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P U A, Raj G, John J, Mohan K M, John F, George J. Aptamers: Features, Synthesis and Applications. Chem Biodivers 2023; 20:e202301008. [PMID: 37709723 DOI: 10.1002/cbdv.202301008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/11/2023] [Accepted: 09/14/2023] [Indexed: 09/16/2023]
Abstract
Aptamers have become a topic of interest among the researchers and scientists since they not only possess all of the benefits of antibodies but also possess special qualities including heat stability, low cost, and limitless uses⋅ Here we give a review about the features, applications, and challenges of aptamers and also how they are beneficial over the antibodies for biomedical applications. Their unique features make aptamers a prominent tool in therapeutics, diagnostics, biosensors and targeted drug delivery. In conclusion, aptamers represent exciting materials for a variety of applications and can be modified to improve their properties and to extend their applications in biomedical field.
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Affiliation(s)
- Aiswarya P U
- Bio-organic Laboratory, Department of Chemistry, Sacred Heart College, Kochi, 682013, India
| | - Gopika Raj
- Bio-organic Laboratory, Department of Chemistry, Sacred Heart College, Kochi, 682013, India
| | - Jinju John
- Bio-organic Laboratory, Department of Chemistry, Sacred Heart College, Kochi, 682013, India
| | - Malavika Mohan K
- Bio-organic Laboratory, Department of Chemistry, Sacred Heart College, Kochi, 682013, India
| | - Franklin John
- Bio-organic Laboratory, Department of Chemistry, Sacred Heart College, Kochi, 682013, India
| | - Jinu George
- Bio-organic Laboratory, Department of Chemistry, Sacred Heart College, Kochi, 682013, India
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2
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Bekkouche I, Kuznetsova MN, Rejepov DT, Vetcher AA, Shishonin AY. Recent Advances in DNA Nanomaterials. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:2449. [PMID: 37686956 PMCID: PMC10490369 DOI: 10.3390/nano13172449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023]
Abstract
Applications of DNA-containing nanomaterials (DNA-NMs) in science and technology are currently attracting increasing attention in the fields of medicine, environment, engineering, etc. Such objects have become important for various branches of science and industries due to their outstanding characteristics such as small size, high controllability, clustering actions, and strong permeability. For these reasons, DNA-NMs deserve a review with respect to their recent advancements. On the other hand, precise cluster control, targeted drug distribution in vivo, and cellular micro-nano operation remain as problems. This review summarizes the recent progress in DNA-NMs and their crossover and integration into multiple disciplines (including in vivo/in vitro, microcircles excisions, and plasmid oligomers). We hope that this review will motivate relevant practitioners to generate new research perspectives and boost the advancement of nanomanipulation.
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Affiliation(s)
- Incherah Bekkouche
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia n.a. P. Lumumba (RUDN), Miklukho-Maklaya St. 6, Moscow 117198, Russia; (M.N.K.); (D.T.R.)
| | - Maria N. Kuznetsova
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia n.a. P. Lumumba (RUDN), Miklukho-Maklaya St. 6, Moscow 117198, Russia; (M.N.K.); (D.T.R.)
| | - Dovlet T. Rejepov
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia n.a. P. Lumumba (RUDN), Miklukho-Maklaya St. 6, Moscow 117198, Russia; (M.N.K.); (D.T.R.)
| | - Alexandre A. Vetcher
- Nanotechnology Scientific and Educational Center, Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia n.a. P. Lumumba (RUDN), Miklukho-Maklaya St. 6, Moscow 117198, Russia; (M.N.K.); (D.T.R.)
- Complementary and Integrative Health Clinic of Dr. Shishonin, 5, Yasnogorskaya Str., Moscow 117588, Russia;
| | - Alexander Y. Shishonin
- Complementary and Integrative Health Clinic of Dr. Shishonin, 5, Yasnogorskaya Str., Moscow 117588, Russia;
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Yu H, Zhu J, Shen G, Deng Y, Geng X, Wang L. Improving aptamer performance: key factors and strategies. Mikrochim Acta 2023; 190:255. [PMID: 37300603 DOI: 10.1007/s00604-023-05836-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/16/2023] [Indexed: 06/12/2023]
Abstract
Aptamers are functional single-stranded oligonucleotide fragments isolated from randomized libraries by Systematic Evolution of Ligands by Exponential Enrichment (SELEX), exhibiting excellent affinity and specificity toward targets. Compared with traditional antibody reagents, aptamers display many desirable properties, such as low variation and high flexibility, and they are suitable for artificial and large-scale synthesis. These advantages make aptamers have a broad application potential ranging from biosensors, bioimaging to therapeutics and other areas of application. However, the overall performance of aptamer pre-selected by SELEX screening is far from being satisfactory. To improve aptamer performance and applicability, various post-SELEX optimization methods have been developed in the last decade. In this review, we first discuss the key factors that influence the performance or properties of aptamers, and then we summarize the key strategies of post-SELEX optimization which have been successfully used to improve aptamer performance, such as truncation, extension, mutagenesis and modification, splitting, and multivalent integration. This review shall provide a comprehensive summary and discussion of post-SELEX optimization methods developed in recent years. Moreover, by discussing the mechanism of each approach, we highlight the importance of choosing the proper method to perform post-SELEX optimization.
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Affiliation(s)
- Hong Yu
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Jiangxiong Zhu
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Guoqing Shen
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Yun Deng
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Xueqing Geng
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Lumei Wang
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China.
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China.
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China.
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Kara N, Ayoub N, Ilgu H, Fotiadis D, Ilgu M. Aptamers Targeting Membrane Proteins for Sensor and Diagnostic Applications. Molecules 2023; 28:molecules28093728. [PMID: 37175137 PMCID: PMC10180177 DOI: 10.3390/molecules28093728] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/07/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023] Open
Abstract
Many biological processes (physiological or pathological) are relevant to membrane proteins (MPs), which account for almost 30% of the total of human proteins. As such, MPs can serve as predictive molecular biomarkers for disease diagnosis and prognosis. Indeed, cell surface MPs are an important class of attractive targets of the currently prescribed therapeutic drugs and diagnostic molecules used in disease detection. The oligonucleotides known as aptamers can be selected against a particular target with high affinity and selectivity by iterative rounds of in vitro library evolution, known as Systematic Evolution of Ligands by EXponential Enrichment (SELEX). As an alternative to antibodies, aptamers offer unique features like thermal stability, low-cost, reuse, ease of chemical modification, and compatibility with various detection techniques. Particularly, immobilized-aptamer sensing platforms have been under investigation for diagnostics and have demonstrated significant value compared to other analytical techniques. These "aptasensors" can be classified into several types based on their working principle, which are commonly electrochemical, optical, or mass-sensitive. In this review, we review the studies on aptamer-based MP-sensing technologies for diagnostic applications and have included new methodological variations undertaken in recent years.
