering Peptide-Modified Surface-Enhanced Raman Spectroscopy Sensors for SARS-CoV-2. ACS Sens 2021. [PMID: 34491043 DOI: 10.1021/acssensors.1c0134410.1021/acssensors.1c01344.s001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2023]
Abstract
COVID-19 remains an ongoing issue across the globe, highlighting the need for a rapid, selective, and accurate sensor for SARS-CoV-2 and its emerging variants. The chemical specificity and signal amplification of surface-enhanced Raman spectroscopy (SERS) could be advantageous for developing a quantitative assay for SARS-CoV-2 with improved speed and accuracy over current testing methods. Here, we have tackled the challenges associated with SERS detection of viruses. As viruses are large, multicomponent species, they can yield different SERS signals, but also other abundant biomolecules present in the sample can generate undesired signals. To improve selectivity in complex biological environments, we have employed peptides as capture probes for viral proteins and developed an angiotensin-converting enzyme 2 (ACE2) mimetic peptide-based SERS sensor for SARS-CoV-2. The unique vibrational signature of the spike protein bound to the peptide-modified surface is identified and used to construct a multivariate calibration model for quantification. The sensor demonstrates a 300 nM limit of detection and high selectivity in the presence of excess bovine serum albumin. This work provides the basis for designing a SERS-based assay for the detection of SARS-CoV-2 as well as engineering SERS biosensors for other viruses in the future.
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Affiliation(s)
- Taylor D Payne
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Stephen J Klawa
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Tengyue Jian
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Sang Hoon Kim
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Micah J Papanikolas
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Ronit Freeman
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Zachary D Schultz
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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14
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Zavyalova E, Ambartsumyan O, Zhdanov G, Gribanyov D, Gushchin V, Tkachuk A, Rudakova E, Nikiforova M, Kuznetsova N, Popova L, Verdiev B, Alatyrev A, Burtseva E, Ignatieva A, Iliukhina A, Dolzhikova I, Arutyunyan A, Gambaryan A, Kukushkin V. SERS-Based Aptasensor for Rapid Quantitative Detection of SARS-CoV-2. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:1394. [PMID: 34070421 PMCID: PMC8228355 DOI: 10.3390/nano11061394] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/21/2021] [Accepted: 05/22/2021] [Indexed: 12/21/2022]
Abstract
During the COVID-19 pandemic, the development of sensitive and rapid techniques for detection of viruses have become vital. Surface-enhanced Raman scattering (SERS) is an appropriate tool for new techniques due to its high sensitivity. SERS materials modified with short-structured oligonucleotides (DNA aptamers) provide specificity for SERS biosensors. Existing SERS-based aptasensors for rapid virus detection are either inapplicable for quantitative determination or have sophisticated and expensive construction and implementation. In this paper, we provide a SERS-aptasensor based on colloidal solutions which combines rapidity and specificity in quantitative determination of SARS-CoV-2 virus, discriminating it from the other respiratory viruses.
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Affiliation(s)
- Elena Zavyalova
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Oganes Ambartsumyan
- Department of Microbiology, Virology and Immunology, I.M. Sechenov First Moscow State Medical University, 125009 Moscow, Russia;
| | - Gleb Zhdanov
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Dmitry Gribanyov
- Institute of Solid State Physics of Russian Academy of Science, 142432 Chernogolovka, Russia;
| | - Vladimir Gushchin
- National Research Center for Epidemiology and Microbiology Named after the Honorary Academician N. F. Gamaleya, 123098 Moscow, Russia; (V.G.); (A.T.); (M.N.); (N.K.); (L.P.); (B.V.); (A.A.); (E.B.); (A.I.); (A.I.); (I.D.)
| | - Artem Tkachuk
- National Research Center for Epidemiology and Microbiology Named after the Honorary Academician N. F. Gamaleya, 123098 Moscow, Russia; (V.G.); (A.T.); (M.N.); (N.K.); (L.P.); (B.V.); (A.A.); (E.B.); (A.I.); (A.I.); (I.D.)
| | - Elena Rudakova
- Institute of Physiologically Active Compounds of Russian Academy of Science, 142432 Chernogolovka, Russia;
| | - Maria Nikiforova
- National Research Center for Epidemiology and Microbiology Named after the Honorary Academician N. F. Gamaleya, 123098 Moscow, Russia; (V.G.); (A.T.); (M.N.); (N.K.); (L.P.); (B.V.); (A.A.); (E.B.); (A.I.); (A.I.); (I.D.)
| | - Nadezhda Kuznetsova
- National Research Center for Epidemiology and Microbiology Named after the Honorary Academician N. F. Gamaleya, 123098 Moscow, Russia; (V.G.); (A.T.); (M.N.); (N.K.); (L.P.); (B.V.); (A.A.); (E.B.); (A.I.); (A.I.); (I.D.)
| | - Liubov Popova
- National Research Center for Epidemiology and Microbiology Named after the Honorary Academician N. F. Gamaleya, 123098 Moscow, Russia; (V.G.); (A.T.); (M.N.); (N.K.); (L.P.); (B.V.); (A.A.); (E.B.); (A.I.); (A.I.); (I.D.)
| | - Bakhtiyar Verdiev
- National Research Center for Epidemiology and Microbiology Named after the Honorary Academician N. F. Gamaleya, 123098 Moscow, Russia; (V.G.); (A.T.); (M.N.); (N.K.); (L.P.); (B.V.); (A.A.); (E.B.); (A.I.); (A.I.); (I.D.)
| | - Artem Alatyrev
- National Research Center for Epidemiology and Microbiology Named after the Honorary Academician N. F. Gamaleya, 123098 Moscow, Russia; (V.G.); (A.T.); (M.N.); (N.K.); (L.P.); (B.V.); (A.A.); (E.B.); (A.I.); (A.I.); (I.D.)
| | - Elena Burtseva
- National Research Center for Epidemiology and Microbiology Named after the Honorary Academician N. F. Gamaleya, 123098 Moscow, Russia; (V.G.); (A.T.); (M.N.); (N.K.); (L.P.); (B.V.); (A.A.); (E.B.); (A.I.); (A.I.); (I.D.)
| | - Anna Ignatieva
- National Research Center for Epidemiology and Microbiology Named after the Honorary Academician N. F. Gamaleya, 123098 Moscow, Russia; (V.G.); (A.T.); (M.N.); (N.K.); (L.P.); (B.V.); (A.A.); (E.B.); (A.I.); (A.I.); (I.D.)
| | - Anna Iliukhina
- National Research Center for Epidemiology and Microbiology Named after the Honorary Academician N. F. Gamaleya, 123098 Moscow, Russia; (V.G.); (A.T.); (M.N.); (N.K.); (L.P.); (B.V.); (A.A.); (E.B.); (A.I.); (A.I.); (I.D.)
