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Singh NK, Wang Y, Wen C, Davis B, Wang X, Lee K, Wang Y. High-affinity one-step aptamer selection using a non-fouling porous hydrogel. Nat Biotechnol 2024; 42:1224-1231. [PMID: 37798416 DOI: 10.1038/s41587-023-01973-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 08/29/2023] [Indexed: 10/07/2023]
Abstract
Aptamers, commonly referred to as chemical antibodies, are used in a wide range of applications including drug delivery and biosensing. However, the process of aptamer selection poses a substantial challenge, as it requires numerous cycles of enrichment and involves issues with nonspecific binding. We present a simple, fast instrument-free method for aptamer enrichment and selection based on a diffusion-binding process in a three-dimensional non-fouling porous hydrogel with immobilized target proteins. Low-affinity aptamer candidates can be rapidly released from the hydrogel, whereas high-affinity candidates are restricted due to their strong binding to the immobilized protein targets. Consequently, a one-step enriched aptamer pool can strongly bind the protein targets. This enrichment is consistent across five proteins with isoelectric points in varying ranges. With thrombin as a representative model, the anti-thrombin aptamer identified from an enriched aptamer pool has been found to have a binding affinity that is comparable to those identified over ten cycles of selection using traditional methods.
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Affiliation(s)
- Naveen K Singh
- Department of Biomedical Engineering, The Penn State University, University Park, PA, USA
- Centre for Biomedical Engineering, Indian Institute of Technology Delhi, Delhi, New Delhi, India
| | - Yixun Wang
- Department of Biomedical Engineering, The Penn State University, University Park, PA, USA
| | - Connie Wen
- Department of Biomedical Engineering, The Penn State University, University Park, PA, USA
| | - Brandon Davis
- Department of Biomedical Engineering, The Penn State University, University Park, PA, USA
| | - Xuelin Wang
- Department of Biomedical Engineering, The Penn State University, University Park, PA, USA
| | - Kyungsene Lee
- Department of Biomedical Engineering, The Penn State University, University Park, PA, USA
| | - Yong Wang
- Department of Biomedical Engineering, The Penn State University, University Park, PA, USA.
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2
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Li H, Jin Z, Lu N, Pan J, Xu J, Yin XB, Zhang M. Fe 3O 4 nanoparticles entrapped in the inner surfaces of N-doped carbon microtubes with enhanced biomimetic activity. Dalton Trans 2024; 53:6974-6982. [PMID: 38563069 DOI: 10.1039/d3dt04310j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Tubular structured composites have attracted great interest in catalysis research owing to their void-confinement effects. In this work, we synthesized a pair of hollow N-doped carbon microtubes (NCMTs) with Fe3O4 nanoparticles (NPs) encapsulated inside NCMTs (Fe3O4@NCMTs) and supported outside NCMTs (NCMTs@Fe3O4) while keeping other structural features the same. The impact of structural effects on the catalytic activities was investigated by comparing a pair of hollow-structured nanocomposites. It was found that the Fe3O4@NCMTs possessed a higher peroxidase-like activity when compared with NCMTs@Fe3O4, demonstrating structural superiority of Fe3O4@NCMTs. Based on the excellent peroxidase-like catalytic activity and stability of Fe3O4@NCMTs, an ultra-sensitive colorimetric method was developed for the detection of H2O2 and GSH with detection limits of 0.15 μM and 0.49 μM, respectively, which has potential application value in biological sciences and biotechnology.
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Affiliation(s)
- Huanhuan Li
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China.
| | - Ziqi Jin
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China.
| | - Na Lu
- College of Materials Science and Engineering, Shanghai University of Engineering Science, Shanghai, 201620, China.
| | - Jianmin Pan
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China.
| | - Jingli Xu
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China.
| | - Xue-Bo Yin
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China.
| | - Min Zhang
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China.
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3
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Park KS, Park TI, Lee JE, Hwang SY, Choi A, Pack SP. Aptamers and Nanobodies as New Bioprobes for SARS-CoV-2 Diagnostic and Therapeutic System Applications. BIOSENSORS 2024; 14:146. [PMID: 38534253 DOI: 10.3390/bios14030146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/10/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024]
Abstract
The global challenges posed by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic have underscored the critical importance of innovative and efficient control systems for addressing future pandemics. The most effective way to control the pandemic is to rapidly suppress the spread of the virus through early detection using a rapid, accurate, and easy-to-use diagnostic platform. In biosensors that use bioprobes, the binding affinity of molecular recognition elements (MREs) is the primary factor determining the dynamic range of the sensing platform. Furthermore, the sensitivity relies mainly on bioprobe quality with sufficient functionality. This comprehensive review investigates aptamers and nanobodies recently developed as advanced MREs for SARS-CoV-2 diagnostic and therapeutic applications. These bioprobes might be integrated into organic bioelectronic materials and devices, with promising enhanced sensitivity and specificity. This review offers valuable insights into advancing biosensing technologies for infectious disease diagnosis and treatment using aptamers and nanobodies as new bioprobes.
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Affiliation(s)
- Ki Sung Park
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Tae-In Park
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Jae Eon Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Seo-Yeong Hwang
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Anna Choi
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Seung Pil Pack
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
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4
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Lin B, Xiao F, Jiang J, Zhao Z, Zhou X. Engineered aptamers for molecular imaging. Chem Sci 2023; 14:14039-14061. [PMID: 38098720 PMCID: PMC10718180 DOI: 10.1039/d3sc03989g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/07/2023] [Indexed: 12/17/2023] Open
Abstract
Molecular imaging, including quantification and molecular interaction studies, plays a crucial role in visualizing and analysing molecular events occurring within cells or organisms, thus facilitating the understanding of biological processes. Moreover, molecular imaging offers promising applications for early disease diagnosis and therapeutic evaluation. Aptamers are oligonucleotides that can recognize targets with a high affinity and specificity by folding themselves into various three-dimensional structures, thus serving as ideal molecular recognition elements in molecular imaging. This review summarizes the commonly employed aptamers in molecular imaging and outlines the prevalent design approaches for their applications. Furthermore, it highlights the successful application of aptamers to a wide range of targets and imaging modalities. Finally, the review concludes with a forward-looking perspective on future advancements in aptamer-based molecular imaging.
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Affiliation(s)
- Bingqian Lin
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University Wuhan 430072 China
| | - Feng Xiao
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University Wuhan 430072 China
| | - Jinting Jiang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University Wuhan 430072 China
| | - Zhengjia Zhao
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University Wuhan 430072 China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University Wuhan 430072 China
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5
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Zhang Z, Jin J, Paluzzi VE, Jin Z, Wen Y, Huang CZ, Li CM, Mao C, Zuo H. AMP Aptamer Programs DNA Tile Cohesion without Canonical Base Pairing. J Am Chem Soc 2023; 145:19503-19507. [PMID: 37638713 DOI: 10.1021/jacs.3c06260] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
Tile-based DNA self-assembly provides a versatile approach for the construction of a wide range of nanostructures for various applications such as nanomedicine and advanced materials. The inter-tile interactions are primarily programmed by base pairing, particularly Watson-Crick base pairing. To further expand the tool box for DNA nanotechnology, herein, we have designed DNA tiles that contain both ligands and aptamers. Upon ligand-aptamer binding, tiles associate into geometrically well-defined nanostructures. This strategy has been demonstrated by the assembly of a series of DNA nanostructures, which have been thoroughly characterized by gel electrophoresis and atomic force microscopy. This new inter-tile cohesion could bring new potentials to DNA self-assembly in the future. For example, the addition of free ligand could modulate the nanostructure formation. In the case of biological ligands, DNA self-assembly could be related to the presence of certain ligands.
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Affiliation(s)
- Zhe Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Jin Jin
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Victoria E Paluzzi
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zhuoer Jin
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Yuandong Wen
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | | | - Chun Mei Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Chengde Mao
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Hua Zuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
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6
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Yuwen L, Zhang S, Chao J. Recent Advances in DNA Nanotechnology-Enabled Biosensors for Virus Detection. BIOSENSORS 2023; 13:822. [PMID: 37622908 PMCID: PMC10452139 DOI: 10.3390/bios13080822] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/05/2023] [Accepted: 08/12/2023] [Indexed: 08/26/2023]
Abstract
Virus-related infectious diseases are serious threats to humans, which makes virus detection of great importance. Traditional virus-detection methods usually suffer from low sensitivity and specificity, are time-consuming, have a high cost, etc. Recently, DNA biosensors based on DNA nanotechnology have shown great potential in virus detection. DNA nanotechnology, specifically DNA tiles and DNA aptamers, has achieved atomic precision in nanostructure construction. Exploiting the programmable nature of DNA nanostructures, researchers have developed DNA nanobiosensors that outperform traditional virus-detection methods. This paper reviews the history of DNA tiles and DNA aptamers, and it briefly describes the Baltimore classification of virology. Moreover, the advance of virus detection by using DNA nanobiosensors is discussed in detail and compared with traditional virus-detection methods. Finally, challenges faced by DNA nanobiosensors in virus detection are summarized, and a perspective on the future development of DNA nanobiosensors in virus detection is also provided.