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Affiliation(s)
- Nilufer Kara
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
| | - Nooraldeen Ayoub
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
- Institute of Biochemistry and Molecular Medicine, University of Bern, CH-3012 Bern, Switzerland
| | - Huseyin Ilgu
- Institute of Biochemistry and Molecular Medicine, University of Bern, CH-3012 Bern, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern, CH-3012 Bern, Switzerland
| | - Muslum Ilgu
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA
- Aptalogic Inc., Ames, IA 50014, USA
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5
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Wang Z, Lou X. Recent Progress in Functional-Nucleic-Acid-Based Fluorescent Fiber-Optic Evanescent Wave Biosensors. BIOSENSORS 2023; 13:bios13040425. [PMID: 37185500 PMCID: PMC10135899 DOI: 10.3390/bios13040425] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/20/2023] [Accepted: 03/25/2023] [Indexed: 05/17/2023]
Abstract
Biosensors capable of onsite and continuous detection of environmental and food pollutants and biomarkers are highly desired, but only a few sensing platforms meet the "2-SAR" requirements (sensitivity, specificity, affordability, automation, rapidity, and reusability). A fiber optic evanescent wave (FOEW) sensor is an attractive type of portable device that has the advantages of high sensitivity, low cost, good reusability, and long-term stability. By utilizing functional nucleic acids (FNAs) such as aptamers, DNAzymes, and rational designed nucleic acid probes as specific recognition ligands, the FOEW sensor has been demonstrated to be a general sensing platform for the onsite and continuous detection of various targets ranging from small molecules and heavy metal ions to proteins, nucleic acids, and pathogens. In this review, we cover the progress of the fluorescent FNA-based FOEW biosensor since its first report in 1995. We focus on the chemical modification of the optical fiber and the sensing mechanisms for the five above-mentioned types of targets. The challenges and prospects on the isolation of high-quality aptamers, reagent-free detection, long-term stability under application conditions, and high throughput are also included in this review to highlight the future trends for the development of FOEW biosensors capable of onsite and continuous detection.
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Affiliation(s)
- Zheng Wang
- Department of Chemistry, Capital Normal University, Xisanhuan North Road. 105, Beijing 100048, China
| | - Xinhui Lou
- Department of Chemistry, Capital Normal University, Xisanhuan North Road. 105, Beijing 100048, China
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6
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Huang Z, Hu B, Wang H. Analytical methods for microplastics in the environment: a review. ENVIRONMENTAL CHEMISTRY LETTERS 2023; 21:383-401. [PMID: 36196263 PMCID: PMC9521859 DOI: 10.1007/s10311-022-01525-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 07/21/2022] [Indexed: 05/06/2023]
Abstract
Microplastic pollution is a recently discovered threat to ecosystems requiring the development of new analytical methods. Here, we review classical and advanced methods for microplastic analysis. Methods include visual analysis, laser diffraction particle, dynamic light scattering, scanning electron microscopy, Fourier-transform infrared spectroscopy, Raman spectroscopy, thermal analysis, mass spectrometry, aptamer and in vitro selection, and flow cytometry.
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Affiliation(s)
- Zike Huang
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083 China
| | - Bo Hu
- School of Engineering, The University of Edinburgh, Edinburgh, EH9 3JW UK
| | - Hui Wang
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083 China
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7
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3dDNA: A Computational Method of Building DNA 3D Structures. Molecules 2022; 27:molecules27185936. [PMID: 36144680 PMCID: PMC9503956 DOI: 10.3390/molecules27185936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/04/2022] [Accepted: 09/08/2022] [Indexed: 02/07/2023] Open
Abstract
Considerable progress has been made in the prediction methods of 3D structures of RNAs. In contrast, no such methods are available for DNAs. The determination of 3D structures of the latter is also increasingly needed for understanding their functions and designing new DNA molecules. Since the number of experimental structures of DNA is limited at present, here, we propose a computational and template-based method, 3dDNA, which combines DNA and RNA template libraries to predict DNA 3D structures. It was benchmarked on three test sets with different numbers of chains, and the results show that 3dDNA can predict DNA 3D structures with a mean RMSD of about 2.36 Å for those with one or two chains and fewer than 4 Å with three or more chains.