| | - Inna Dolzhikova
- National Research Center for Epidemiology and Microbiology Named after the Honorary Academician N. F. Gamaleya, 123098 Moscow, Russia; (V.G.); (A.T.); (M.N.); (N.K.); (L.P.); (B.V.); (A.A.); (E.B.); (A.I.); (A.I.); (I.D.)
| | - Alexander Arutyunyan
- Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Alexandra Gambaryan
- Chumakov Federal Scientific Center for Research and Development of Immune and Biological Products RAS, 108819 Moscow, Russia;
| | - Vladimir Kukushkin
- Institute of Solid State Physics of Russian Academy of Science, 142432 Chernogolovka, Russia;
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15
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Shi Y, Li Z, Liu PY, Nguyen BTT, Wu W, Zhao Q, Chin LK, Wei M, Yap PH, Zhou X, Zhao H, Yu D, Tsai DP, Liu AQ. On-Chip Optical Detection of Viruses: A Review. ADVANCED PHOTONICS RESEARCH 2021; 2:2000150. [PMID: 33786535 PMCID: PMC7994989 DOI: 10.1002/adpr.202000150] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/31/2020] [Indexed: 05/17/2023]
Abstract
The current outbreak of the coronavirus disease-19 (COVID-19) pandemic worldwide has caused millions of fatalities and imposed a severe impact on our daily lives. Thus, the global healthcare system urgently calls for rapid, affordable, and reliable detection toolkits. Although the gold-standard nucleic acid amplification tests have been widely accepted and utilized, they are time-consuming and labor-intensive, which exceedingly hinder the mass detection in low-income populations, especially in developing countries. Recently, due to the blooming development of photonics, various optical chips have been developed to detect single viruses with the advantages of fast, label-free, affordable, and point of care deployment. Herein, optical approaches especially in three perspectives, e.g., flow-free optical methods, optofluidics, and surface-modification-assisted approaches, are summarized. The future development of on-chip optical-detection methods in the wave of emerging new ideas in nanophotonics is also briefly discussed.
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Affiliation(s)
- Yuzhi Shi
- School of Electrical and Electronic EngineeringNanyang Technological UniversitySingapore639798Singapore
| | - Zhenyu Li
- School of Electrical and Electronic EngineeringNanyang Technological UniversitySingapore639798Singapore
- National Key Laboratory of Science and Technology on Micro/Nano FabricationInstitute of MicroelectronicsPeking UniversityBeijing100871China
| | - Patricia Yang Liu
- School of Electrical and Electronic EngineeringNanyang Technological UniversitySingapore639798Singapore
| | - Binh Thi Thanh Nguyen
- School of Electrical and Electronic EngineeringNanyang Technological UniversitySingapore639798Singapore
| | - Wenshuai Wu
- School of Electrical and Electronic EngineeringNanyang Technological UniversitySingapore639798Singapore
| | - Qianbin Zhao
- School of Electrical and Electronic EngineeringNanyang Technological UniversitySingapore639798Singapore
| | - Lip Ket Chin
- School of Electrical and Electronic EngineeringNanyang Technological UniversitySingapore639798Singapore
- Center for Systems BiologyMassachusetts General HospitalBostonMA02141USA
| | - Minggui Wei
- School of Electrical and Electronic EngineeringNanyang Technological UniversitySingapore639798Singapore
| | - Peng Huat Yap
- Lee Kong Chian School of MedicineNanyang Technological UniversitySingapore308232Singapore
| | - Xiaohong Zhou
- State Key Joint Laboratory of ESPCSchool of EnvironmentTsinghua UniversityBeijing100084China
| | - Hongwei Zhao
- State Key Laboratory of Marine Resource Utilization of South China SeaHainan UniversityHaikou570228China
| | - Dan Yu
- Beijing Pediatric Research InstituteBeijing Children's HospitalCapital Medical UniversityNational Center for Children's HealthBeijing100045China
| | - Din Ping Tsai
- Department of Electronic and Information EngineeringThe Hong Kong Polytechnic UniversityHung HomKowloonHong KongChina
| | - Ai Qun Liu
- School of Electrical and Electronic EngineeringNanyang Technological UniversitySingapore639798Singapore
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16
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Selection and applications of functional nucleic acids for infectious disease detection and prevention. Anal Bioanal Chem 2021; 413:4563-4579. [PMID: 33506341 PMCID: PMC7840224 DOI: 10.1007/s00216-020-03124-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 11/30/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023]
Abstract
Infectious diseases caused by pathogenic microorganisms such as viruses and bacteria pose a great threat to human health. Although a significant progress has been obtained in the diagnosis and prevention of infectious diseases, it still remains challenging to develop rapid and cost-effective detection approaches and overcome the side effects of therapeutic agents and pathogen resistance. Functional nucleic acids (FNAs), especially the most widely used aptamers and DNAzymes, hold the advantages of high stability and flexible design, which make them ideal molecular recognition tools for bacteria and viruses, as well as potential therapeutic drugs for infectious diseases. This review summarizes important advances in the selection and detection of bacterial- and virus-associated FNAs, along with their potential prevention ability of infectious disease in recent years. Finally, the challenges and future development directions are concluded.
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17
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Soler M, Estevez MC, Cardenosa-Rubio M, Astua A, Lechuga LM. How Nanophotonic Label-Free Biosensors Can Contribute to Rapid and Massive Diagnostics of Respiratory Virus Infections: COVID-19 Case. ACS Sens 2020; 5:2663-2678. [PMID: 32786383 PMCID: PMC7447078 DOI: 10.1021/acssensors.0c01180] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/07/2020] [Indexed: 12/23/2022]
Abstract
The global sanitary crisis caused by the emergence of the respiratory virus SARS-CoV-2 and the COVID-19 outbreak has revealed the urgent need for rapid, accurate, and affordable diagnostic tests to broadly and massively monitor the population in order to properly manage and control the spread of the pandemic. Current diagnostic techniques essentially rely on polymerase chain reaction (PCR) tests, which provide the required sensitivity and specificity. However, its relatively long time-to-result, including sample transport to a specialized laboratory, delays massive detection. Rapid lateral flow tests (both antigen and serological tests) are a remarkable alternative for rapid point-of-care diagnostics, but they exhibit critical limitations as they do not always achieve the required sensitivity for reliable diagnostics and surveillance. Next-generation diagnostic tools capable of overcoming all the above limitations are in demand, and optical biosensors are an excellent option to surpass such critical issues. Label-free nanophotonic biosensors offer high sensitivity and operational robustness with an enormous potential for integration in compact autonomous devices to be delivered out-of-the-lab at the point-of-care (POC). Taking the current COVID-19 pandemic as a critical case scenario, we provide an overview of the diagnostic techniques for respiratory viruses and analyze how nanophotonic biosensors can contribute to improving such diagnostics. We review the ongoing published work using this biosensor technology for intact virus detection, nucleic acid detection or serological tests, and the key factors for bringing nanophotonic POC biosensors to accurate and effective COVID-19 diagnosis on the short term.