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Affiliation(s)
- Lihui Yuwen
- State Key Laboratory of Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (L.Y.); (S.Z.)
| | - Shifeng Zhang
- State Key Laboratory of Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (L.Y.); (S.Z.)
| | - Jie Chao
- School of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
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7
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Alkhamis O, Canoura J, Willis C, Wang L, Perry J, Xiao Y. Comparison of Aptamer Signaling Mechanisms Reveals Disparities in Sensor Response and Strategies to Eliminate False Signals. J Am Chem Soc 2023. [PMID: 37217444 DOI: 10.1021/jacs.3c03640] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Aptamers are nucleic acid-based affinity reagents that have been incorporated into a variety of molecular sensor formats. However, many aptamer sensors exhibit insufficient sensitivity and specificity for real-world applications, and although considerable effort has been dedicated to improving sensitivity, sensor specificity has remained largely neglected and understudied. In this work, we have developed a series of sensors using aptamers for the small-molecule drugs flunixin, fentanyl, and furanyl fentanyl and compare their performance─in particular, focusing on their specificity. Contrary to expectations, we observe that sensors using the same aptamer operating under the same physicochemical conditions produce divergent responses to interferents depending on their signal transduction mechanism. For instance, aptamer beacon sensors are susceptible to false-positives from interferents that weakly associate with DNA, while strand-displacement sensors suffer from false-negatives due to interferent-associated signal suppression when both the target and interferent are present. Biophysical analyses suggest that these effects arise from aptamer-interferent interactions that are either nonspecific or induce aptamer conformational changes that are distinct from those induced by true target-binding events. We also demonstrate strategies for improving the sensitivity and specificity of aptamer sensors with the development of a "hybrid beacon," wherein the incorporation of a complementary DNA competitor into an aptamer beacon selectively hinders interferent─but not target─binding and signaling, while simultaneously overcoming signal suppression by interferents. Our results highlight the need for systematic and thorough testing of aptamer sensor response and new aptamer selection methods that optimize specificity more effectively than traditional counter-SELEX.
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Affiliation(s)
- Obtin Alkhamis
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695, United States
| | - Juan Canoura
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695, United States
| | - Connor Willis
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695, United States
| | - Linlin Wang
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695, United States
| | - Jacob Perry
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695, United States
| | - Yi Xiao
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695, United States
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8
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Ferrari E. Gold Nanoparticle-Based Plasmonic Biosensors. BIOSENSORS 2023; 13:bios13030411. [PMID: 36979623 PMCID: PMC10046074 DOI: 10.3390/bios13030411] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/16/2023] [Accepted: 03/20/2023] [Indexed: 06/10/2023]
Abstract
One of the emerging technologies in molecular diagnostics of the last two decades is the use of gold nanoparticles (AuNPs) for biosensors. AuNPs can be functionalized with various biomolecules, such as nucleic acids or antibodies, to recognize and bind to specific targets. AuNPs present unique optical properties, such as their distinctive plasmonic band, which confers a bright-red color to AuNP solutions, and their extremely high extinction coefficient, which makes AuNPs detectable by the naked eye even at low concentrations. Ingenious molecular mechanisms triggered by the presence of a target analyte can change the colloidal status of AuNPs from dispersed to aggregated, with a subsequent visible change in color of the solution due to the loss of the characteristic plasmonic band. This review describes how the optical properties of AuNPs have been exploited for the design of plasmonic biosensors that only require the simple mixing of reagents combined with a visual readout and focuses on the molecular mechanisms involved. This review illustrates selected examples of AuNP-based plasmonic biosensors and promising approaches for the point-of-care testing of various analytes, spanning from the viral RNA of SARS-CoV-2 to the molecules that give distinctive flavor and color to aged whisky.
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Affiliation(s)
- Enrico Ferrari
- Department of Life Sciences, University of Lincoln, Lincoln LN6 7TS, UK
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9
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Non-viral nucleic acid delivery approach: A boon for state-of-the-art gene delivery. J Drug Deliv Sci Technol 2023. [DOI: 10.1016/j.jddst.2023.104152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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10
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Ebadollahi A, Valizadeh B, Panahandeh S, Mirhosseini H, Zolfaghari M, Changbunjong T. Nanoencapsulation of Acetamiprid by Sodium Alginate and Polyethylene Glycol Enhanced Its Insecticidal Efficiency. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:nano12172971. [PMID: 36080008 PMCID: PMC9457968 DOI: 10.3390/nano12172971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/20/2022] [Accepted: 08/21/2022] [Indexed: 06/01/2023]
Abstract
Nanoformulation has been considered one of the newly applied methods in integrated pest management strategies. In this research, a conventional neonicotinoid insecticide acetamiprid was nanoencapsulated via AL (Sodium Alginate) and PEG (Polyethylene Glycol) and tested against the elm leaf beetle Xanthogaleruca luteola. The synthesized particles had spherical-like morphology and nanoscale based on TEM (Transmission Electron Microscopy) and DLS (Dynamic Light Scattering). The encapsulation efficiency and loading percentages of acetamiprid in AL and PEG were 92.58% and 90.15%, and 88.46% and 86.79%, respectively. Leaf discs treated with different formulations by the leaf-dipping method were used for oral toxicity assays. The LC50 values (Lethal Concentration to kill 50% of insect population) of acetamiprid and Al- and PEG-nanoencapsulated formulations on third-instar larvae were 0.68, 0.04, and 0.08 ppm, respectively. Based on the highest relative potency, AL-encapsulated acetamiprid had the most toxicity. The content of energy reserve protein, glucose, and triglyceride and the activity of detoxifying enzymes esterase and glutathione S-transferase of the larvae treated by LC50 values of nanoformulations were also decreased. According to the current findings, the nanoencapsulation of acetamiprid by Al and PEG can increase its insecticidal performance in terms of lethal and sublethal toxicity.
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Affiliation(s)
- Asgar Ebadollahi
- Department of Plant Sciences, Moghan College of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil 5697194781, Iran
| | - Bita Valizadeh
- Department of Plant Protection, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman 7616913439, Iran
| | - Saleh Panahandeh
- Department of Plant Protection, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman 7616913439, Iran
| | - Hadiseh Mirhosseini
- Department of Chemistry, Faculty of Science, Shahid Bahonar University of Kerman, Kerman 7616913439, Iran
| | - Maryam Zolfaghari
- Department of Plant Protection, Faculty of Agricultural Sciences, University of Guilan, Rasht 416351314, Iran
| | - Tanasak Changbunjong
- Department of Pre-Clinic and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand
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11
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El-Husseini DM, Sayour AE, Melzer F, Mohamed MF, Neubauer H, Tammam RH. Generation and Selection of Specific Aptamers Targeting Brucella Species through an Enhanced Cell-SELEX Methodology. Int J Mol Sci 2022; 23:ijms23116131. [PMID: 35682807 PMCID: PMC9180945 DOI: 10.3390/ijms23116131] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 02/07/2023] Open
Abstract
Brucellae are Gram-negative, aerobic, non-motile coccobacilli causing brucellosis in man and animals. The disease is one of the most significant yet neglected global zoonoses. Especially in developing countries, brucellosis is causing public health problems and economic losses to private animal owners and national revenues. Composed of oligonucleotides, aptamers are chemical analogues of antibodies that are promising components for developing aptamer-based rapid, sensitive, and specific tests to identify the Brucella group of bacteria. For this purpose, aptamers were generated and selected by an enhanced protocol of cell systematic evolution of ligands by exponential enrichment (cell-SELEX). This enhanced cell-SELEX procedure involved the combination of both conventional and toggle cell-SELEX to boost the specificity and binding affinity to whole Brucella cells. This procedure, combined with high-throughput sequencing of the resulting aptamer pools, comprehensive bioinformatics analysis, and wet lab validation assays, led to the selection of a highly sensitive and specific aptamer for those Brucella species known to circulate in Egypt. The isolated candidate aptamer showed dissociation constant (KD) values of 43.5 ± 11, 61.5 ± 8, and 56 ± 10.8 nM for B. melitensis, B. abortus, and B. suis, respectively. This is the first development of a Brucella-specific aptamer using an enhanced combination of conventional and toggle cell-SELEX to the authors’ best knowledge.
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Affiliation(s)
- Dalia M. El-Husseini
- Biotechnology Department, Animal Health Research Institute, Agricultural Research Center, Dokki, Giza 12618, Egypt
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743 Jena, Germany;
- Correspondence: (D.M.E.-H.); (F.M.)
| | - Ashraf E. Sayour
- Molecular Biomimetics Research Group, Animal Health Research Institute, Agricultural Research Center, Dokki, Giza 12618, Egypt;
| | - Falk Melzer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743 Jena, Germany;
- Correspondence: (D.M.E.-H.); (F.M.)
| | - Magda F. Mohamed
- Chemistry Department, Faculty of Science, Cairo University, Giza 12613, Egypt; (M.F.M.); (R.H.T.)
| | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743 Jena, Germany;
| | - Reham H. Tammam
- Chemistry Department, Faculty of Science, Cairo University, Giza 12613, Egypt; (M.F.M.); (R.H.T.)