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8
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Khaksari S, Ameri AR, Taghdisi SM, Sabet M, Javad Ghaani Bami SM, Abnous K, Mousavi Shaegh SA. A microfluidic electrochemical aptasensor for highly sensitive and selective detection of A549 cells as integrin α6β4-containing cell model via IDA aptamers. Talanta 2022; 252:123781. [DOI: 10.1016/j.talanta.2022.123781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 07/19/2022] [Accepted: 07/24/2022] [Indexed: 11/30/2022]
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9
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Shabir G, Shafique I, Saeed A. Ultrasound Assisted Synthesis of 5‐7 Membered Heterocyclic Rings in Organic Molecules. J Heterocycl Chem 2022. [DOI: 10.1002/jhet.4527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ghulam Shabir
- Department of Chemistry Quaid‐I‐Azam University Islamabad Pakistan
- College of Arts and Science University of Chakwal Punjab Pakistan
| | - Imran Shafique
- Department of Chemistry Quaid‐I‐Azam University Islamabad Pakistan
| | - Aamer Saeed
- Department of Chemistry Quaid‐I‐Azam University Islamabad Pakistan
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10
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Ogurcovs A, Kadiwala K, Sledevskis E, Krasovska M, Plaksenkova I, Butanovs E. Effect of DNA Aptamer Concentration on the Conductivity of a Water-Gated Al:ZnO Thin-Film Transistor-Based Biosensor. SENSORS (BASEL, SWITZERLAND) 2022; 22:3408. [PMID: 35591098 PMCID: PMC9101190 DOI: 10.3390/s22093408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 02/01/2023]
Abstract
Field-effect transistor-based biosensors (bio-FETs) are promising candidates for the rapid high-sensitivity and high-selectivity sensing of various analytes in healthcare, clinical diagnostics, and the food industry. However, bio-FETs still have several unresolved problems that hinder their technological transfer, such as electrical stability. Therefore, it is important to develop reliable, efficient devices and establish facile electrochemical characterization methods. In this work, we have fabricated a flexible biosensor based on an Al:ZnO thin-film transistor (TFT) gated through an aqueous electrolyte on a polyimide substrate. In addition, we demonstrated techniques for establishing the operating range of such devices. The Al:ZnO-based devices with a channel length/width ratio of 12.35 and a channel thickness of 50 nm were produced at room temperature via magnetron sputtering. These Al:ZnO-based devices exhibited high field-effect mobility (μ = 6.85 cm2/Vs) and threshold voltage (Vth = 654 mV), thus showing promise for application on temperature-sensitive substrates. X-ray photoelectron spectroscopy was used to verify the chemical composition of the deposited films, while the morphological aspects of the films were assessed using scanning electron and atomic force microscopies. The gate-channel electric capacitance of 40 nF/cm2 was determined using electrochemical impedance spectroscopy, while the electrochemical window of the gate-channel system was determined as 1.8 V (from -0.6 V to +1.2 V) using cyclic voltammetry. A deionized water solution of 10 mer (CCC AAG GTC C) DNA aptamer (molar weight -2972.9 g/mol) in a concentration ranging from 1-1000 pM/μL was used as an analyte. An increase in aptamer concentration caused a proportional decrease in the TFT channel conductivity. The techniques demonstrated in this work can be applied to optimize the operating parameters of various semiconductor materials in order to create a universal detection platform for biosensing applications, such as multi-element FET sensor arrays based on various composition nanostructured films, which use advanced neural network signal processing.
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Affiliation(s)
- Andrejs Ogurcovs
- Institute of Solid State Physics, University of Latvia, Kengaraga Street 8, LV-1063 Riga, Latvia; (K.K.); (E.B.)
| | - Kevon Kadiwala
- Institute of Solid State Physics, University of Latvia, Kengaraga Street 8, LV-1063 Riga, Latvia; (K.K.); (E.B.)
| | - Eriks Sledevskis
- G. Liberts’ Innovative Microscopy Centre, Department of Technology, Institute of Life Sciences and Technology, Daugavpils University, Parades Street 1A, LV-5401 Daugavpils, Latvia; (E.S.); (M.K.)
| | - Marina Krasovska
- G. Liberts’ Innovative Microscopy Centre, Department of Technology, Institute of Life Sciences and Technology, Daugavpils University, Parades Street 1A, LV-5401 Daugavpils, Latvia; (E.S.); (M.K.)
| | - Ilona Plaksenkova
- Laboratory of Genomics and Biotechnology, Department of Biotechnology, Institute of Life Sciences and Technology, Daugavpils University, Parades Street 1A, LV-5401 Daugavpils, Latvia;
| | - Edgars Butanovs
- Institute of Solid State Physics, University of Latvia, Kengaraga Street 8, LV-1063 Riga, Latvia; (K.K.); (E.B.)
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Dutta S, Corni S, Brancolini G. Atomistic Simulations of Functionalized Nano-Materials for Biosensors Applications. Int J Mol Sci 2022; 23:1484. [PMID: 35163407 PMCID: PMC8835741 DOI: 10.3390/ijms23031484] [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: 12/15/2021] [Revised: 12/30/2021] [Accepted: 12/31/2021] [Indexed: 12/24/2022] Open
Abstract
Nanoscale biosensors, a highly promising technique in clinical analysis, can provide sensitive yet label-free detection of biomolecules. The spatial and chemical specificity of the surface coverage, the proper immobilization of the bioreceptor as well as the underlying interfacial phenomena are crucial elements for optimizing the performance of a biosensor. Due to experimental limitations at the microscopic level, integrated cross-disciplinary approaches that combine in silico design with experimental measurements have the potential to present a powerful new paradigm that tackles the issue of developing novel biosensors. In some cases, computational studies can be seen as alternative approaches to assess the microscopic working mechanisms of biosensors. Nonetheless, the complex architecture of a biosensor, associated with the collective contribution from "substrate-receptor-analyte" conjugate in a solvent, often requires extensive atomistic simulations and systems of prohibitive size which need to be addressed. In silico studies of functionalized surfaces also require ad hoc force field parameterization, as existing force fields for biomolecules are usually unable to correctly describe the biomolecule/surface interface. Thus, the computational studies in this field are limited to date. In this review, we aim to introduce fundamental principles that govern the absorption of biomolecules onto functionalized nanomaterials and to report state-of-the-art computational strategies to rationally design nanoscale biosensors. A detailed account of available in silico strategies used to drive and/or optimize the synthesis of functionalized nanomaterials for biosensing will be presented. The insights will not only stimulate the field to rationally design functionalized nanomaterials with improved biosensing performance but also foster research on the required functionalization to improve biomolecule-surface complex formation as a whole.
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Affiliation(s)
- Sutapa Dutta
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy; (S.D.); (S.C.)
- Institute of Nanoscience, CNR-NANO S3, Via G. Campi 213/A, 41125 Modena, Italy
| | - Stefano Corni
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy; (S.D.); (S.C.)