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Affiliation(s)
| | | | - Maria Cardenosa-Rubio
- Nanobiosensors and Bioanalytical Applications (NanoB2A),
Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, BIST and
CIBER-BBN, 08193 Bellaterra, Barcelona, Spain
| | - Alejandro Astua
- Nanobiosensors and Bioanalytical Applications (NanoB2A),
Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, BIST and
CIBER-BBN, 08193 Bellaterra, Barcelona, Spain
| | - Laura M. Lechuga
- Nanobiosensors and Bioanalytical Applications (NanoB2A),
Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, BIST and
CIBER-BBN, 08193 Bellaterra, Barcelona, Spain
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18
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Ekrami E, Pouresmaieli M, Barati F, Asghari S, Ziarani FR, Shariati P, Mamoudifard M. Potential Diagnostic Systems for Coronavirus Detection: a Critical Review. Biol Proced Online 2020; 22:21. [PMID: 32884452 PMCID: PMC7462115 DOI: 10.1186/s12575-020-00134-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/23/2020] [Indexed: 02/06/2023] Open
Abstract
Abstract Currently there are no effective anti-viral drugs for SARS-CoV-2, so the primary line of defense is to detect infected cases as soon as possible. The high rate of contagion for this virus and the highly nonspecific symptoms of the disease (Coronovirus disease 2019, (Covid-19)) that it causes, such as respiratory symptoms, cough, dyspnea, fever, and viral pneumonia, require the urgent establishment of precise and fast diagnostic tests to verify suspected cases, screen patients, and conduct virus surveillance. Nowadays, several virus detection methods are available for viral diseases, which act on specific properties of each virus or virus family, therefore, further investigations and trials are needed to find a highly efficient and accurate detection method to detect and prevent the outcomes of the disease. Hence, there is an urgent need for more and precise studies in this field. In this review, we discussed the properties of a new generation of coronaviruses (SARS-CoV-2) following routine virus detection methods and proposed new strategies and the use of potential samples for SARS-CoV-2 detection. Graphical Abstract ![]()
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Affiliation(s)
- Elena Ekrami
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Mahdi Pouresmaieli
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Fatemeh Barati
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Sahar Asghari
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Farzad Ramezani Ziarani
- Department of Microbiology, School of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Parvin Shariati
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Matin Mamoudifard
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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19
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A simple and sensitive aptasensor based on SERS for trace analysis of kanamycin in milk. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2020. [DOI: 10.1007/s11694-020-00553-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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20
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Ambartsumyan O, Gribanyov D, Kukushkin V, Kopylov A, Zavyalova E. SERS-Based Biosensors for Virus Determination with Oligonucleotides as Recognition Elements. Int J Mol Sci 2020; 21:ijms21093373. [PMID: 32397680 PMCID: PMC7247000 DOI: 10.3390/ijms21093373] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 01/22/2023] Open
Abstract
Viral infections are among the main causes of morbidity and mortality of humans; sensitive and specific diagnostic methods for the rapid identification of viral pathogens are required. Surface-enhanced Raman spectroscopy (SERS) is one of the most promising techniques for routine analysis due to its excellent sensitivity, simple and low-cost instrumentation and minimal required sample preparation. The outstanding sensitivity of SERS is achieved due to tiny nanostructures which must be assembled before or during the analysis. As for specificity, it may be provided using recognition elements. Antibodies, complimentary nucleic acids and aptamers are the most usable recognition elements for virus identification. Here, SERS-based biosensors for virus identification with oligonucleotides as recognition elements are reviewed, and the potential of these biosensors is discussed.
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Affiliation(s)
| | - Dmitry Gribanyov
- Institute of Solid State Physics RAS, Chernogolovka 142432, Russia;
| | - Vladimir Kukushkin
- Institute of Solid State Physics RAS, Chernogolovka 142432, Russia;
- Correspondence: (V.K.); (E.Z.); Tel.: +7-495-939-3149 (E.Z.)
| | - Alexey Kopylov
- Chemistry Department, Lomonosov Moscow State University, Moscow 119991, Russia;
| | - Elena Zavyalova
- Chemistry Department, Lomonosov Moscow State University, Moscow 119991, Russia;
- Correspondence: (V.K.); (E.Z.); Tel.: +7-495-939-3149 (E.Z.)
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21
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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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22
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Zou X, Wu J, Gu J, Shen L, Mao L. Application of Aptamers in Virus Detection and Antiviral Therapy. Front Microbiol 2019; 10:1462. [PMID: 31333603 PMCID: PMC6618307 DOI: 10.3389/fmicb.2019.01462] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 06/11/2019] [Indexed: 12/19/2022] Open
Abstract
Viral infections can cause serious diseases for humans and animals. Accurate and early detection of viruses is often crucial for clinical diagnosis and therapy. Aptamers are mostly single-stranded nucleotide sequences that are artificially synthesized by an in vitro technology known as the Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Similar to antibodies, aptamers bind specifically to their targets. However, compared with antibody, aptamers are easy to synthesize and modify and can bind to a broad range of targets. Thus, aptamers are promising for detecting viruses and treating viral infections. In this review, we briefly introduce aptamer-based biosensors (aptasensors) and describe their applications in rapid detection of viruses and as antiviral agents in treating infections. We summarize available data about the use of aptamers to detect and inhibit viruses. Furthermore, for the first time, we list aptamers specific to different viruses that have been screened out but have not yet been used for detecting viruses or treating viral infections. Finally, we analyze barriers and developing perspectives in the application of aptamer-based virus detection and therapeutics.
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Affiliation(s)
- Xinran Zou
- Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China.,Jiangsu Key Laboratory of Laboratory Medicine, Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Jing Wu
- Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China.,Jiangsu Key Laboratory of Laboratory Medicine, Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Jiaqi Gu
- Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China.,Jiangsu Key Laboratory of Laboratory Medicine, Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Li Shen
- Zhenjiang Center for Disease Control and Prevention, Jiangsu, China
| | - Lingxiang Mao
- Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China
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23
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Kukushkin VI, Ivanov NM, Novoseltseva AA, Gambaryan AS, Yaminsky IV, Kopylov AM, Zavyalova EG. Highly sensitive detection of influenza virus with SERS aptasensor. PLoS One 2019; 14:e0216247. [PMID: 31022287 PMCID: PMC6483365 DOI: 10.1371/journal.pone.0216247] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/16/2019] [Indexed: 12/20/2022] Open
Abstract
Highly sensitive and rapid technology of surface enhanced Raman scattering (SERS) was applied to create aptasensors for influenza virus detection. SERS achieves 106−109 times signal amplification, yielding excellent sensitivity, whereas aptamers to hemagglutinin provide a specific recognition of the influenza virus. Aptamer RHA0385 was demonstrated to have essentially broad strain-specificity toward both recombinant hemagglutinins and the whole viruses. To achieve high sensitivity, a sandwich of primary aptamers, influenza virus and secondary aptamers was assembled. Primary aptamers were attached to metal particles of a SERS substrate, and influenza viruses were captured and bound with secondary aptamers labelled with Raman-active molecules. The signal was affected by the concentration of both primary and secondary aptamers. The limit of detection was as low as 1 · 10−4 hemagglutination units per probe as tested for the H3N2 virus (A/England/42/72). Aptamer-based sensors provided recognition of various influenza viral strains, including H1, H3, and H5 hemagglutinin subtypes. Therefore, the aptasensors could be applied for fast and low-cost strain-independent determination of influenza viruses.