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12
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Jang K, Westbay JH, Asher SA. DNA-Crosslinked 2D Photonic Crystal Hydrogels for Detection of Adenosine Actuated by an Adenosine-Binding Aptamer. ACS Sens 2022; 7:1648-1656. [PMID: 35623053 DOI: 10.1021/acssensors.1c02424] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
There is a need to develop versatile sensing motifs that can be used to detect a variety of chemical targets in resource-limited settings, for example, at the point of care. While numerous sensing technologies have been developed toward this effort, these technologies can be overly complex and require a skilled technician, extensive sample preparation, or sophisticated instrumentation to use, limiting their generalizability and application in resource-limited settings. Here, we report a novel sensing motif that utilizes DNA-crosslinked two-dimensional photonic crystal (2DPC) hydrogels. These hydrogel sensors contain a DNA aptamer recognition group that binds a target analyte. As proof of concept, we fabricated 2DPC hydrogels using a well-studied adenosine-binding aptamer. This adenosine aptamer is duplexed with a partially complementary strand and forms responsive crosslinks in the hydrogel polymer network. When adenosine is introduced, aptamer-adenosine binding occurs, breaking the DNA crosslinks and causing the hydrogel to swell. This in turn increases the particle spacing of an embedded 2DPC array, shifting the 2DPC Bragg diffraction. Thus, adenosine concentration can be monitored through 2DPC Bragg diffraction measurements. A linear range of 20 μM to 2 mM was observed. The detection limits were calculated to be 13.9 μM in adenosine-binding buffer and 26.7 μM in fetal bovine serum. This reported sensing motif has a readout that is simple and rapid and requires minimal equipment. We hypothesize that this sensing motif is generalizable and that other sensors can be easily fabricated by simply exchanging the aptamer that serves as a molecular recognition group.
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Affiliation(s)
- Kyeongwoo Jang
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - James H. Westbay
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sanford A. Asher
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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13
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Liu F, Li N, Shang Y, Wang Y, Liu Q, Ma Z, Jiang Q, Ding B. A DNA‐Based Plasmonic Nanodevice for Cascade Signal Amplification. Angew Chem Int Ed Engl 2022; 61:e202114706. [DOI: 10.1002/anie.202114706] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Indexed: 11/09/2022]
Affiliation(s)
- Fengsong Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication National Center for Nanoscience and Technology Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Na Li
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication National Center for Nanoscience and Technology Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Yingxu Shang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication National Center for Nanoscience and Technology Beijing 100190 China
| | - Yiming Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication National Center for Nanoscience and Technology Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Qing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication National Center for Nanoscience and Technology Beijing 100190 China
| | - Zhentao Ma
- He'nan Institute of Advanced Technology School of Materials Science and Engineering Zhengzhou University Zhengzhou 450001 China
| | - Qiao Jiang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication National Center for Nanoscience and Technology Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication National Center for Nanoscience and Technology Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
- He'nan Institute of Advanced Technology School of Materials Science and Engineering Zhengzhou University Zhengzhou 450001 China
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14
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Xu R, Abune L, Davis B, Ouyang L, Zhang G, Wang Y, Zhe J. Ultrasensitive detection of small biomolecules using aptamer-based molecular recognition and nanoparticle counting. Biosens Bioelectron 2022; 203:114023. [DOI: 10.1016/j.bios.2022.114023] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 01/11/2022] [Accepted: 01/17/2022] [Indexed: 01/12/2023]
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15
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Chatterjee S, Lou XY, Liang F, Yang YW. Surface-functionalized gold and silver nanoparticles for colorimetric and fluorescent sensing of metal ions and biomolecules. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214461] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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16
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Mendes BB, Conniot J, Avital A, Yao D, Jiang X, Zhou X, Sharf-Pauker N, Xiao Y, Adir O, Liang H, Shi J, Schroeder A, Conde J. Nanodelivery of nucleic acids. NATURE REVIEWS. METHODS PRIMERS 2022; 2:24. [PMID: 35480987 PMCID: PMC9038125 DOI: 10.1038/s43586-022-00104-y] [Citation(s) in RCA: 179] [Impact Index Per Article: 89.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/09/2022] [Indexed: 12/11/2022]
Abstract
There is growing need for a safe, efficient, specific and non-pathogenic means for delivery of gene therapy materials. Nanomaterials for nucleic acid delivery offer an unprecedented opportunity to overcome these drawbacks; owing to their tunability with diverse physico-chemical properties, they can readily be functionalized with any type of biomolecules/moieties for selective targeting. Nucleic acid therapeutics such as antisense DNA, mRNA, small interfering RNA (siRNA) or microRNA (miRNA) have been widely explored to modulate DNA or RNA expression Strikingly, gene therapies combined with nanoscale delivery systems have broadened the therapeutic and biomedical applications of these molecules, such as bioanalysis, gene silencing, protein replacement and vaccines. Here, we overview how to design smart nucleic acid delivery methods, which provide functionality and efficacy in the layout of molecular diagnostics and therapeutic systems. It is crucial to outline some of the general design considerations of nucleic acid delivery nanoparticles, their extraordinary properties and the structure-function relationships of these nanomaterials with biological systems and diseased cells and tissues.
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Affiliation(s)
- Bárbara B. Mendes
- NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
- Centre for Toxicogenomics and Human Health, Genetics, Oncology and Human Toxicology, NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
- These authors contributed equally: Bárbara B. Mendes, João Conniot, Aviram Avital, Dongbao Yao, Xingya Jiang, Xiang Zhou, Noga Sharf-Pauker, Yuling Xiao, Omer Adir
| | - João Conniot
- NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
- Centre for Toxicogenomics and Human Health, Genetics, Oncology and Human Toxicology, NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
- These authors contributed equally: Bárbara B. Mendes, João Conniot, Aviram Avital, Dongbao Yao, Xingya Jiang, Xiang Zhou, Noga Sharf-Pauker, Yuling Xiao, Omer Adir
| | - Aviram Avital
- Department of Chemical Engineering, Technion — Israel Institute of Technology, Haifa, Israel
- The Norman Seiden Multidisciplinary Program for Nanoscience and Nanotechnology, Technion — Israel Institute of Technology, Haifa, Israel
- These authors contributed equally: Bárbara B. Mendes, João Conniot, Aviram Avital, Dongbao Yao, Xingya Jiang, Xiang Zhou, Noga Sharf-Pauker, Yuling Xiao, Omer Adir
| | - Dongbao Yao
- Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
- These authors contributed equally: Bárbara B. Mendes, João Conniot, Aviram Avital, Dongbao Yao, Xingya Jiang, Xiang Zhou, Noga Sharf-Pauker, Yuling Xiao, Omer Adir
| | - Xingya Jiang
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- These authors contributed equally: Bárbara B. Mendes, João Conniot, Aviram Avital, Dongbao Yao, Xingya Jiang, Xiang Zhou, Noga Sharf-Pauker, Yuling Xiao, Omer Adir
| | - Xiang Zhou
- Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
- These authors contributed equally: Bárbara B. Mendes, João Conniot, Aviram Avital, Dongbao Yao, Xingya Jiang, Xiang Zhou, Noga Sharf-Pauker, Yuling Xiao, Omer Adir
| | - Noga Sharf-Pauker
- Department of Chemical Engineering, Technion — Israel Institute of Technology, Haifa, Israel
- The Norman Seiden Multidisciplinary Program for Nanoscience and Nanotechnology, Technion — Israel Institute of Technology, Haifa, Israel
- These authors contributed equally: Bárbara B. Mendes, João Conniot, Aviram Avital, Dongbao Yao, Xingya Jiang, Xiang Zhou, Noga Sharf-Pauker, Yuling Xiao, Omer Adir
| | - Yuling Xiao
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- These authors contributed equally: Bárbara B. Mendes, João Conniot, Aviram Avital, Dongbao Yao, Xingya Jiang, Xiang Zhou, Noga Sharf-Pauker, Yuling Xiao, Omer Adir
| | - Omer Adir
- Department of Chemical Engineering, Technion — Israel Institute of Technology, Haifa, Israel
- The Norman Seiden Multidisciplinary Program for Nanoscience and Nanotechnology, Technion — Israel Institute of Technology, Haifa, Israel
- These authors contributed equally: Bárbara B. Mendes, João Conniot, Aviram Avital, Dongbao Yao, Xingya Jiang, Xiang Zhou, Noga Sharf-Pauker, Yuling Xiao, Omer Adir
| | - Haojun Liang
- Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at the Microscale, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Jinjun Shi
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Avi Schroeder
- Department of Chemical Engineering, Technion — Israel Institute of Technology, Haifa, Israel
| | - João Conde
- NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
- Centre for Toxicogenomics and Human Health, Genetics, Oncology and Human Toxicology, NOVA Medical School, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
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17
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Zhao Y, Yavari K, Wang Y, Pi K, Van Cappellen P, Liu J. Deployment of functional DNA-based biosensors for environmental water analysis. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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18
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Liu F, Li N, Shang Y, Wang Y, Liu Q, Ma Z, Jiang Q, Ding B. A DNA‐based plasmonic nanodevice for cascade signal amplification. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202114706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Fengsong Liu
- National Center for Nanoscience and Technology CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CHINA
| | - Na Li
- National Center for Nanoscience and Technology CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CHINA
| | - Yingxu Shang
- National Center for Nanoscience and Technology CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CHINA
| | - Yiming Wang
- National Center for Nanoscience and Technology CAS Key Labortory of Nanosystem and Hierarchical Fabrication CHINA
| | - Qing Liu
- National Center for Nanoscience and Technology CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CHINA
| | - Zhentao Ma
- Zhengzhou University School of Materials Science and Engineering CHINA
| | - Qiao Jiang
- National Center for Nanoscience and Technology CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CHINA
| | - Baoquan Ding
- National Center for Nanoscience and Technology, China CAS Key Laboratory of Nanosystem and Hierarchical Fabrication No. 11, BeiYiTiao, ZhongGuanCun 100190 Beijing CHINA
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19
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Moradi R, Khalili NP, Septiani NLW, Liu CH, Doustkhah E, Yamauchi Y, Rotkin SV. Nanoarchitectonics for Abused-Drug Biosensors. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2104847. [PMID: 34882957 DOI: 10.1002/smll.202104847] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/14/2021] [Indexed: 06/13/2023]
Abstract
Rapid, accessible, and highly accurate biosensors for the detection of addictive and abused drugs are needed to reduce the adverse personal and societal impacts of addiction. Modern sensors that utilize next-generation technologies, e.g., nanobiotechnology and nanoarchitectonics, have triggered revolutionary progress in the field as they allow accurate detection and tracking of trace levels of major classes of drugs. This paper reviews advances in the field of biosensors for the detection of commonly abused drugs, both prescribed such as codeine and morphine, and illegal narcotics like cocaine.