- Institute of Nanoscience, CNR-NANO S3, Via G. Campi 213/A, 41125 Modena, Italy
| | - Giorgia Brancolini
- Institute of Nanoscience, CNR-NANO S3, Via G. Campi 213/A, 41125 Modena, Italy
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Bakhshandeh B, Sorboni SG, Haghighi DM, Ahmadi F, Dehghani Z, Badiei A. New analytical methods using carbon-based nanomaterials for detection of Salmonella species as a major food poisoning organism in water and soil resources. CHEMOSPHERE 2022; 287:132243. [PMID: 34537453 DOI: 10.1016/j.chemosphere.2021.132243] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/21/2021] [Accepted: 09/11/2021] [Indexed: 06/13/2023]
Abstract
Salmonella is one of the most prevalent causing agents of food- and water-borne illnesses, posing an ongoing public health threat. These food-poisoning bacteria contaminate the resources at different stages such as production, aggregation, processing, distribution, as well as marketing. According to the high incidence of salmonellosis, effective strategies for early-stage detection are required at the highest priority. Since traditional culture-dependent methods and polymerase chain reaction are labor-intensive and time-taking, identification of early and accurate detection of Salmonella in food and water samples can prevent significant health economic burden and lessen the costs. The immense potentiality of biosensors in diagnosis, such as simplicity in operation, the ability of multiplex analysis, high sensitivity, and specificity, have driven research in the evolution of nanotechnology, innovating newer biosensors. Carbon nanomaterials enhance the detection sensitivity of biosensors while obtaining low levels of detection limits due to their possibility to immobilize huge amounts of bioreceptor units at insignificant volume. Moreover, conjugation and functionalization of carbon nanomaterials with metallic nanoparticles or organic molecules enables surface functional groups. According to these remarkable properties, carbon nanomaterials are widely exploited in the development of novel biosensors. To be specific, carbon nanomaterials such as carbon nanotubes, graphene and fullerenes function as transducers in the analyte recognition process or surface immobilizers for biomolecules. Herein the potential application of carbon nanomaterials in the development of novel Salmonella biosensors platforms is reviewed comprehensively. In addition, the current problems and critical analyses of the future perspectives of Salmonella biosensors are discussed.
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Affiliation(s)
- Behnaz Bakhshandeh
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran; Department of Microbiology, Faculty of Biology, College of Science, University of Tehran, Tehran, Iran.
| | | | - Dorrin Mohtadi Haghighi
- Department of Pharmaceutics, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Ahmadi
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Zahra Dehghani
- Department of Cellular and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Alireza Badiei
- School of Chemistry, College of Science, University of Tehran, Tehran, Iran
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Carbon-Based Nanocomposite Smart Sensors for the Rapid Detection of Mycotoxins. NANOMATERIALS 2021; 11:nano11112851. [PMID: 34835617 PMCID: PMC8621137 DOI: 10.3390/nano11112851] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 10/01/2021] [Accepted: 10/11/2021] [Indexed: 01/07/2023]
Abstract
Carbon-based nanomaterials have become the subject of intensive interest because their intriguing physical and chemical properties are different from those of their bulk counterparts, leading to novel applications in smart sensors. Mycotoxins are secondary metabolites with different structures and toxic effects produced by fungi. Mycotoxins have low molecular weights and highly diverse molecular structures, which can induce a spectrum of biological effects in humans and animals even at low concentrations. A tremendous amount of biosensor platforms based on various carbon nanocomposites have been developed for the determination of mycotoxins. Therefore, the contents of this review are based on a balanced combination of our own studies and selected research studies performed by academic groups worldwide. We first address the vital preparation methods of biorecognition unit (antibodies, aptamers, molecularly imprinted polymers)-functionalized carbon-based nanomaterials for sensing mycotoxins. Then, we summarize various types of smart sensors for the detection of mycotoxins. We expect future research on smart sensors to show a significant impact on the detection of mycotoxins in food products.
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14
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Xeno-Nucleic Acid (XNA) 2'-Fluoro-Arabino Nucleic Acid (FANA) Aptamers to the Receptor-Binding Domain of SARS-CoV-2 S Protein Block ACE2 Binding. Viruses 2021; 13:v13101983. [PMID: 34696413 PMCID: PMC8539646 DOI: 10.3390/v13101983] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 01/03/2023] Open
Abstract
The causative agent of COVID-19, SARS-CoV-2, gains access to cells through interactions of the receptor-binding domain (RBD) on the viral S protein with angiotensin-converting enzyme 2 (ACE2) on the surface of human host cells. Systematic evolution of ligands by exponential enrichment (SELEX) was used to generate aptamers (nucleic acids selected for high binding affinity to a target) to the RBD made from 2ʹ-fluoro-arabinonucleic acid (FANA). The best selected ~79 nucleotide aptamers bound the RBD (Arg319-Phe541) and the larger S1 domain (Val16-Arg685) of the 1272 amino acid S protein with equilibrium dissociation constants (KD,app) of ~10–20 nM, and binding half-life for the RBD, S1 domain, and full trimeric S protein of 53 ± 18, 76 ± 5, and 127 ± 7 min, respectively. Aptamers inhibited the binding of the RBD to ACE2 in an ELISA assay. Inhibition, on a per weight basis, was similar to neutralizing antibodies that were specific for RBD. Aptamers demonstrated high specificity, binding with about 10-fold lower affinity to the related S1 domain from the original SARS virus, which also binds to ACE2. Overall, FANA aptamers show affinities comparable to previous DNA aptamers to RBD and S1 protein and directly block receptor interactions while using an alternative Xeno-nucleic acid (XNA) platform.
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15
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Liu L, Han Z, An F, Gong X, Zhao C, Zheng W, Mei L, Zhou Q. Aptamer-based biosensors for the diagnosis of sepsis. J Nanobiotechnology 2021; 19:216. [PMID: 34281552 PMCID: PMC8287673 DOI: 10.1186/s12951-021-00959-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/09/2021] [Indexed: 12/15/2022] Open
Abstract
Sepsis, the syndrome of infection complicated by acute organ dysfunction, is a serious and growing global problem, which not only leads to enormous economic losses but also becomes one of the leading causes of mortality in the intensive care unit. The detection of sepsis-related pathogens and biomarkers in the early stage plays a critical role in selecting appropriate antibiotics or other drugs, thereby preventing the emergence of dangerous phases and saving human lives. There are numerous demerits in conventional detection strategies, such as high cost, low efficiency, as well as lacking of sensitivity and selectivity. Recently, the aptamer-based biosensor is an emerging strategy for reasonable sepsis diagnosis because of its accessibility, rapidity, and stability. In this review, we first introduce the screening of suitable aptamer. Further, recent advances of aptamer-based biosensors in the detection of bacteria and biomarkers for the diagnosis of sepsis are summarized. Finally, the review proposes a brief forecast of challenges and future directions with highly promising aptamer-based biosensors.