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Affiliation(s)
- Vladimir I. Kukushkin
- Institute of Solid State Physics RAS, Chernogolovka, Moscow district, Russian Federation
| | - Nikita M. Ivanov
- Chemistry Department, Lomonosov Moscow State University, Moscow, Russian Federation
| | | | - Alexandra S. Gambaryan
- Chumakov Federal Scientific Center for Research and Development of Immune and Biological Products RAS, Moscow, Russian Federation
| | - Igor V. Yaminsky
- Chemistry Department, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Alexey M. Kopylov
- Chemistry Department, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Elena G. Zavyalova
- Chemistry Department, Lomonosov Moscow State University, Moscow, Russian Federation
- * E-mail:
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24
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Cai S, Yan J, Xiong H, Liu Y, Peng D, Liu Z. Investigations on the interface of nucleic acid aptamers and binding targets. Analyst 2019; 143:5317-5338. [PMID: 30357118 DOI: 10.1039/c8an01467a] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nucleic acid aptamers are single-stranded DNA or RNA of 20-100 nucleotides in length that have attracted substantial scientific interest due to their ability to specifically bind to target molecules via the formation of three-dimensional structures. Compared to traditional protein antibodies, aptamers have several advantages, such as their small size, high binding affinity, specificity, flexible structure, being chemical synthesizable and modifiable, good biocompatibility, high stability and low immunogenicity, which all contribute to their widely applications in the biomedical field. To date, much progress has been made in the study and applications of aptamers, however, detailed information on how aptamers bind to their targets is still scarce. Over the past few decades, many methods have been introduced to investigate the aptamer-target binding process, such as measuring the main kinetic or thermodynamic parameters, detecting the structural changes of the binding complexes, etc. Apart from traditional physicochemical methods, various types of molecular docking programs have been applied to simulate the aptamer-target interactions, while these simulations also have limitations. To facilitate the further research on the interactions, herein, we provide a brief review to illustrate the recent advances in the study of aptamer-target interactions. We summarize the binding targets of aptamers, such as small molecules, macromolecules, and even cells. Their binding constants (KD) are also summarized. Methods to probe the aptamer-target binding process, such as surface plasmon resonance (SPR), circular dichroism spectroscopy (CD), isothermal titration calorimetry (ITC), footprinting assay, truncation and mutation assay, nuclear magnetic resonance spectroscopy (NMR), X-ray crystallography and molecular docking simulation are indicated. The binding forces mediating the aptamer-target interactions, such as hydrogen bonding, electrostatic interaction, the hydrophobic effect, π-π stacking and van der Waals forces are summarized. The challenges and future perspectives are also discussed.
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Affiliation(s)
- Shundong Cai
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, PR China.
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25
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Leblebici P, Leirs K, Spasic D, Lammertyn J. Encoded particle microfluidic platform for rapid multiplexed screening and characterization of aptamers against influenza A nucleoprotein. Anal Chim Acta 2018; 1053:70-80. [PMID: 30712571 DOI: 10.1016/j.aca.2018.11.055] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/20/2018] [Accepted: 11/26/2018] [Indexed: 02/03/2023]
Abstract
Aptamers represent interesting bioreceptor alternatives to antibodies when developing a bioassay and are selected by the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) process. After selection, an extensive characterization process is essential to verify the binding affinity and specificity of aptamer candidates, which is the most time-consuming and costly step. In this study, we assessed a new microfluidic platform, namely Evalution™, as a rapid and high throughput aptamer characterization platform. To do this, we first selected aptamers against influenza A nucleoprotein (infA NP) by performing magnetic bead-based SELEX. The selected aptamer candidates were subsequently screened using Evalution™ for their binding kinetics and specificity towards infA NP. All aptamers showed dissociation constants (KD) in the low nanomolar range (from 13 to 41 nM), and differential binding behavior towards control proteins, such as BSA and influenza B nucleoprotein (infB NP). Among 5 selected candidates, one aptamer (NP5) exhibited a significant discrimination between infA NP and infB NP and was further used to benchmark the kinetic analysis of Evalution™ (KD = 41 nM) with an SPR platform (KD = 17 nM). These results suggested that NP5 has the potential to be used for developing sensitive and infA NP specific aptamer-based assay. Moreover, the presented platform proved to be an efficient aptamer characterization tool for performing typical aptamer characterization experiments like binding kinetics (due to the real-time monitoring feature) and specificity assessment in a high-throughput manner due to the multiplexing capacity.
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Affiliation(s)
- Pelin Leblebici
- Department of Biosystems, Biosensors Group, KU Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
| | - Karen Leirs
- Department of Biosystems, Biosensors Group, KU Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
| | - Dragana Spasic
- Department of Biosystems, Biosensors Group, KU Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems, Biosensors Group, KU Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium.
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26
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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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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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28
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Kim S, Jeong SN, Bae S, Chung H, Yoo SY. Sensitive Surface Enhanced Raman Scattering-Based Detection of a BIGH3 Point Mutation Associated with Avellino Corneal Dystrophy. Anal Chem 2016; 88:11288-11292. [PMID: 27934116 DOI: 10.1021/acs.analchem.6b03320] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Surface enhanced Raman scattering (SERS) is highly useful for sensitive analytical sensing; however, its practical availability for detecting a point mutation associated with disease in clinical sample was rarely proved. Herein, we present a toehold-mediated, DNA displacement-based, SERS sensor for detecting point mutations in the BIGH3 gene associated with the most common corneal dystrophies (CDs) in a clinical setting. To diagnose Avellino corneal dystrophy (ACD), selectivity was ensured by exploring optimal DNA displacement conditions such as length of toehold and hybridization temperature. A SERS-efficient Ag@Au bimetallic nanodendrite was employed to ensure sensitivity. Optimization for a clinical setting showed that discrimination was maximized when toehold length was 6-mer (T6), and hybridization temperature was 36 °C. On the basis of tests that used clinical homozygous and heterozygous CD samples, a single-base mismatched DNA sequence was identifiable within 30 min with a limit of detection (LOD) of 400 fM. From the results, we conclude that our toehold-mediated, DNA displacement-based, SERS sensor allows a rapid and sensitive detection of a BIGH3 gene point mutation associated with Avellino corneal dystrophy, indicating the practical ability of the method to diagnose genetic diseases caused by point mutations.