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Affiliation(s)
- Rasoul Moradi
- Nanotechnology Laboratory, School of Engineering and Applied Science, Khazar University, Baku, Az1096, Azerbaijan
- Department of Chemical Engineering, School of Engineering and Applied Science, Khazar University, Baku, Az1096, Azerbaijan
| | - Nazila Pour Khalili
- Nanotechnology Laboratory, School of Engineering and Applied Science, Khazar University, Baku, Az1096, Azerbaijan
- Center for Cell Pathology Research, Department of Biological Science, Khazar University, Baku, Az1096, Azerbaijan
| | - Ni Luh Wulan Septiani
- Advanced Functional Materials Research Group, Institut Teknologi Bandung, Bandung, 40132, Indonesia
| | - Chia-Hung Liu
- Department of Urology, School of Medicine, College of Medicine, and TMU Research Center of Urology and Kidney, Taipei Medical University, No. 250, Wu-Hsing Street, Taipei, 110, Taiwan
- Department of Urology, Shuang Ho Hospital, Taipei Medical University, No. 291, Zhongzheng Road, Zhonghe District, New Taipei City, 23561, Taiwan
| | - Esmail Doustkhah
- International Center for Materials Nanoarchitechtonics (WPI-MANA), National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan
- JST-ERATO Yamauchi Materials Space-Tectonics Project and International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan
| | - Yusuke Yamauchi
- JST-ERATO Yamauchi Materials Space-Tectonics Project and International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan
- School of Chemical Engineering and Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Slava V Rotkin
- Department of Engineering Science and Mechanics, Materials Research Institute, The Pennsylvania State University, Millennium Science Complex, University Park, PA, 16802, USA
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20
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Recent trends and emerging strategies for aptasensing technologies for illicit drugs detection. J Electroanal Chem (Lausanne) 2022. [DOI: 10.1016/j.jelechem.2022.116128] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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21
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Alkhamis O, Canoura J, Bukhryakov KV, Tarifa A, DeCaprio AP, Xiao Y. DNA Aptamer–Cyanine Complexes as Generic Colorimetric Small‐Molecule Sensors. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Obtin Alkhamis
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
- Department of Chemistry North Carolina State University 2620 Yarbrough Dr. Raleigh NC 27695 USA
| | - Juan Canoura
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
- Department of Chemistry North Carolina State University 2620 Yarbrough Dr. Raleigh NC 27695 USA
| | - Konstantin V. Bukhryakov
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Anamary Tarifa
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Anthony P. DeCaprio
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Yi Xiao
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
- Department of Chemistry North Carolina State University 2620 Yarbrough Dr. Raleigh NC 27695 USA
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22
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Huang W, Huang S, Chen G, Ouyang G. Biocatalytic Metal-Organic Framework: Promising Materials for Biosensing. Chembiochem 2022; 23:e202100567. [PMID: 35025113 DOI: 10.1002/cbic.202100567] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/11/2022] [Indexed: 11/10/2022]
Abstract
The high-efficient and specific catalysis of enzyme allow it to recognize a myriad of substrate that impels the biosensing. Nevertheless, the fragility of natural enzymes severely restricts their practical applications. Metal-organic frameworks (MOFs) with porous network and attractive functions have been intelligently employed as supports to encase enzymes for protecting them against hash environments. More importantly, the customizable construction and composition affords the intrinsic enzyme-like activity of some MOFs (known as nanozymes), which provides an alternative guideline to construct robust enzymes mimics. Herein, this review will introduce the concept of these biocatalytic MOFs, with the special emphasis on how the biocatalytic processes operated in these MOFs materials can reverse the plight of native enzymes-based biosensing. In addition, the present challenges and future outlooks in this research field are briefly put forward.
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Affiliation(s)
- Wei Huang
- Sun Yat-Sen University, School of Chemical Engineering and Technology, CHINA
| | - Siming Huang
- Guangzhou Medical University, School of pharmaceutical sciences, CHINA
| | - Guosheng Chen
- Sun Yat-Sen University, School of Chemistry, No. 135, Xingang Xi Road, Guangzhou, 510275, P. R. China, 510275, Guangzhou, CHINA
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23
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Guo K, Song Z, Wang G, Tang C. Detecting Redox Potentials Using Porous Boron Nitride/ATP-DNA Aptamer/Methylene Blue Biosensor to Monitor Microbial Activities. MICROMACHINES 2022; 13:mi13010083. [PMID: 35056248 PMCID: PMC8777636 DOI: 10.3390/mi13010083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 12/30/2021] [Accepted: 12/31/2021] [Indexed: 02/05/2023]
Abstract
Microbial activity has gained attention because of its impact on the environment and the quality of people’s lives. Most of today’s methods, which include genome sequencing and electrochemistry, are costly and difficult to manage. Our group proposed a method using the redox potential change to detect microbial activity, which is rooted in the concept that metabolic activity can change the redox potential of a microbial community. The redox potential change was captured by a biosensor consisting of porous boron nitride, ATP-DNA aptamer, and methylene blue as the fluorophore. This assembly can switch on or off when there is a redox potential change, and this change leads to a fluorescence change that can be examined using a multipurpose microplate reader. The results show that this biosensor can detect microbial community changes when its composition is changed or toxic metals are ingested.
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Affiliation(s)
- Kai Guo
- Correspondence: (K.G.); (C.T.)
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24
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Le NH, Cathcart N, Kitaev V, Chen JIL. Core-satellite assembly of gold nanoshells on solid gold nanoparticles for a color coding plasmonic nanosensor. Analyst 2021; 147:155-164. [PMID: 34860213 DOI: 10.1039/d1an01421h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We present core-satellite assemblies comprising a solid gold nanoparticle as the core and hollow decahedral gold nanoshells as satellites for tuning the optical properties of the plasmonic structure for sensing. The core-satellite assemblies were fabricated on a substrate via the layer-by-layer assembly of nanoparticles linked by DNA. We used finite-difference time-domain simulations to help guide the geometrical design, and characterized the optical properties and morphology of the solid-shell nanoparticle assemblies using darkfield microscopy, single-nanostructure spectroscopy, and scanning electron microscopy. Plasmon coupling yielded resonant peaks at longer wavelengths in the red to near-infrared range for solid-shell assemblies compared with solid-solid nanoparticle assemblies. We examined sensing with the solid-shell assemblies using adenosine triphosphate (ATP) as a model target and ATP-aptamer as the linker. Binding of ATP induced disassembly and led to a decrease in the scattering intensity and a color change from red to green. The new morphology of the core-satellite assembly enabled plasmonic color-coding of multiplexed sensors. We demonstrate this potential by fabricating two types of assemblies using DNA linkers that target different molecules - ATP and a model nucleic acid. Our work expands the capability of chip-based plasmonic nanoparticle assemblies for the analysis of multiple, different types of biomolecules in small sample sizes including the microenvironment and single cells.
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Affiliation(s)
- Nguyen H Le
- Department of Chemistry, York University, 4700 Keele Street Toronto, Ontario, M3J 1P3, Canada.
| | - Nicole Cathcart
- Department of Chemistry, York University, 4700 Keele Street Toronto, Ontario, M3J 1P3, Canada. .,Department of Chemistry and Biochemistry, Wilfrid Laurier University, 75 University Ave. W., Waterloo, Ontario N2L 3C5, Canada
| | - Vladimir Kitaev
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, 75 University Ave. W., Waterloo, Ontario N2L 3C5, Canada
| | - Jennifer I L Chen
- Department of Chemistry, York University, 4700 Keele Street Toronto, Ontario, M3J 1P3, Canada.
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25
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Chang Y, Xia N, Huang Y, Sun Z, Liu L. In Situ Assembly of Nanomaterials and Molecules for the Signal Enhancement of Electrochemical Biosensors. NANOMATERIALS 2021; 11:nano11123307. [PMID: 34947656 PMCID: PMC8705329 DOI: 10.3390/nano11123307] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/30/2021] [Accepted: 12/04/2021] [Indexed: 02/07/2023]
Abstract
The physiochemical properties of nanomaterials have a close relationship with their status in solution. As a result of its better simplicity than that of pre-assembled aggregates, the in situ assembly of nanomaterials has been integrated into the design of electrochemical biosensors for the signal output and amplification. In this review, we highlight the significant progress in the in situ assembly of nanomaterials as the nanolabels for enhancing the performances of electrochemical biosensors. The works are discussed based on the difference in the interactions for the assembly of nanomaterials, including DNA hybridization, metal ion-ligand coordination, metal-thiol and boronate ester interactions, aptamer-target binding, electrostatic attraction, and streptavidin (SA)-biotin conjugate. We further expand the range of the assembly units from nanomaterials to small organic molecules and biomolecules, which endow the signal-amplified strategies with more potential applications.