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Affiliation(s)
- Lubin Liu
- Institute for Translational Medicine, Department of Stomatology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266003, China
- School of Stomatology, Qingdao University, Qingdao, 266003, China
| | - Zeyu Han
- Institute for Translational Medicine, Department of Stomatology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266003, China
- School of Stomatology, Qingdao University, Qingdao, 266003, China
| | - Fei An
- Institute for Translational Medicine, Department of Stomatology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266003, China
- School of Stomatology, Qingdao University, Qingdao, 266003, China
| | - Xuening Gong
- Institute for Translational Medicine, Department of Stomatology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266003, China
- School of Stomatology, Qingdao University, Qingdao, 266003, China
| | - Chenguang Zhao
- Institute for Translational Medicine, Department of Stomatology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266003, China
- School of Stomatology, Qingdao University, Qingdao, 266003, China
| | - Weiping Zheng
- Institute for Translational Medicine, Department of Stomatology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266003, China
- School of Stomatology, Qingdao University, Qingdao, 266003, China
| | - Li Mei
- School of Stomatology, Qingdao University, Qingdao, 266003, China
| | - Qihui Zhou
- Institute for Translational Medicine, Department of Stomatology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266003, China.
- School of Stomatology, Qingdao University, Qingdao, 266003, China.
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16
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Ferreira-Bravo IA, DeStefano JJ. Xeno-nucleic Acid (XNA) 2'-Fluoro-Arabino Nucleic Acid (FANA) Aptamers to the Receptor Binding Domain of SARS-CoV-2 S Protein Block ACE2 Binding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34282416 DOI: 10.1101/2021.07.13.452259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The causative agent of COVID-19, SARS-CoV-2, gains access to cells through interactions of the receptor binding domain (RBD) on the viral S protein with angiotensin converting enzyme 2 (ACE2) on the surface of human host cells. Systematic Evolution of Ligands by Exponential Enrichment (SELEX) was used to generate aptamers (nucleic acids selected for high binding affinity to a target) to the RBD made from 2'-fluoroarabinonucleic acid (FANA). The best selected ~ 79 nucleotide aptamers bound the RBD (Arg319-Phe541) and the larger S1 domain (Val16-Arg685) of the 1272 amino acid S protein with equilibrium dissociation constants ( K D,app ) of ~ 10-20 nM and a binding half-life for the RBD of 53 ± 18 minutes. Aptamers inhibited the binding of the RBD to ACE2 in an ELISA assay. Inhibition, on a per weight basis, was similar to neutralizing antibodies that were specific for RBD. Aptamers demonstrated high specificity, binding with about 10-fold lower affinity to the related S1 domain from the original SARS virus, which also binds to ACE2. Overall, FANA aptamers show affinities comparable to previous DNA aptamers to RBD and S protein and directly block receptor interactions while using an alternative Xeno-nucleic acid (XNA) platform.
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17
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Rahman MM, Lee DJ, Jo A, Yun SH, Eun JB, Im MH, Shim JH, Abd El-Aty AM. Onsite/on-field analysis of pesticide and veterinary drug residues by a state-of-art technology: A review. J Sep Sci 2021; 44:2310-2327. [PMID: 33773036 DOI: 10.1002/jssc.202001105] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 03/12/2021] [Accepted: 03/13/2021] [Indexed: 11/08/2022]
Abstract
Pesticides and veterinary drugs are generally employed to control pests and insects in crop and livestock farming. However, remaining residues are considered potentially hazardous to human health and the environment. Therefore, regular monitoring is required for assessing and legislation of pesticides and veterinary drugs. Various approaches to determining residues in various agricultural and animal food products have been reported. Most analytical methods involve sample extraction, purification (cleanup), and detection. Traditional sample preparation is time-consuming labor-intensive, expensive, and requires a large amount of toxic organic solvent, along with high probability for the decomposition of a compound before the analysis. Thus, modern sample preparation techniques, such as the quick, easy, cheap, effective, rugged, and safe method, have been widely accepted in the scientific community for its versatile application; however, it still requires a laboratory setup for the extraction and purification processes, which also involves the utilization of a toxic solvent. Therefore, it is crucial to elucidate recent technologies that are simple, portable, green, quick, and cost-effective for onsite and infield residue detections. Several technologies, such as surface-enhanced Raman spectroscopy, quantum dots, biosensing, and miniaturized gas chromatography, are now available. Further, several onsite techniques, such as ion mobility-mass spectrometry, are now being upgraded; some of them, although unable to analyze field sample directly, can analyze a large number of compounds within very short time (such as time-of-flight and Orbitrap mass spectrometry). Thus, to stay updated with scientific advances and analyze organic contaminants effectively and safely, it is necessary to study all of the state-of-art technology.
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Affiliation(s)
- Md Musfiqur Rahman
- Natural Products Chemistry Laboratory, Chonnam National University, Gwangju, Republic of Korea
| | - Dong Ju Lee
- Natural Products Chemistry Laboratory, Chonnam National University, Gwangju, Republic of Korea
| | - Ara Jo
- Natural Products Chemistry Laboratory, Chonnam National University, Gwangju, Republic of Korea
| | - Seung Hee Yun
- Natural Products Chemistry Laboratory, Chonnam National University, Gwangju, Republic of Korea
| | - Jong-Bang Eun
- Department of Food Science and Technology and BK 21 plus Program, Graduate School of Chonnam National University, Gwangju, Republic of Korea
| | - Moo-Hyeog Im
- Department of Food Engineering, Daegu University, Gyeongbuk, Republic of Korea
| | - Jae-Han Shim
- Natural Products Chemistry Laboratory, Chonnam National University, Gwangju, Republic of Korea
| | - A M Abd El-Aty
- Department of Pharmacology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt.,Department of Medical Pharmacology, Medical Faculty, Ataturk University, Erzurum, Turkey
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18
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19
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The assessment of three dimensional modelling design for single strand DNA aptamers for computational chemistry application. Biophys Chem 2020; 267:106492. [PMID: 33035750 DOI: 10.1016/j.bpc.2020.106492] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/17/2020] [Accepted: 09/29/2020] [Indexed: 11/23/2022]
Abstract
Aptamers are oligonucleotides and peptides around 15-100 bases in length and are suitable as detection probes or as therapeutics molecules. There are growing interests in the aptamer screening approach through computational simulation methods. DNA and RNA modelling lacks of validation on their predicted 3D structures due to less number of validation tools, unlike protein structures. We suggest an approach to design the stem-loop/hairpin for the three dimensional structure of DNA aptamers through serial applications of computational prediction methods by comparing the simulated structures with the experimental data deposited in PDB Data bank, followed by MD simulations. The result shows minimal structural differences were observed between the designed and the original NMR aptamers, and the stem-loop conformational structures were also retained during the MD thus suggesting the proposed aptamers designing methods are able to synthesize a high quality molecular structure of hairpin aptamers, comparable to the NMR structures.