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Affiliation(s)
- Saetbyeol Kim
- Department of Chemistry and Research Institute for Convergence of Basic Sciences, Hanyang University , Seoul, 04763, Republic of Korea
| | - Su-Nam Jeong
- BIO-IT Foundry Technology Institute, Pusan National University , Busan, 46287, Republic of Korea.,Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital , Yangsan, Gyeongsangnam-do 50612, Republic of Korea
| | - Sangsu Bae
- Department of Chemistry and Research Institute for Convergence of Basic Sciences, Hanyang University , Seoul, 04763, Republic of Korea
| | - Hoeil Chung
- Department of Chemistry and Research Institute for Convergence of Basic Sciences, Hanyang University , Seoul, 04763, Republic of Korea
| | - So Young Yoo
- BIO-IT Foundry Technology Institute, Pusan National University , Busan, 46287, Republic of Korea.,Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital , Yangsan, Gyeongsangnam-do 50612, Republic of Korea
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29
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Liao W, Lu X. Determination of chemical hazards in foods using surface-enhanced Raman spectroscopy coupled with advanced separation techniques. Trends Food Sci Technol 2016. [DOI: 10.1016/j.tifs.2016.05.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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30
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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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31
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Choi J, Martin SJH, Tripp RA, Tompkins SM, Dluhy RA. Detection of neuraminidase stalk motifs associated with enhanced N1 subtype influenza A virulence via Raman spectroscopy. Analyst 2015; 140:7748-60. [PMID: 26460183 PMCID: PMC4687448 DOI: 10.1039/c5an00977d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Oligonucleotides corresponding to neuraminidase (NA) stalk motifs that have been associated with enhanced influenza virulence have been identified using surface-enhanced Raman spectroscopy (SERS). 5'-Thiolated ssDNA oligonucleotides were immobilized onto a hexadecyltrimethylammonium bromide (CTAB) coated Au nanoparticles (AuNP). Three synthetic RNA sequences corresponding to specific amino acid deletions in the influenza NA stalk region were attached to the CTAB-modified AuNPs. Two of these sequences were specific to sequences with amino acid deletions associated with increased virulence, and one was a low virulence sequence with no amino acid deletions. Hybridization of synthetic matched and mismatched DNA-RNA complexes were detected based on the intrinsic SERS spectra. In addition, this platform was used to analyze RNA sequences isolated from laboratory grown influenza viruses having the NA stalk motif associated with enhanced virulence, including A/WSN/33/H1N1, A/Anhui/1/2005/H5N, and A/Vietnam/1203/2004/H5N1 strains. Multivariate feature selection methods were employed to determine the specific wavenumbers in the Raman spectra that contributed the most information for class discrimination. A one-way analysis of variance (ANOVA) test identified 884 and 1196 wavenumbers as being highly significant in the high and low virulence spectra, respectively (p < 0.01). A post-hoc Tukey Honestly Significance Difference (HSD) test identified the wavenumbers that played a major role in differentiating the DNA-RNA hybrid classes. An estimate of the spectral variability, based on the Wilcoxon rank sum test, found the major source of variation to be predominately between the different classes, and not within the classes, thus confirming that the spectra reflected real class differences and not sampling artifacts. The multivariate classification methods partial least squares discriminant analysis (PLS-DA) and support vector machine discriminant analysis (SVM-DA) were able to distinguish between different NA stalk-motifs linked to NA-enhanced influenza virus virulence (NA-EIV) with >95% sensitivity and specificity in both synthetic RNA sequences as well as the isolated viral RNA. This study demonstrates the feasibility of SERS for direct identification of influenza NA stalk mutations associated with virulence without sample amplification or labeling.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Cetrimonium
- Cetrimonium Compounds/chemistry
- DNA Probes/chemistry
- DNA Probes/genetics
- Gold/chemistry
- Humans
- Immobilized Nucleic Acids/chemistry
- Immobilized Nucleic Acids/genetics
- Influenza A Virus, H1N1 Subtype/enzymology
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/pathogenicity
- Influenza A Virus, H5N1 Subtype/enzymology
- Influenza A Virus, H5N1 Subtype/genetics
- Influenza A Virus, H5N1 Subtype/pathogenicity
- Influenza, Human/virology
- Metal Nanoparticles/chemistry
- Metal Nanoparticles/ultrastructure
- Mutation
- Neuraminidase/chemistry
- Neuraminidase/genetics
- RNA, Viral/analysis
- RNA, Viral/genetics
- Spectrum Analysis, Raman/methods
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Affiliation(s)
- JooYoung Choi
- Department of Chemistry, University of Georgia, Athens, GA 30602, USA.
| | - Sharon J H Martin
- Department of Chemistry, University of Georgia, Athens, GA 30602, USA.
| | - Ralph A Tripp
- Department of Infectious Disease, University of Georgia, Athens, GA 30602, USA
| | - S Mark Tompkins
- Department of Infectious Disease, University of Georgia, Athens, GA 30602, USA
| | - Richard A Dluhy
- Department of Chemistry, University of Georgia, Athens, GA 30602, USA.
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Lim JY, Nam JS, Yang SE, Shin H, Jang YH, Bae GU, Kang T, Lim KI, Choi Y. Identification of Newly Emerging Influenza Viruses by Surface-Enhanced Raman Spectroscopy. Anal Chem 2015; 87:11652-9. [DOI: 10.1021/acs.analchem.5b02661] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Jae-young Lim
- Department
of Bio-convergence Engineering, Korea University, Seoul, 136-713, Korea
| | - Jung-soo Nam
- Department of Medical & Pharmaceutical Sciences, Sookmyung Women’s University, Seoul, 140-742, Korea
| | - Se-eun Yang
- Department
of Bio-convergence Engineering, Korea University, Seoul, 136-713, Korea
| | - Hyunku Shin
- Department
of Bio-convergence Engineering, Korea University, Seoul, 136-713, Korea
| | - Yoon-ha Jang
- Department of Medical & Pharmaceutical Sciences, Sookmyung Women’s University, Seoul, 140-742, Korea
| | - Gyu-Un Bae
- Research
Center for Cell Fate Control, College of Pharmacy, Sookmyung Women’s University, Seoul, 140-742, Korea
| | - Taewook Kang
- Department of Chemical & Biomolecular Engineering, Sogang University, Seoul, 121-742, Korea
| | - Kwang-il Lim
- Department of Medical & Pharmaceutical Sciences, Sookmyung Women’s University, Seoul, 140-742, Korea
| | - Yeonho Choi
- Department
of Bio-convergence Engineering, Korea University, Seoul, 136-713, Korea
- School
of Biomedical Engineering, Korea University, Seoul, 136-713, Korea
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33
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van den Kieboom CH, van der Beek SL, Mészáros T, Gyurcsányi RE, Ferwerda G, de Jonge MI. Aptasensors for viral diagnostics. Trends Analyt Chem 2015; 74:58-67. [PMID: 32287539 PMCID: PMC7112930 DOI: 10.1016/j.trac.2015.05.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We discuss progress in aptamer-based detection of viruses. We consider the use of aptasensors for point-of-care diagnostics of viruses. Aptamers have distinct advantages over antibodies for virus recognition. There is strong demand for multiplexed diagnostic measurement of pathogens.