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Affiliation(s)
| | | | | | | | - Lin Liu
- Correspondence: (Z.S.); (L.L.)
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26
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Kim JM, Lee C, Lee Y, Lee J, Park SJ, Park S, Nam JM. Synthesis, Assembly, Optical Properties, and Sensing Applications of Plasmonic Gap Nanostructures. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2006966. [PMID: 34013617 DOI: 10.1002/adma.202006966] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/30/2020] [Indexed: 06/12/2023]
Abstract
Plasmonic gap nanostructures (PGNs) have been extensively investigated mainly because of their strongly enhanced optical responses, which stem from the high intensity of the localized field in the nanogap. The recently developed methods for the preparation of versatile nanogap structures open new avenues for the exploration of unprecedented optical properties and development of sensing applications relying on the amplification of various optical signals. However, the reproducible and controlled preparation of highly uniform plasmonic nanogaps and the prediction, understanding, and control of their optical properties, especially for nanogaps in the nanometer or sub-nanometer range, remain challenging. This is because subtle changes in the nanogap significantly affect the plasmonic response and are of paramount importance to the desired optical performance and further applications. Here, recent advances in the synthesis, assembly, and fabrication strategies, prediction and control of optical properties, and sensing applications of PGNs are discussed, and perspectives toward addressing these challenging issues and the future research directions are presented.
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Affiliation(s)
- Jae-Myoung Kim
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
| | - Chungyeon Lee
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
| | - Yeonhee Lee
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
| | - Jinhaeng Lee
- Department of Chemistry, Sungkyunkwan University, Suwon, 16419, South Korea
| | - So-Jung Park
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 03760, South Korea
| | - Sungho Park
- Department of Chemistry, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Jwa-Min Nam
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
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27
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Alkhamis O, Canoura J, Bukhryakov KV, Tarifa A, DeCaprio AP, Xiao Y. DNA Aptamer-Cyanine Complexes as Generic Colorimetric Small-Molecule Sensors. Angew Chem Int Ed Engl 2021; 61:e202112305. [PMID: 34706127 DOI: 10.1002/anie.202112305] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Indexed: 12/31/2022]
Abstract
Aptamers are promising biorecognition elements for sensors. However, aptamer-based assays often lack the requisite levels of sensitivity and/or selectivity because they typically employ structure-switching aptamers with attenuated affinity and/or utilize reporters that require aptamer labeling or which are susceptible to false positives. Dye-displacement assays offer a label-free, sensitive means for overcoming these issues, wherein target binding liberates a dye that is complexed with the aptamer, producing an optical readout. However, broad utilization of these assays has been limited. Here, we demonstrate a rational approach to develop colorimetric cyanine dye-displacement assays that can be broadly applied to DNA aptamers regardless of their structure, sequence, affinity, or the physicochemical properties of their targets. Our approach should accelerate the development of mix-and-measure assays that could be applied for diverse analytical applications.
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Affiliation(s)
- Obtin Alkhamis
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA.,Department of Chemistry, North Carolina State University, 2620 Yarbrough Dr., Raleigh, NC, 27695, USA
| | - Juan Canoura
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA.,Department of Chemistry, North Carolina State University, 2620 Yarbrough Dr., Raleigh, NC, 27695, USA
| | - Konstantin V Bukhryakov
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Anamary Tarifa
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Anthony P DeCaprio
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Yi Xiao
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA.,Department of Chemistry, North Carolina State University, 2620 Yarbrough Dr., Raleigh, NC, 27695, USA
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28
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Zhang F, Liu J. Interactions of the Cocaine and Quinine Aptamer with Gold Nanoparticles under the Dilute Biosensor and Concentrated NMR Conditions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:11939-11947. [PMID: 34591480 DOI: 10.1021/acs.langmuir.1c02239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The cocaine aptamer was later found to bind quinine with an even higher affinity. In this work, we used a fluorescently labeled aptamer named MN4 to study its adsorption by gold nanoparticles (AuNPs), and the subsequent displacement by the nonlabeled aptamer and by quinine. Without washing, 14% of the preadsorbed MN4 strands were displaced by 4000-fold excess of free MN4, whereas no displacement was observed after washing, suggesting that washing removed weakly adsorbed aptamers. In a previous paper, rapid exchange was observed with NMR by directly mixing AuNPs and concentrated MN4, and our work has unified the dilute and concentrated aptamer conditions. The difference is attributable to the conformation of the adsorbed aptamer, where dilute aptamers are adsorbed in a collapsed state with a much higher affinity to AuNPs. In addition, the preadsorbed MN4 aptamer cannot be desorbed by adding quinine, indicating that direct desorption-based fluorescent sensors cannot be made. Finally, based on the similar color responses to both the aptamer and its nonbinding mutants, the label-free colorimetric detection method cannot be directly applied for the detection of quinine. This work indicated that different experimental conditions need to be carefully compared to have a unified understanding of aptamer/AuNP systems.
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Affiliation(s)
- Fang Zhang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, People's Republic of China
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada
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29
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Comparison of Duplex and Quadruplex Folding Structure Adenosine Aptamers for Carbon Nanotube Field Effect Transistor Aptasensors. NANOMATERIALS 2021; 11:nano11092280. [PMID: 34578596 PMCID: PMC8468449 DOI: 10.3390/nano11092280] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/25/2021] [Accepted: 08/30/2021] [Indexed: 12/24/2022]
Abstract
Carbon nanotube field effect transistor (CNT FET) aptasensors have been investigated for the detection of adenosine using two different aptamer sequences, a 35-mer and a 27-mer. We found limits of detection for adenosine of 100 pM and 320 nM for the 35-mer and 27-mer aptamers, with dissociation constants of 1.2 nM and 160 nM, respectively. Upon analyte recognition the 35-mer adenosine aptamer adopts a compact G-quadruplex structure while the 27-mer adenosine aptamer changes to a folded duplex. Using the CNT FET aptasensor platform adenosine could be detected with high sensitivity over the range of 100 pM to 10 µM, highlighting the suitability of the CNT FET aptasensor platform for high performance adenosine detection. The aptamer restructuring format is critical for high sensitivity with the G-quadraplex aptasensor having a 130-fold smaller dissociation constant than the duplex forming aptasensor.
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Pavase TR, Lin H, Soomro MA, Zheng H, Li X, Wang K, Li Z. Visual detection of tropomyosin, a major shrimp allergenic protein using gold nanoparticles (AuNPs)-assisted colorimetric aptasensor. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:382-394. [PMID: 37073291 PMCID: PMC10077205 DOI: 10.1007/s42995-020-00085-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 11/05/2020] [Indexed: 05/03/2023]
Abstract
A gold nanoparticle-based label-free colorimetric assay was developed to detect the shrimp allergenic protein tropomyosin (TM), an important biomarker responsible for severe clinical reactivity to shellfish. In a gold nanoparticles (AuNPs)-tropomyosin-binding aptamer (TMBA) complex, the aptamer adsorbs onto the surface of AuNPs and dissociates in the presence of TM. In addition, AuNPs tend to aggregate in the presence of ionic salt, revealing a color change (i.e., wine-red to purple/blue) with a shift in the maximum absorption peak from 520 nm. In the presence of specific binding TM, the aptamer folds into a tertiary structure where it more efficiently stabilizes AuNPs toward the salt-induced aggregation with a hypsochromic shift in the absorption spectra compared to the stabilized AuNPs by aptamer alone. Based on the aggregation and sensitive spectral transformation principle, the AuNPs-based colorimetric aptasensor was successfully applied to detect TM with a range of 10-200 nmol/L and a low detection limit of 40 nmol/L in water samples. The reliability, selectivity, and sensitivity of the aptasensor was then tested with food samples spiked with TM. The observed detection limit was as low as 70 nmol/L in shrimp, 90 nmol/L in tofu, and 80 nmol/L in eggs, respectively. We anticipate the proposed AuNPs-based colorimetric aptasensor assay possesses a high potential for the easy and efficient visual colorimetric detection of TM. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-020-00085-5.
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Affiliation(s)
- Tushar Ramesh Pavase
- Food Safety Laboratory, Department of Food Science and Engineering, College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
| | - Hong Lin
- Food Safety Laboratory, Department of Food Science and Engineering, College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
| | - Maqsood Ahmed Soomro
- Fish Molecular Immunology Laboratory, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
| | - Hongwei Zheng
- Food Safety Laboratory, Department of Food Science and Engineering, College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
| | - Xiaxia Li
- Food Safety Laboratory, Department of Food Science and Engineering, College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
| | - Kexin Wang
- Food Safety Laboratory, Department of Food Science and Engineering, College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
| | - Zhenxing Li
- Food Safety Laboratory, Department of Food Science and Engineering, College of Food Science and Engineering, Ocean University of China, Qingdao, 266003 China
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Martin DR, Sibuyi NR, Dube P, Fadaka AO, Cloete R, Onani M, Madiehe AM, Meyer M. Aptamer-Based Diagnostic Systems for the Rapid Screening of TB at the Point-of-Care. Diagnostics (Basel) 2021; 11:1352. [PMID: 34441287 PMCID: PMC8391981 DOI: 10.3390/diagnostics11081352] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/07/2021] [Accepted: 07/12/2021] [Indexed: 12/17/2022] Open
Abstract
The transmission of Tuberculosis (TB) is very rapid and the burden it places on health care systems is felt globally. The effective management and prevention of this disease requires that it is detected early. Current TB diagnostic approaches, such as the culture, sputum smear, skin tuberculin, and molecular tests are time-consuming, and some are unaffordable for low-income countries. Rapid tests for disease biomarker detection are mostly based on immunological assays that use antibodies which are costly to produce, have low sensitivity and stability. Aptamers can replace antibodies in these diagnostic tests for the development of new rapid tests that are more cost effective; more stable at high temperatures and therefore have a better shelf life; do not have batch-to-batch variations, and thus more consistently bind to a specific target with similar or higher specificity and selectivity and are therefore more reliable. Advancements in TB research, in particular the application of proteomics to identify TB specific biomarkers, led to the identification of a number of biomarker proteins, that can be used to develop aptamer-based diagnostic assays able to screen individuals at the point-of-care (POC) more efficiently in resource-limited settings.