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20
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Li T, Ou G, Chen X, Li Z, Hu R, Li Y, Yang Y, Liu M. Naked-eye based point-of-care detection of E.coli O157: H7 by a signal-amplified microfluidic aptasensor. Anal Chim Acta 2020; 1130:20-28. [PMID: 32892935 DOI: 10.1016/j.aca.2020.07.031] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/14/2020] [Indexed: 02/02/2023]
Abstract
Fast and sensitive detection of E.coli O157: H7 is significantly essential for clinical management as well as for transmission prevention during disease outbreaks. Though many types of detection strategies have been implemented for measuring E.coli O157: H7, most of them still rely on complex instruments or tedious/laborious setups, which restrict their applications in resource-limited scenarios. Herein, we introduce an eye-based microfluidic aptasensor (EA-Sensor) for fast detection of E.coli O157: H7 without the assist of any instruments. We demonstrate the perfect coupling of aptamer sensing, hybridization chain reaction (HCR)-amplification and a distance-based visualized readout to quantitatively determine the pathogen concentration. We first used gel-electrophoresis assay to evaluate the system and the results proved that E.coli O157: H7 was well recognized by the aptamer and HCR could increase the signal by about 100 folds. In addition, the Aptamer specificity and signal-amplification ability were verified on the EA-Sensor for sensing E.coli O157: H7 by naked eyes. Furthermore, we demonstrated that E.coli O157: H7 in milk could be accurately and conveniently measured with good performance. With the benefits of operation integration and strategy integration, our EA-Sensor shows advantages of high specificity, easy operation, efficient amplification and visualized readout, which offers a favorable point-of-care tool for E.coli O157: H7 or other pathogen detection in resource-constrained settings.
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Affiliation(s)
- Tao Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Gaozhi Ou
- School of Sports, China University of Geosciences, Wuhan, 430074, China
| | - Xuliang Chen
- Department of Cardiovascular Surgery, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Zheyu Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Rui Hu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Ying Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 10049, China.
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 10049, China.
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 10049, China
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21
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Endoh T, Sugimoto N. Signaling Aptamer Optimization through Selection Using RNA-Capturing Microsphere Particles. Anal Chem 2020; 92:7955-7963. [PMID: 32363852 DOI: 10.1021/acs.analchem.0c01338] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An RNA signaling aptamer is composed of two units: a sensing aptamer that binds the input target molecule and a working aptamer that binds the output target molecule to result in a detectable signal. A conformational change of the signaling aptamer that induces an allosteric interaction with the output target molecule in response to the input target molecule depends on a junction region, which connects the two aptamer units. Efficient and effective optimization of the junction region remains a technical challenge. In this study, we demonstrate a simple strategy for optimizing the junction region through functional RNA selection using RNA-capturing microsphere particles. From approximately 0.2 million sequence variants, a signaling aptamer that enabled intracellular detection of S-adenosyl methionine with a high signal-to-noise ratio, which is approximately 2-fold higher relative fluorescence increment compared to the previously reported signaling aptamer, was obtained after single round of selection. The technology demonstrated here can be used to select RNA sequences that carry out specific functions in response to particular stimuli.
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Affiliation(s)
- Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe 650-0047, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe 650-0047, Japan.,Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe 650-0047, Japan
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22
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Wang J, Yang D, Guo X, Song Q, Tan L, Dong L. A novel RNA aptamer-modified riboswitch as chemical sensor. Anal Chim Acta 2019; 1100:240-249. [PMID: 31987147 DOI: 10.1016/j.aca.2019.11.071] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/20/2019] [Accepted: 11/30/2019] [Indexed: 12/19/2022]
Abstract
In this study, a novel label- and immobilization-free RNA aptamer-modified riboswitch-based biosensor was developed by using RNA aptamer modified secondary-structural scaffolds to control the identity of the ribosomal binding sequence (RBS). In the developed sensor, the duplex RNA aptamers-modified cis-repressor sequence is introduced upstream to the RBS of the indicating gene (gfp gene), leading to formatting an RNA bubble due to the none-complementary state of the RNA aptamers in the hairpin structure of the cis-repressor sequence. Without the presence of the target molecule, the ribosome cannot identify the RBS of the indicating gene as the RBS is hidden by the introduced cis-repressor, consequently, the indicating gene in the sensor would not be expressed, demonstrating the absence of the target. On the contrary, with the presence of the target molecule, the binding of aptamer with the target would induce the enlargement of the RNA bubble, leading to the separation of the cis-repressor sequence and RBS. Hence, the indicating gene would be expressed, manifesting the existence of the target. In addition, the developed sensor can quantitatively report the target concentrations by measuring the gfp gene-encoded GFP (green fluorescent protein) concentration. The approach proposed in this study can be used to construct sensors for detecting various chemicals by introducing the corresponding aptamers, therefore, this strategy can potentially provide a new set of analytical tools in the field of analytical chemistry.
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Affiliation(s)
- Jing Wang
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400044, China; College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China; Key Laboratory of Low-grade Energy Utilization Technologies & Systems of the Ministry of Education, Chongqing University, Chongqing, 40004, PR China
| | - Dongmei Yang
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400044, China
| | - Xiaogang Guo
- Chongqing Key Laboratory of Inorganic Special Functional Materials, College of Chemistry and Chemical Engineering, Yangtze Normal University, Chongqing, 408100, China
| | - Qitao Song
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Luxi Tan
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400044, China; Key Laboratory of Low-grade Energy Utilization Technologies & Systems of the Ministry of Education, Chongqing University, Chongqing, 40004, PR China.
| | - Lichun Dong
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400044, China; Key Laboratory of Low-grade Energy Utilization Technologies & Systems of the Ministry of Education, Chongqing University, Chongqing, 40004, PR China.