Novel viral diagnostic tools need to be affordable, fast, accurate and easy to use with sensitivity and specificity equivalent or superior to current standards. At present, viral diagnostics are based on direct detection of viral components or indirect detection by measuring antibodies generated in response to viral infection. While sensitivity of detection and quantification are still important challenges, we expect major advances from new assay formats and synthetic binding molecules, such as aptamers. Compared to traditional antibody-based detection, aptamers could provide faster adaptation to continuously evolving virus strains and higher discriminating capacity between specific virus serotypes. Aptamers are very stable and easily modifiable, so are ideal molecules for detection and chemical sensing applications. Here, we review the use of aptasensors for detection of viral pathogens and consider the feasibility of aptasensors to become standard devices for point-of-care diagnostics of viruses.
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Affiliation(s)
- Corné H van den Kieboom
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Center, Nijmegen, Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Tamás Mészáros
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary.,MTA-BME Research Group for Technical Analytical Chemistry, Budapest University of Technology and Economics, Budapest, Hungary
| | - Róbert E Gyurcsányi
- MTA-BME Lendület Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Budapest, Hungary
| | - Gerben Ferwerda
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Marien I de Jonge
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Center, Nijmegen, Netherlands
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Davydova A, Vorobjeva M, Pyshnyi D, Altman S, Vlassov V, Venyaminova A. Aptamers against pathogenic microorganisms. Crit Rev Microbiol 2015; 42:847-65. [PMID: 26258445 PMCID: PMC5022137 DOI: 10.3109/1040841x.2015.1070115] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
An important current issue of modern molecular medicine and biotechnology is the search for new approaches to early diagnostic assays and adequate therapy of infectious diseases. One of the promising solutions to this problem might be a development of nucleic acid aptamers capable of interacting specifically with bacteria, protozoa, and viruses. Such aptamers can be used for the specific recognition of infectious agents as well as for blocking of their functions. The present review summarizes various modern SELEX techniques used in this field, and of several currently identified aptamers against viral particles and unicellular organisms, and their applications. The prospects of applying nucleic acid aptamers for the development of novel detection systems and antibacterial and antiviral drugs are discussed.
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Affiliation(s)
- Anna Davydova
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
| | - Maria Vorobjeva
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
| | - Dmitrii Pyshnyi
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
| | - Sidney Altman
- b Department of Molecular, Cellular and Developmental Biology , Yale University , New Haven , CT , USA
| | - Valentin Vlassov
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
| | - Alya Venyaminova
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
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Sivanesan A, Izake EL, Agoston R, Ayoko GA, Sillence M. Reproducible and label-free biosensor for the selective extraction and rapid detection of proteins in biological fluids. J Nanobiotechnology 2015; 13:43. [PMID: 26104688 PMCID: PMC4477471 DOI: 10.1186/s12951-015-0102-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 06/05/2015] [Indexed: 11/29/2022] Open
Abstract
Erythropoietin (EPO), a glycoprotein hormone of ∼34 kDa, is an important hematopoietic growth factor, mainly produced in the kidney and controls the number of red blood cells circulating in the blood stream. Sensitive and rapid recombinant human EPO (rHuEPO) detection tools that improve on the current laborious EPO detection techniques are in high demand for both clinical and sports industry. A sensitive aptamer-functionalized biosensor (aptasensor) has been developed by controlled growth of gold nanostructures (AuNS) over a gold substrate (pAu/AuNS). The aptasensor selectively binds to rHuEPO and, therefore, was used to extract and detect the drug from horse plasma by surface enhanced Raman spectroscopy (SERS). Due to the nanogap separation between the nanostructures, the high population and distribution of hot spots on the pAu/AuNS substrate surface, strong signal enhancement was acquired. By using wide area illumination (WAI) setting for the Raman detection, a low RSD of 4.92% over 150 SERS measurements was achieved. The significant reproducibility of the new biosensor addresses the serious problem of SERS signal inconsistency that hampers the use of the technique in the field. The WAI setting is compatible with handheld Raman devices. Therefore, the new aptasensor can be used for the selective extraction of rHuEPO from biological fluids and subsequently screened with handheld Raman spectrometer for SERS based in-field protein detection.
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Affiliation(s)
- Arumugam Sivanesan
- Nanotechnology and Molecular Sciences Discipline, Faculty of Science and Engineering, Queensland University of Technology, 2 George St., Brisbane, QLD, 4001, Australia.
| | - Emad L Izake
- Nanotechnology and Molecular Sciences Discipline, Faculty of Science and Engineering, Queensland University of Technology, 2 George St., Brisbane, QLD, 4001, Australia.
| | - Roland Agoston
- Nanotechnology and Molecular Sciences Discipline, Faculty of Science and Engineering, Queensland University of Technology, 2 George St., Brisbane, QLD, 4001, Australia.
| | - Godwin A Ayoko
- Nanotechnology and Molecular Sciences Discipline, Faculty of Science and Engineering, Queensland University of Technology, 2 George St., Brisbane, QLD, 4001, Australia.
| | - Martin Sillence
- Discipline of Biosciences, Faculty of Science and Engineering, Queensland University of Technology, 2 George St., Brisbane, QLD, 4001, Australia.
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Guerrini L, Arenal R, Mannini B, Chiti F, Pini R, Matteini P, Alvarez-Puebla RA. SERS Detection of Amyloid Oligomers on Metallorganic-Decorated Plasmonic Beads. ACS APPLIED MATERIALS & INTERFACES 2015; 7:9420-9428. [PMID: 25897657 DOI: 10.1021/acsami.5b01056] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Protein misfolded proteins are among the most toxic endogenous species of macromolecules. These chemical entities are responsible for neurodegenerative disorders such as Alzheimer's, Parkinson's, Creutzfeldt-Jakob's and different non-neurophatic amyloidosis. Notably, these oligomers show a combination of marked heterogeneity and low abundance in body fluids, which have prevented a reliable detection by immunological methods so far. Herein we exploit the selectivity of proteins to react with metallic ions and the sensitivity of surface-enhanced Raman spectroscopy (SERS) toward small electronic changes in coordination compounds to design and engineer a reliable optical sensor for protein misfolded oligomers. Our strategy relies on the functionalization of Au nanoparticle-decorated polystyrene beads with an effective metallorganic Raman chemoreceptor, composed by Al(3+) ions coordinated to 4-mercaptobenzoic acid (MBA) with high Raman cross-section, that selectively binds aberrant protein oligomers. The mechanical deformations of the MBA phenyl ring upon complexation with the oligomeric species are registered in its SERS spectrum and can be quantitatively correlated with the concentration of the target biomolecule. The SERS platform used here appears promising for future implementation of diagnostic tools of aberrant species associated with protein deposition diseases, including those with a strong social and economic impact, such as Alzheimer's and Parkinson's diseases.