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Affiliation(s)
- Darius Riziki Martin
- DSI/Mintek Nanotechnology Innovation Centre-Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (D.R.M.); (N.R.S.); (P.D.); (A.O.F.); (A.M.M.)
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa;
| | - Nicole Remaliah Sibuyi
- DSI/Mintek Nanotechnology Innovation Centre-Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (D.R.M.); (N.R.S.); (P.D.); (A.O.F.); (A.M.M.)
| | - Phumuzile Dube
- DSI/Mintek Nanotechnology Innovation Centre-Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (D.R.M.); (N.R.S.); (P.D.); (A.O.F.); (A.M.M.)
| | - Adewale Oluwaseun Fadaka
- DSI/Mintek Nanotechnology Innovation Centre-Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (D.R.M.); (N.R.S.); (P.D.); (A.O.F.); (A.M.M.)
| | - Ruben Cloete
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa;
| | - Martin Onani
- Department of Chemistry, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa;
| | - Abram Madimabe Madiehe
- DSI/Mintek Nanotechnology Innovation Centre-Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (D.R.M.); (N.R.S.); (P.D.); (A.O.F.); (A.M.M.)
| | - Mervin Meyer
- DSI/Mintek Nanotechnology Innovation Centre-Biolabels Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa; (D.R.M.); (N.R.S.); (P.D.); (A.O.F.); (A.M.M.)
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Yu H, Alkhamis O, Canoura J, Liu Y, Xiao Y. Advances and Challenges in Small‐Molecule DNA Aptamer Isolation, Characterization, and Sensor Development. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202008663] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Haixiang Yu
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Obtin Alkhamis
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Juan Canoura
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Yingzhu Liu
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Yi Xiao
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
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Yu H, Alkhamis O, Canoura J, Liu Y, Xiao Y. Advances and Challenges in Small-Molecule DNA Aptamer Isolation, Characterization, and Sensor Development. Angew Chem Int Ed Engl 2021; 60:16800-16823. [PMID: 33559947 PMCID: PMC8292151 DOI: 10.1002/anie.202008663] [Citation(s) in RCA: 156] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 11/16/2021] [Indexed: 12/12/2022]
Abstract
Aptamers are short oligonucleotides isolated in vitro from randomized libraries that can bind to specific molecules with high affinity, and offer a number of advantages relative to antibodies as biorecognition elements in biosensors. However, it remains difficult and labor-intensive to develop aptamer-based sensors for small-molecule detection. Here, we review the challenges and advances in the isolation and characterization of small-molecule-binding DNA aptamers and their use in sensors. First, we discuss in vitro methodologies for the isolation of aptamers, and provide guidance on selecting the appropriate strategy for generating aptamers with optimal binding properties for a given application. We next examine techniques for characterizing aptamer-target binding and structure. Afterwards, we discuss various small-molecule sensing platforms based on original or engineered aptamers, and their detection applications. Finally, we conclude with a general workflow to develop aptamer-based small-molecule sensors for real-world applications.
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Affiliation(s)
- Haixiang Yu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Obtin Alkhamis
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Juan Canoura
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Yingzhu Liu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Yi Xiao
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
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Lee ES, Kim EJ, Park TK, Bae DW, Cha SS, Kim TW, Kim YP. Gold nanoparticle-assisted SELEX as a visual monitoring platform for the development of small molecule-binding DNA aptasensors. Biosens Bioelectron 2021; 191:113468. [PMID: 34233257 DOI: 10.1016/j.bios.2021.113468] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/09/2021] [Accepted: 06/26/2021] [Indexed: 02/07/2023]
Abstract
To resolve time-consuming and imperceptible monitoring problems in the traditional systematic evolution of ligands by exponential enrichment (SELEX), we report gold nanoparticle-assisted SELEX (GNP-SELEX) as a visual, proofreading, and self-monitoring platform and its application to small molecule-binding single-stranded DNA (ssDNA) aptasensors. Through the colorimetric changes between rounds, GNP-SELEX enabled the rapid determination of target-specific aptamer library enrichment with neither target modification nor extra monitoring process. We identified ssDNA aptamers with high selectivity and binding affinity by targeting two small molecules (brassinolide; BL and bisphenol A; BPA) as a model. The rational design of selected aptamers by 3D molecular simulation increased their ability to detect BL or BPA in real samples as bioreceptors. These results suggest that GNP-SELEX is useful as a self-monitoring platform to discover ssDNA aptamers as well as to develop aptasensors for diverse targets in a rapid and simple way.
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Affiliation(s)
- Eun-Song Lee
- Department of Life Science, Hanyang University, Seoul, 04763, Republic of Korea; Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, Republic of Korea
| | - Eun-Ji Kim
- Department of Life Science, Hanyang University, Seoul, 04763, Republic of Korea
| | - Tae-Ki Park
- Department of Life Science, Hanyang University, Seoul, 04763, Republic of Korea
| | - Da-Woon Bae
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Sun-Shin Cha
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Tae-Wuk Kim
- Department of Life Science, Hanyang University, Seoul, 04763, Republic of Korea; Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, Republic of Korea; Research Institute for Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea.
| | - Young-Pil Kim
- Department of Life Science, Hanyang University, Seoul, 04763, Republic of Korea; Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, Republic of Korea; Research Institute for Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea; Department of HY-KIST Bio-Convergence, Hanyang University, Seoul, 04763, Republic of Korea.
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Hou Y, Zhu L, Hao H, Zhang Z, Ding C, Zhang G, Bi J, Yan S, Liu G, Hou H. A novel photoelectrochemical aptamer sensor based on rare-earth doped Bi2WO6 and Ag2S for the rapid detection of Vibrio parahaemolyticus. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106132] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Li Y, Liu J. Aptamer-based strategies for recognizing adenine, adenosine, ATP and related compounds. Analyst 2021; 145:6753-6768. [PMID: 32909556 DOI: 10.1039/d0an00886a] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Adenine is a key nucleobase, adenosine is an endogenous regulator of the immune system, while adenosine triphosphate (ATP) is the energy source of many biological reactions. Selective detection of these molecules is useful for understanding biological processes, biochemical reactions and signaling. Since 1993, various aptamers have been reported to bind to adenine and its derivatives. In addition, the adenine riboswitch was later discovered. This review summarizes the efforts for the selection of RNA and DNA aptamers for adenine derivatives, and we pay particular attention to the specificity of binding. In addition, other molecular recognition strategies based on rational sequence design are also introduced. Most of the work in the field was performed on the classic DNA aptamer for adenosine and ATP reported by the Szostak group. Based on this aptamer, some representative applications such as the design of fluorescent, colorimetric and electrochemical biosensors, intracellular imaging, and ATP-responsive materials are also described. In addition, we critically review the limit of the reported aptamers and also important problems in the field, which can give future research opportunities.
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Affiliation(s)
- Yuqing Li
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
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Billet B, Chovelon B, Fiore E, Oukacine F, Petrillo MA, Faure P, Ravelet C, Peyrin E. Aptamer Switches Regulated by Post-Transition/Transition Metal Ions. Angew Chem Int Ed Engl 2021; 60:12346-12350. [PMID: 33742515 DOI: 10.1002/anie.202102254] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Indexed: 12/11/2022]
Abstract
We introduced an aptamer switch design that relies on the ability of post-transition/transition metal ions to trigger, through their coordination to nucleobases, substantial DNA destabilization. In the absence of molecular target, the addition of one such metal ion to usual aptamer working solutions promotes the formation of an alternative, inert DNA state. Upon exposure to the cognate compound, the equilibrium is shifted towards the competent DNA form. The switching process was preferentially activated by metal ions of intermediate base over phosphate complexation preference (i.e. Pb2+ , Cd2+ ) and operated with diversely structured DNA molecules. This very simple aptamer switch scheme was applied to the detection of small organics using the fluorescence anisotropy readout mode. We envision that the approach could be adapted to a variety of signalling methods that report on changes in the surface charge density of DNA receptors.