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23
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Thrombin Aptamer-Modified Metal-Organic Framework Nanoparticles: Functional Nanostructures for Sensing Thrombin and the Triggered Controlled Release of Anti-Blood Clotting Drugs. SENSORS 2019; 19:s19235260. [PMID: 31795428 PMCID: PMC6929137 DOI: 10.3390/s19235260] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/14/2019] [Accepted: 11/23/2019] [Indexed: 12/11/2022]
Abstract
This paper features the synthesis of thrombin-responsive, nucleic acid-gated, UiO-68 metal-organic framework nanoparticles (NMOFs) loaded with the drug Apixaban or rhodamine 6G as a drug model. Apixaban acts as an inhibitor of blood clots formation. The loads in the NMOFs are locked by duplex nucleic acids that are composed of anchor nucleic acids linked to the NMOFs that are hybridized with the anti-thrombin aptamer. In the presence of thrombin, the duplex gating units are separated through the formation of thrombin-aptamer complexes. The unlocking of the NMOFs releases the drug (or the drug model). The release of the drug is controlled by the concentration of thrombin. The Apixaban-loaded NMOFs revealed improved inhibition, as compared to free Apixaban, toward blood clot formation. This is reflected by their longer time intervals for inducing clot formation and the decreased doses of the drug required to affect clots formation. The beneficial effects of the Apixaban-loaded NMOFs are attributed to the slow-release mechanism induced by the NMOFs carriers, where the inhibition of factor Xa in the blood clotting cycle retards the formation of thrombin, which slows down the release of the drug.
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24
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Rose KM, Alves Ferreira-Bravo I, Li M, Craigie R, Ditzler MA, Holliger P, DeStefano JJ. Selection of 2'-Deoxy-2'-Fluoroarabino Nucleic Acid (FANA) Aptamers That Bind HIV-1 Integrase with Picomolar Affinity. ACS Chem Biol 2019; 14:2166-2175. [PMID: 31560515 PMCID: PMC7005942 DOI: 10.1021/acschembio.9b00237] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
Systematic Evolution
of Ligands by Exponential Enrichment (SELEX)
is the iterative process by which nucleic acids that can bind with
high affinity and specificity (termed aptamers) to specific protein
targets are selected. Using a SELEX protocol adapted for Xeno-Nucleic
Acid (XNA) as a suitable substrate for aptamer generation, 2′-fluoroarabinonucleic
acid (FANA) was used to select several related aptamers to HIV-1 integrase
(IN). IN bound FANA aptamers with equilibrium dissociation constants
(KD,app) of ∼50–100 pM in
a buffer with 200 mM NaCl and 6 mM MgCl2. Comparisons to
published HIV-1 IN RNA and DNA aptamers as well as IN genomic binding
partners indicated that FANA aptamers bound more than 2 orders of
magnitude more tightly to IN. Using a combination of RNA folding algorithms
and covariation analysis, all strong binding aptamers demonstrated
a common four-way junction structure, despite significant sequence
variation. IN aptamers were selected from the same starting library
as FA1, a FANA aptamer that binds with pM affinity to HIV-1 Reverse
Transcriptase (RT). It contains a 20-nucleotide 5′ DNA sequence
followed by 59 FANA nucleotides. IN-1.1 (one of the selected aptamers)
potently inhibited IN activity and intasome formation in vitro. Replacing
the FANA nucleotides of IN-1.1 with 2′-fluororibonucleic acid
(F-RNA), which has the same chemical formula but with a ribose rather
than arabinose sugar conformation, dramatically reduced binding, suggesting
that FANA adopts unique structural conformations that promote binding
to HIV-1 IN.
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25
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Ma F, Qi L, Einarson O, Sen D, Yu HZ. Divergent Pair of Ultrasensitive Mechanoelectronic Nanoswitches Made out of DNA. Anal Chem 2019; 91:8244-8251. [DOI: 10.1021/acs.analchem.9b00896] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fen Ma
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry (Ministry of Education), College of Chemistry and Materials Science, Northwest University, Xi′an, Shaanxi 710127, China
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26
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Wang C, Tan R, Li J, Zhang Z. Exonuclease I-assisted fluorescent method for ochratoxin A detection using iron-doped porous carbon, nitrogen-doped graphene quantum dots, and double magnetic separation. Anal Bioanal Chem 2019; 411:2405-2414. [PMID: 30828760 DOI: 10.1007/s00216-019-01684-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 01/29/2019] [Accepted: 02/11/2019] [Indexed: 01/21/2023]
Abstract
In this paper, a fluorescent method was developed for ochratoxin A (OTA) detection that uses iron-doped porous carbon (MPC) and aptamer-functionalized nitrogen-doped graphene quantum dots (NGQDs-Apt) as probes. In this method, the adsorbance of the NGQDs-Apt on the MPC due to a π-π interaction between the aptamer and the MPC results in the quenching of the fluorescence of the NGQDs-Apt. However, since OTA interacts strongly with the aptamer, the presence of OTA leads to the detachment of the NGQDs-Apt from the MPC, resulting in the resumption of fluorescence from the NGQDs-Apt. When exonuclease I (Exo I) is also added to the solution, this exonuclease specifically digests the aptamer, leading to the release of the OTA back into the solution. This free OTA then interacts with another MPC-NGQDs-Apt system, inducing the release of more NGQDs into the solution, which enhances the fluorescent intensity compared to that of the system with no Exo I. Utilizing this behavior of OTA in the presence of NGQDs-Apt, it was possible to detect concentrations of OTA ranging from 10 to 5000 nM, with a limit of detection of 2.28 nM. Our method was tested by applying it to the detection of OTA in wheat and corn samples. This method has four advantages: (1) the magnetic porous carbon is easy to prepare, its porosity enhances its loading capacity for NGQDs, it highly efficiently quenches the fluorescence of the NGQDs, and its magnetic properties facilitate the separation of the MPC from other species in solution; (2) applying double magnetic separation decreases the background signal; (3) Exo I digests the free aptamer effectively, which allows the resulting free OTA to induce the release of more NGQDs-Apt, ultimately enhancing the fluorescent signal; and (4) the proposed method presented high sensitivity and a wide linear detection range. This method may prove helpful in food safety analysis and new biosensor development (achieved by using different aptamer sequences to that used in the present work). Graphical abstract Exonuclease I (Exo I)-assisted fluorescent method for ochratoxin A (OTA) detection using magnetic porous carbon (MPC), nitrogen-doped graphene quantum dots (NGQDs), and double magnetic separation.