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Affiliation(s)
- Luca Guerrini
- †Universitat Rovira i Virgili and Centro de Tecnologia Quimica de Cataluña, C/de Marcel·lí Domingo s/n, N5, 43007 Tarragona, Spain
- ‡Medcom Advance SA, Viladecans Busines Park, Edificio Brasil, C/Bertran i Musitu, 83-85, 08840 Viladecans, Barcelona, Spain
| | - Raul Arenal
- §Laboratorio de Microscopias Avanzadas (LMA), Instituto de Nanociencia de Aragon (INA), Universidad de Zaragoza, 50018 Zaragoza, Spain
- ∥Fundación ARAID, 50018 Zaragoza, Spain
| | - Benedetta Mannini
- ⊥Department of Biomedical Experimental and Clinical Sciences, University of Florence, 50134 Florence, Italy
| | - Fabrizio Chiti
- ⊥Department of Biomedical Experimental and Clinical Sciences, University of Florence, 50134 Florence, Italy
| | - Roberto Pini
- #Institute of Applied Physics Nello Carrara, National Research Council, via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
| | - Paolo Matteini
- #Institute of Applied Physics Nello Carrara, National Research Council, via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
| | - Ramon A Alvarez-Puebla
- †Universitat Rovira i Virgili and Centro de Tecnologia Quimica de Cataluña, C/de Marcel·lí Domingo s/n, N5, 43007 Tarragona, Spain
- ‡Medcom Advance SA, Viladecans Busines Park, Edificio Brasil, C/Bertran i Musitu, 83-85, 08840 Viladecans, Barcelona, Spain
- ○ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
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37
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Aptamers in diagnostics and treatment of viral infections. Viruses 2015; 7:751-80. [PMID: 25690797 PMCID: PMC4353915 DOI: 10.3390/v7020751] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 01/13/2015] [Accepted: 02/12/2015] [Indexed: 02/07/2023] Open
Abstract
Aptamers are in vitro selected DNA or RNA molecules that are capable of binding a wide range of nucleic and non-nucleic acid molecules with high affinity and specificity. They have been conducted through the process known as SELEX (Systematic Evolution of Ligands by Exponential Enrichment). It serves to reach specificity and considerable affinity to target molecules, including those of viral origin, both proteins and nucleic acids. Properties of aptamers allow detecting virus infected cells or viruses themselves and make them competitive to monoclonal antibodies. Specific aptamers can be used to interfere in each stage of the viral replication cycle and also inhibit its penetration into cells. Many current studies have reported possible application of aptamers as a treatment or diagnostic tool in viral infections, e.g., HIV (Human Immunodeficiency Virus), HBV (Hepatitis B Virus), HCV (Hepatitis C Virus), SARS (Severe Acute Respiratory Syndrome), H5N1 avian influenza and recently spread Ebola. This review presents current developments of using aptamers in the diagnostics and treatment of viral diseases.
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38
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Rivera-Betancourt OE, Karls R, Grosse-Siestrup B, Helms S, Quinn F, Dluhy RA. Identification of mycobacteria based on spectroscopic analyses of mycolic acid profiles. Analyst 2014; 138:6774-85. [PMID: 24071725 DOI: 10.1039/c3an01157g] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This report examines lipophilic extracts containing mycolic acids isolated from tuberculosis (MTB) and non-tuberculosis (NTM) mycobacterial strains using chromatography, mass spectrometry (MS), nuclear magnetic resonance (NMR), and Raman spectroscopy. Gas chromatography-MS was used to identify major fatty acid mycolate components, while proton NMR confirmed the presence of characteristic cis- and trans-cyclopropane rings within different mycolic acid sub-types. Surface-enhanced Raman (SERS) spectra were obtained from the mycolic acids extracted from the bacterial cell envelopes of the MTB or NTM mycobacterial species. The Raman spectral profiles were used to develop a classification method based on chemometrics for identification of the mycobacterial species. Multivariate statistical analysis methods, including principal component analysis (PCA), hierarchical cluster analysis (HCA), and partial least squares discriminant analysis (PLS-DA) of the SERS spectra enabled differentiation of NTM mycobacteria from one another with 100% accuracy. These methods are also sensitive enough to differentiate clinically-isolated MTB strains that differed only by the presence or absence of a single extracytoplasmic sigma factor with 83-100% sensitivity and 80-100% specificity. The current work is the first report on discrimination of mycobacteria strains based on the SERS spectra of the constituent mycolic acids in lipophilic extracts. These results suggest that SERS can be used as an accurate and sensitive method for species and strain discrimination in mycobacteria.
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Negri P, Choi JY, Jones C, Tompkins SM, Tripp R, Dluhy RA. Identification of virulence determinants in influenza viruses. Anal Chem 2014; 86:6911-7. [PMID: 24937567 PMCID: PMC4116746 DOI: 10.1021/ac500659f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 06/17/2014] [Indexed: 01/15/2023]
Abstract
To date there is no rapid method to screen for highly pathogenic avian influenza strains that may be indicators of future pandemics. We report here the first development of an oligonucleotide-based spectroscopic assay to rapidly and sensitively detect a N66S mutation in the gene coding for the PB1-F2 protein associated with increased virulence in highly pathogenic pandemic influenza viruses. 5'-Thiolated ssDNA oligonucleotides were employed as probes to capture RNA isolated from six influenza viruses, three having N66S mutations, two without the N66S mutation, and one deletion mutant not encoding the PB1-F2 protein. Hybridization was detected without amplification or labeling using the intrinsic surfaced-enhanced Raman spectrum of the DNA-RNA complex. Multivariate analysis identified target RNA binding from noncomplementary sequences with 100% sensitivity, 100% selectivity, and 100% correct classification in the test data set. These results establish that optical-based diagnostic methods are able to directly identify diagnostic indicators of virulence linked to highly pathogenic pandemic influenza viruses without amplification or labeling.