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Affiliation(s)
- Blandine Billet
- DPM UMR 5063, University Grenoble Alpes, CNRS, 38041, Grenoble, France.,Biochemistry, Toxicology and Pharmacology Department, Grenoble site Nord CHU- Biology and Pathology Institute, 38041, Grenoble, France
| | - Benoit Chovelon
- DPM UMR 5063, University Grenoble Alpes, CNRS, 38041, Grenoble, France.,Biochemistry, Toxicology and Pharmacology Department, Grenoble site Nord CHU- Biology and Pathology Institute, 38041, Grenoble, France
| | - Emmanuelle Fiore
- DPM UMR 5063, University Grenoble Alpes, CNRS, 38041, Grenoble, France
| | - Farid Oukacine
- DPM UMR 5063, University Grenoble Alpes, CNRS, 38041, Grenoble, France
| | | | - Patrice Faure
- DPM UMR 5063, University Grenoble Alpes, CNRS, 38041, Grenoble, France.,Biochemistry, Toxicology and Pharmacology Department, Grenoble site Nord CHU- Biology and Pathology Institute, 38041, Grenoble, France
| | - Corinne Ravelet
- DPM UMR 5063, University Grenoble Alpes, CNRS, 38041, Grenoble, France
| | - Eric Peyrin
- DPM UMR 5063, University Grenoble Alpes, CNRS, 38041, Grenoble, France
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Billet B, Chovelon B, Fiore E, Oukacine F, Petrillo M, Faure P, Ravelet C, Peyrin E. Aptamer Switches Regulated by Post‐Transition/Transition Metal Ions. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Blandine Billet
- DPM UMR 5063 University Grenoble Alpes CNRS 38041 Grenoble France
- Biochemistry, Toxicology and Pharmacology Department Grenoble site Nord CHU- Biology and Pathology Institute 38041 Grenoble France
| | - Benoit Chovelon
- DPM UMR 5063 University Grenoble Alpes CNRS 38041 Grenoble France
- Biochemistry, Toxicology and Pharmacology Department Grenoble site Nord CHU- Biology and Pathology Institute 38041 Grenoble France
| | - Emmanuelle Fiore
- DPM UMR 5063 University Grenoble Alpes CNRS 38041 Grenoble France
| | - Farid Oukacine
- DPM UMR 5063 University Grenoble Alpes CNRS 38041 Grenoble France
| | | | - Patrice Faure
- DPM UMR 5063 University Grenoble Alpes CNRS 38041 Grenoble France
- Biochemistry, Toxicology and Pharmacology Department Grenoble site Nord CHU- Biology and Pathology Institute 38041 Grenoble France
| | - Corinne Ravelet
- DPM UMR 5063 University Grenoble Alpes CNRS 38041 Grenoble France
| | - Eric Peyrin
- DPM UMR 5063 University Grenoble Alpes CNRS 38041 Grenoble France
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Lu C, Saint-Pierre C, Gasparutto D, Roupioz Y, Ravelet C, Peyrin E, Buhot A. Melting Curve Analysis of Aptachains: Adenosine Detection with Internal Calibration. BIOSENSORS 2021; 11:112. [PMID: 33917864 PMCID: PMC8068264 DOI: 10.3390/bios11040112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/22/2021] [Accepted: 04/06/2021] [Indexed: 12/14/2022]
Abstract
Small molecules are ubiquitous in nature and their detection is relevant in various domains. However, due to their size, sensitive and selective probes are difficult to select and the detection methods are generally indirect. In this study, we introduced the use of melting curve analysis of aptachains based on split-aptamers for the detection of adenosine. Aptamers, short oligonucleotides, are known to be particularly efficient probes compared to antibodies thanks to their advantageous probe/target size ratio. Aptachains are formed from dimers with dangling ends followed by the split-aptamer binding triggered by the presence of the target. The high melting temperature of the dimers served as a calibration for the detection/quantification of the target based on the height and/or temperature shift of the aptachain melting peak.
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Affiliation(s)
- Chenze Lu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China;
- University Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, F-38000 Grenoble, France; (C.S.-P.); (D.G.); (Y.R.)
- University Grenoble Alpes, CNRS, DPM, F-38000 Grenoble, France; (C.R.); (E.P.)
| | - Christine Saint-Pierre
- University Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, F-38000 Grenoble, France; (C.S.-P.); (D.G.); (Y.R.)
| | - Didier Gasparutto
- University Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, F-38000 Grenoble, France; (C.S.-P.); (D.G.); (Y.R.)
| | - Yoann Roupioz
- University Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, F-38000 Grenoble, France; (C.S.-P.); (D.G.); (Y.R.)
| | - Corinne Ravelet
- University Grenoble Alpes, CNRS, DPM, F-38000 Grenoble, France; (C.R.); (E.P.)
| | - Eric Peyrin
- University Grenoble Alpes, CNRS, DPM, F-38000 Grenoble, France; (C.R.); (E.P.)
| | - Arnaud Buhot
- University Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, F-38000 Grenoble, France; (C.S.-P.); (D.G.); (Y.R.)
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Niu C, Wang C, Li F, Zheng X, Xing X, Zhang C. Aptamer assisted CRISPR-Cas12a strategy for small molecule diagnostics. Biosens Bioelectron 2021; 183:113196. [PMID: 33839534 DOI: 10.1016/j.bios.2021.113196] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 01/03/2021] [Accepted: 03/20/2021] [Indexed: 12/26/2022]
Abstract
Molecular diagnostics are vital for the identification, prevention, and treatment of numerous diseases and are of particular demand in point-of-care (POC) settings. Nevertheless, most reported biosensors based on the CRISPR-Cas system have focused on nucleic-acid targets. Here, we report a versatile diagnostic strategy for small molecules called Molecular Radar (Random Molecular Aptamer-Dependent CRISPR-Assist Reporter), The workflow is simple, convenient, and rapid (conducted at 37 °C in under 25 min), indicating the substantial potential of the proposed assay could be adapted into a biosensor for POC settings and on-site molecular diagnostics. This strategy is based on the CRISPR Cas12a-assisted fluorescence reporter system that consists of Cas12a, CRISPR RNA (crRNA), a single-stranded DNA (ssDNA) probe labeled with a fluorophore at the 5' end and a quencher at the 3' end (F-Q probe), and a single-stranded DNA aptamer for the target molecule. In the presence of a target molecule, the aptamer binds to this small molecule with high specificity and affinity, resulting in a decrease of aptamer hybridized to the crRNA-Cas12a duplex. This decrease in activated Cas12a leads to a significant reduction in fluorescence signal. In this study, adenosine-5'-triphosphate (ATP) was selected as model target molecule and an ATP detect method was developed with high specificity and sensitivity with a linear range from 25 to 500 μM and a detection limit of 104 nM. Moreover, the particular characteristics of CRISPR-Cas12a that we report here for the first time have enriched our understanding of Cas12a and provided guidance for further research on CRISPR-Cas12a-based biosensors.
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Affiliation(s)
- Chenqi Niu
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Chuyi Wang
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Fan Li
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Xiang Zheng
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Xinhui Xing
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Chong Zhang
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China.
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Wang XN, Zhao Y, Li JL, Pang JD, Wang Q, Li B, Zhou HC. Biomimetic catalysts of iron-based metal-organic frameworks with high peroxidase-mimicking activity for colorimetric biosensing. Dalton Trans 2021; 50:3854-3861. [PMID: 33656021 DOI: 10.1039/d0dt02504f] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The field of metal-organic framework (MOF)-based biomimetic catalysts has achieved great progress but is still in its infancy. The systematic investigation of the tailored construction of MOF-based biomimetic catalysts is required for further development. Herein, two iron-based MOFs, namely, [(Fe3O)2(H2O)4(HCOO)(L)2]n (HUST-5: H6L = hexakis(4-formylphenoxy) cyclotriphosphazene; HUST = Huazhong University of Science and Technology) and [(Fe3O)(H2O)3(L)]n (HUST-7) have been fabricated through the assembly of different iron clusters and hexa-carboxylate ligand under the control of the added acid species. The two MOFs exhibit distinct secondary building units (SBUs) and topological structures, which could be used as biomimetic catalysts for the systematic comparisons of structural characteristics and the catalytic activity. Both MOFs possess catalytic activity similar to that of natural peroxidases towards the catalysis of the oxidation of a variety of substrates. Significantly, HUST-5 and HUST-7 can effectively catalyze the oxidation of 3,3',5,5'-tetramethylbenzidine (TMB) by H2O2 accompanied by significant colorimetric biosensing. With same compositions, different catalytic performances were obtained due to differences in the porous structures and characteristics of SBUs in two Fe-MOFs, which was also validated by theoretical calculation results. Furthermore, the phenomenon of colorimetric biosensing could be significantly suppressed by the addition of ascorbic acid (AA) during the oxidation process of TMB. It was observed from these findings that a facile colorimetric biosensing platform for detecting H2O2 and ascorbic acid has been successfully explored. Therefore, this work provides another unique perspective for the tailor-made preparation of stable MOF-based peroxidase mimics with excellent catalytic performance and colorimetric biosensing.