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Affiliation(s)
- Pierre Negri
- Department
of Chemistry, University of Georgia, Athens, Georgia 30602 United States
| | - Joo Young Choi
- Department
of Chemistry, University of Georgia, Athens, Georgia 30602 United States
| | - Cheryl Jones
- Department
of Infectious Disease, University of Georgia, Athens, Georgia 30602 United States
| | - S. Mark Tompkins
- Department
of Infectious Disease, University of Georgia, Athens, Georgia 30602 United States
| | - Ralph
A. Tripp
- Department
of Infectious Disease, University of Georgia, Athens, Georgia 30602 United States
| | - Richard A. Dluhy
- Department
of Chemistry, University of Georgia, Athens, Georgia 30602 United States
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Rivera-Betancourt OE, Sheppard ES, Krause DC, Dluhy RA. Layer-by-layer polyelectrolyte encapsulation of Mycoplasma pneumoniae for enhanced Raman detection. Analyst 2014; 139:4287-95. [PMID: 25017005 DOI: 10.1039/c4an00596a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Mycoplasma pneumoniae is a major cause of respiratory disease in humans and accounts for as much as 20% of all community-acquired pneumonia. Existing mycoplasma diagnosis is primarily limited by the poor success rate at culturing the bacteria from clinical samples. There is a critical need to develop a new platform for mycoplasma detection that has high sensitivity, specificity, and expediency. Here we report the layer-by-layer (LBL) encapsulation of M. pneumoniae cells with Ag nanoparticles in a matrix of the polyelectrolytes poly(allylamine hydrochloride) (PAH) and poly(styrene sulfonate) (PSS). We evaluated nanoparticle encapsulated mycoplasma cells as a platform for the differentiation of M. pneumoniae strains using surface enhanced Raman scattering (SERS) combined with multivariate statistical analysis. Three separate M. pneumoniae strains (M129, FH and II-3) were studied. Scanning electron microscopy and fluorescence imaging showed that the Ag nanoparticles were incorporated between the oppositely charged polyelectrolyte layers. SERS spectra showed that LBL encapsulation provides excellent spectral reproducibility. Multivariate statistical analysis of the Raman spectra differentiated the three M. pneumoniae strains with 97-100% specificity and sensitivity, and low (0.1-0.4) root mean square error. These results indicated that nanoparticle and polyelectrolyte encapsulation of M. pneumoniae is a potentially powerful platform for rapid and sensitive SERS-based bacterial identification.
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Negri P, Dluhy RA. Detection of genetic markers related to high pathogenicity in influenza by SERS. Analyst 2013; 138:4877-84. [PMID: 23833767 PMCID: PMC3767290 DOI: 10.1039/c3an00774j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We have developed a method for the detection of genetic markers associated with high pathogenicity in influenza. The assay consists of an array of 5'-thiolated ssDNA oligonucleotides immobilized on the surface of a Ag nanorod substrate that serve as capture probes for the detection of synthetic RNA sequences coding for a genetic mutation in the influenza PB1-F2 protein. Hybridization of the DNA probes to their complementary RNA sequences was detected using surface-enhanced Raman spectroscopy (SERS). Multivariate statistical analysis was used to differentiate the spectra of the complementary DNA probe-RNA target hybrids from those of the non-complementary DNA probes containing a single base pair polymorphism. Hierarchical cluster analysis (HCA) was able to distinguish with 100% accuracy the spectra of the complementary DNA probe-RNA target from the spectra of the immobilized DNA probes alone, or the DNA probes incubated with non-complementary RNA sequences. Linearity of response and limits of sensitivity of the SERS-based assays were determined using a partial least squares (PLS) regression model; detection limits computed by PLS was determined to be ~10 nM. The binding affinity of the DNA probes to their complementary RNA sequences was confirmed using enzyme-linked immunosorbent assay (ELISA); however, the detection limits observed using ELISA were approximately 10× higher (~100 nM) than those determined by PLS analysis of the SERS spectra.
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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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Özalp VC, Bilecen K, Kavruk M, Öktem HA. Antimicrobial aptamers for detection and inhibition of microbial pathogen growth. Future Microbiol 2013; 8:387-401. [PMID: 23464374 DOI: 10.2217/fmb.12.149] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Discovery of alternative sources of antimicrobial agents are essential in the ongoing battle against microbial pathogens. Legislative and scientific challenges considerably hinder the discovery and use of new antimicrobial drugs, and new approaches are in urgent demand. On the other hand, rapid, specific and sensitive detection of airborne pathogens is becoming increasingly critical for public health. In this respect affinity oligonucleotides, aptamers, provide unique opportunities for the development of nanotechnological solutions for such medical applications. In recent years, aptamers specifically recognizing microbial cells and viruses showed great potential in a range of analytical and therapeutic applications. This article describes the significant advances in the development of aptamers targeting specific pathogens. Therapeutic application of aptamers as neutralizing agents demonstrates great potential as a future source of antimicrobial agent.
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Affiliation(s)
- Veli Cengiz Özalp
- Nanobiz Ltd, MetuTechnopolis, Galium block, 2nd Floor, No. 18, 06800 Ankara, Turkey
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Detection of receptor-induced glycoprotein conformational changes on enveloped virions by using confocal micro-Raman spectroscopy. J Virol 2013; 87:3130-42. [PMID: 23283947 DOI: 10.1128/jvi.03220-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Conformational changes in the glycoproteins of enveloped viruses are critical for membrane fusion, which enables viral entry into cells and the pathological cell-cell fusion (syncytia) associated with some viral infections. However, technological capabilities for identifying viral glycoproteins and their conformational changes on actual enveloped virus surfaces are generally scarce, challenging, and time-consuming. Our model, Nipah virus (NiV), is a syncytium-forming biosafety level 4 pathogen with a high mortality rate (40 to 75%) in humans. Once the NiV attachment glycoprotein (G) (NiV-G) binds the cell receptor ephrinB2 or -B3, G triggers conformational changes in the fusion glycoprotein (F) that result in membrane fusion and viral entry. We demonstrate that confocal micro-Raman spectroscopy can, within minutes, simultaneously identify specific G and F glycoprotein signals and receptor-induced conformational changes in NiV-F on NiV virus-like particles (VLPs). First, we identified reproducible G- and F-specific Raman spectral features on NiV VLPs containing M (assembly matrix protein), G, and/or F or on NiV/vesicular stomatitis virus (VSV) pseudotyped virions via second-derivative transformations and principal component analysis (PCA). Statistical analyses validated our PCA models. Dynamic temperature-induced conformational changes in F and G or receptor-induced target membrane-dependent conformational changes in F were monitored in NiV pseudovirions in situ in real time by confocal micro-Raman spectroscopy. Advantageously, Raman spectroscopy can identify specific protein signals in relatively impure samples. Thus, this proof-of-principle technological development has implications for the rapid identification and biostability characterization of viruses in medical, veterinary, and food samples and for the analysis of virion glycoprotein conformational changes in situ during viral entry.
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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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45
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Wei X, Zheng L, Luo F, Lin Z, Guo L, Qiu B, Chen G. Fluorescence biosensor for the H5N1 antibody based on a metal–organic framework platform. J Mater Chem B 2013; 1:1812-1817. [DOI: 10.1039/c3tb00501a] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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46
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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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