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Affiliation(s)
- Xiao-Ning Wang
- Hubei Key Laboratory of Biomass Fibers and Eco-dyeing & Finishing, College of Chemistry and Chemical Engineering, Wuhan Textile University, Wuhan, Hubei 430073, PR China
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Wu R, Wang Y, Zhu Z, Yu C, Li H, Li B, Dong S. Low-Noise Solid-State Nanopore Enhancing Direct Label-Free Analysis for Small Dimensional Assemblies Induced by Specific Molecular Binding. ACS APPLIED MATERIALS & INTERFACES 2021; 13:9482-9490. [PMID: 33476120 DOI: 10.1021/acsami.0c20359] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Solid-state nanopores show special potential as a new single-molecular characterization for nucleic acid assemblies and molecular machines. However, direct recognition of small dimensional species is still quite difficult due the lower resolution compared with biological pores. We recently reported a very efficient noise-reduction and resolution-enhancement mechanism via introducing high-dielectric additives (e.g., formamide) into conical glass nanopore (CGN) test buffer. Based on this advance, here, for the first time, we apply a bare CGN to directly recognize small dimensional assemblies induced by small molecules. Cocaine and its split aptamer (Capt assembly) are chosen as the model set. By introducing 20% formamide into CGN test buffer, high cocaine-specific distinguishing of the 113 nt Capt assembly has been realized without any covalent label or additional signaling strategies. The signal-to-background discrimination is much enhanced compared with control characterizations such as gel electrophoresis and fluorescence resonance energy transfer (FRET). As a further innovation, we verify that low-noise CGN can also enhance the resolution of small conformational/size changes happening on the side chain of large dimensional substrates. Long duplex concatamers generated from the hybridization chain reaction (HCR) are selected as the model substrates. In the presence of cocaine, low-noise CGN has sensitively captured the current changes when the 26 nt aptamer segment is assembled on the side chain of HCR duplexes. This paper proves that the introduction of the low-noise mechanism has significantly improved the resolution of the solid-state nanopore at smaller and finer scales and thus may direct extensive and deeper research in the field of CGN-based analysis at both single-molecular and statistical levels, such as molecular recognition, assembly characterization, structure identification, information storage, and target index.
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Affiliation(s)
- Ruiping Wu
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Yesheng Wang
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Zhentong Zhu
- College of Chemistry & Chemical Engineering, Northwest Normal University, Lanzhou, Gansu 730070, P. R. China
| | - Chunmiao Yu
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Huan Li
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Bingling Li
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Shaojun Dong
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
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Yang H, Hu P, Tang J, Cheng Y, Wang F, Chen Z. A bifunctional electrochemical aptasensor based on AuNPs-coated ERGO nanosheets for sensitive detection of adenosine and thrombin. J Solid State Electrochem 2021. [DOI: 10.1007/s10008-021-04916-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Mao L, Wang Q, Luo Y, Gao Y. Detection of Ag + ions via an anti-aggregation mechanism using unmodified gold nanoparticles in the presence of thiamazole. Talanta 2021; 222:121506. [PMID: 33167219 DOI: 10.1016/j.talanta.2020.121506] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 08/02/2020] [Accepted: 08/03/2020] [Indexed: 12/01/2022]
Abstract
The present study proposed a novel and highly selective and sensitive method for Ag+ ion detection based on gold nanoparticles (AuNPs) anti-aggregation. Thiamazole can induce AuNPs aggregation due to electrostatic interactions, which result in color transitions in the AuNPs solution from red to blue. However, the presence of Ag+ ions results in the preferential combination of the pyridinic nitrogen of thiamazole with the Ag+ ions. In addition, the Ag+ ions oxidize the sulfhydryl groups(-SH), which inhibit AuNPs aggregation and prompt a color change from blue to red. As a result, the present study established a method for Ag+ ion determination by AuNPs-thiamazole colorimetric probe based on the aforementioned anti-aggregation mechanism. The probe dynamic range was easily tuned via adjustments of the thiamazole amount. The relationship between the Ag+ concentration and AuNPs aggregation was monitored by ultraviolet-visible light (UV-Vis) spectroscopy at a dynamic range of 0.1 nM-9 μM and at a detection limit of 0.042 nM. The river water and tap water recovery analysis validated the successful operation of this colorimetric sensor in environmental monitoring.
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Affiliation(s)
- Lihui Mao
- College of Science and Technology, Xinyang College, Xinyang, 464000, China.
| | - Qianqian Wang
- College of Science and Technology, Xinyang College, Xinyang, 464000, China
| | - Yuhao Luo
- College of Science and Technology, Xinyang College, Xinyang, 464000, China
| | - Yongping Gao
- College of Science and Technology, Xinyang College, Xinyang, 464000, China
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Abstract
Optical sensors are always fascinating for chemists due to their selectivity, sensitivity, robustness and cost-effective nature.
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Affiliation(s)
- Hafiz Muhammad Junaid
- Institute of Chemistry
- University of the Punjab
- Quaid-e-Azam Campus
- Lahore 54590
- Pakistan
| | - Amber Rehana Solangi
- National Centre of Excellence in Analytical Chemistry
- University of Sindh
- Jamshoro
- Pakistan
| | - Madeeha Batool
- Institute of Chemistry
- University of the Punjab
- Quaid-e-Azam Campus
- Lahore 54590
- Pakistan
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46
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Logic Gates Based on DNA Aptamers. Pharmaceuticals (Basel) 2020; 13:ph13110417. [PMID: 33238657 PMCID: PMC7700249 DOI: 10.3390/ph13110417] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/19/2020] [Accepted: 11/20/2020] [Indexed: 02/08/2023] Open
Abstract
DNA bio-computing is an emerging trend in modern science that is based on interactions among biomolecules. Special types of DNAs are aptamers that are capable of selectively forming complexes with target compounds. This review is devoted to a discussion of logic gates based on aptamers for the purposes of medicine and analytical chemistry. The review considers different approaches to the creation of logic gates and identifies the general algorithms of their creation, as well as describes the methods of obtaining an output signal which can be divided into optical and electrochemical. Aptameric logic gates based on DNA origami and DNA nanorobots are also shown. The information presented in this article can be useful when creating new logic gates using existing aptamers and aptamers that will be selected in the future.
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Abstract
Further complications associated with infection by severe acute respiratory syndrome coronavirus 2 (a.k.a. SARS-CoV-2) continue to be reported. Very recent findings reveal that 20-30% of patients at high risk of mortality from COVID-19 infection experience blood clotting that leads to stroke and sudden death. Timely assessment of the severity of blood clotting will be of enormous help to clinicians in determining the right blood-thinning medications to prevent stroke or other life-threatening consequences. Therefore, rapid identification of blood-clotting-related proteins in the plasma of COVID-19 patients would save many lives. Several nanotechnology-based approaches are being developed to diagnose patients at high risk of death due to complications from COVID-19 infections, including blood clots. This Perspective outlines (i) the significant potential of nanomedicine in assessing the risk of blood clotting and its severity in SARS-CoV-2 infected patients and (ii) its synergistic roles with advanced mass-spectrometry-based proteomics approaches in identifying the important protein patterns that are involved in the occurrence and progression of this disease. The combination of such powerful tools might help us understand the clotting phenomenon and pave the way for development of new diagnostics and therapeutics in the fight against COVID-19.
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Affiliation(s)
- Amir Ata Saei
- Division
of Physiological Chemistry I, Department of Medical Biochemistry and
Biophysics, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Shahriar Sharifi
- Precision
Health Program and Department of Radiology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Morteza Mahmoudi
- Precision
Health Program and Department of Radiology, Michigan State University, East Lansing, Michigan 48824, United States
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Thermodynamic analysis of cooperative ligand binding by the ATP-binding DNA aptamer indicates a population-shift binding mechanism. Sci Rep 2020; 10:18944. [PMID: 33144644 PMCID: PMC7609719 DOI: 10.1038/s41598-020-76002-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 10/22/2020] [Indexed: 01/27/2023] Open
Abstract
The ATP-binding DNA aptamer is often used as a model system for developing new aptamer-based biosensor methods. This aptamer follows a structure-switching binding mechanism and is unusual in that it binds two copies of its ligand. We have used isothermal titration calorimetry methods to study the binding of ATP, ADP, AMP and adenosine to the ATP-binding aptamer. Using both individual and global fitting methods, we show that this aptamer follows a positive cooperative binding mechanism. We have determined the binding affinity and thermodynamics for both ligand-binding sites. By separating the ligand-binding sites by an additional four base pairs, we engineered a variant of this aptamer that binds two adenosine ligands in an independent manner. Together with NMR and thermal stability experiments, these data indicate that the ATP-binding DNA aptamer follows a population-shift binding mechanism that is the source of the positive binding cooperativity by the aptamer.
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Zhou J, Li Y, Wang W, Lu Z, Han H, Liu J. Kanamycin Adsorption on Gold Nanoparticles Dominates Its Label-Free Colorimetric Sensing with Its Aptamer. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:11490-11498. [PMID: 32907335 DOI: 10.1021/acs.langmuir.0c01786] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A short kanamycin-binding aptamer has been widely used for detecting kanamycin. One of the popular signaling methods is based on the color change of gold nanoparticles (AuNPs) to develop label-free colorimetric biosensors. The general perception was that aptamer binding to its target would inhibit aptamer adsorption by the AuNPs. This inhibited adsorption results in the aggregation of the AuNPs and a color change upon addition of salt. However, the potential adsorption of kanamycin was ignored. Herein, we carefully studied the adsorption of kanamycin on AuNPs and performed a comprehensive analysis using two mutated aptamers and a randomly sequenced DNA which were not supposed to bind kanamycin. In addition, a total of six antibiotics were studied over a wide concentration range. As low as 90 nM kanamycin can induce the aggregation of 3 nM citrate-capped AuNPs, indicating very strong adsorption of kanamycin. The color change was independent of DNA sequence, and all the tested sequences showed a similar color response, regardless of aptamer. Among the different antibiotics, kanamycin and streptomycin induced a color change but not the other four. Our results support an alternative mechanism that kanamycin and streptomycin adsorption by the AuNPs was the main reason for the color change instead of aptamer binding.
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Affiliation(s)
- Jiaojiao Zhou
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Yuqing Li
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | | | | | | | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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Ahmed SR, Chand R, Kumar S, Mittal N, Srinivasan S, Rajabzadeh AR. Recent biosensing advances in the rapid detection of illicit drugs. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.116006] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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