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Affiliation(s)
- Chengke Wang
- College of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China.
| | - Rong Tan
- College of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Jiangyu Li
- College of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Zexiang Zhang
- College of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China
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27
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Yuan Z, Xu M, Wu T, Zhang X, Shen Y, Ernest U, Gui L, Wang F, He Q, Chen H. Design and synthesis of NQO1 responsive fluorescence probe and its application in bio-imaging for cancer diagnosis. Talanta 2019; 198:323-329. [PMID: 30876568 DOI: 10.1016/j.talanta.2019.02.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 01/27/2019] [Accepted: 02/03/2019] [Indexed: 12/31/2022]
Abstract
As an over-expressed flavoprotein in several kinds of tumor cells, NAD(P)H: quinone oxidoreductase-1 (NQO1) is considered as a potent biomarker in early-stage cancer diagnosis. Developing a fast, selective and sensitive method of monitoring NQO1 on cellular level will greatly promote cancer diagnosis in clinical practice. In this paper, a fast NQO1 responsive fluorescence probe SYZ-30 containing quinone acid and 7-nitro-2,1,3-benzoxadiazole (NBD) fluorophore is constructed. The probe could selectively respond to NQO1 and rapidly emit strong fluorescence in vitro within only 5 min. Notably, the peak fluorescent intensities at 550 nm showed a linear relationship with NQO1 concentrations in the range of 3-30 ng/ml and limit of detection (LOD) was 0.0667 ng/ml. Furthermore, it was validated that the probe has good biocompatibility and could be applied for bio-imaging in NQO1 over-expressed cancer cells, together with its mitochondria targeting ability. Importantly, confocal fluorescence imaging confirmed the NQO1 detection ability on cellular level, which can be used for real-time detection of several cancer subtypes like adenocarcinoma. To conclude, the probe is rapidly responsive, highly sensitive and selective which will potentially become a practical tool for early cancer detection and diagnosis.
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Affiliation(s)
- Zhenwei Yuan
- Department of Biomedical Engineering, School of Engineering, China Pharmaceutical University, 24 Tongjia Lane, Gulou District, Nanjing 210009, China
| | - Mingjun Xu
- Department of Biomedical Engineering, School of Engineering, China Pharmaceutical University, 24 Tongjia Lane, Gulou District, Nanjing 210009, China
| | - Tianze Wu
- High School Affiliated to Nanjing University, 83 Gulou Street, Gulou District, Nanjing 210009, China
| | - Xinyi Zhang
- Department of Biomedical Engineering, School of Engineering, China Pharmaceutical University, 24 Tongjia Lane, Gulou District, Nanjing 210009, China
| | - Yuanzhi Shen
- Department of Biomedical Engineering, School of Engineering, China Pharmaceutical University, 24 Tongjia Lane, Gulou District, Nanjing 210009, China
| | - Umeorah Ernest
- Department of Biomedical Engineering, School of Engineering, China Pharmaceutical University, 24 Tongjia Lane, Gulou District, Nanjing 210009, China
| | - Lijuan Gui
- Department of Biomedical Engineering, School of Engineering, China Pharmaceutical University, 24 Tongjia Lane, Gulou District, Nanjing 210009, China
| | - Fei Wang
- Department of Biomedical Engineering, School of Engineering, China Pharmaceutical University, 24 Tongjia Lane, Gulou District, Nanjing 210009, China
| | - Qing He
- Department of Biomedical Engineering, School of Engineering, China Pharmaceutical University, 24 Tongjia Lane, Gulou District, Nanjing 210009, China
| | - Haiyan Chen
- Department of Biomedical Engineering, School of Engineering, China Pharmaceutical University, 24 Tongjia Lane, Gulou District, Nanjing 210009, China.
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A novel photosensitive dual-sensor for simultaneous detection of nucleic acids and small chemical molecules. Biosens Bioelectron 2018; 127:108-117. [PMID: 30594890 DOI: 10.1016/j.bios.2018.12.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/03/2018] [Accepted: 12/07/2018] [Indexed: 02/05/2023]
Abstract
Sensors that can rapidly and specifically detect nucleic acids and chemical molecules can revolutionize the diagnosis and treatment of diseases by allowing molecular-level informations to be used during the routine medicines. In this study, we demonstrated a novel dual-sensor that can be used to simultaneously detect any nucleic acids and chemical molecules whose binding aptamers can be found or synthesized. In the developed dual-sensor, the specifically designed PTG (a photosensitive azobenzene derivative carrying one photoisomerizable azobenzene moiety, one threoninol terminal and one guanidinium terminal) molecules are introduced into the unwinding region of two T7 promoters, and two DNA bubbles are introduced upstream of the two T7 promoters. Without the target, the indicating gene in the dual-tensor would not be expressed since the binding with RNAPs (RNA polymerases) cannot melt the T7 promoter for the indicating gene due to the integration of the DNA double strands via the PTG molecules, manifesting the absence of the target nucleic acid and chemical molecule. While with the presence of the target nucleic acid and/or chemical molecule, the indicating gene would be expressed as the T7 promoter contained in the enlarged DNA bubble can be melted and transcribed by the bound RNAPs as the enlarged DNA bubble can help the separation of the two DNA strands, demonstrating the existence of target nucleic acid and/or chemical molecule.
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29
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Beheshti-Marnani A, Hatefi-Mehrjardi A, Es'haghi Z. A sensitive biosensing method for detecting of ultra-trace amounts of AFB1 based on "Aptamer/reduced graphene oxide" nano-bio interaction. Colloids Surf B Biointerfaces 2018; 175:98-105. [PMID: 30522013 DOI: 10.1016/j.colsurfb.2018.11.087] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 11/19/2018] [Accepted: 11/30/2018] [Indexed: 12/20/2022]
Abstract
A simple, low-cost and sensitive label-free aptasensor assembled with assisting reduced graphene oxide nanosheets as the signal amplifier was fabricated and applied for detecting ultra-low levels of Aflatoxin B1(AFB1) through a nano-bio interaction system. The conditions of different modified glassy carbon electrodes as the base of aptasensor were investigated by cyclic voltammetry (CV), differential pulse voltammetry (DPV) and electrochemical impedance spectroscopy (EIS). The performance of the fabricated aptasensor was evaluated by FESEM, HRTEM and AFM images. The proposed biosensor detected AFB1sensitively in a wide linear range (0.5 nM-4μM) by DPV with a considerable low limit of detection (LOD = 0.07 nM) and good repeatability (RSD = 2.9) and stability. Finally, the present aptasensor was applied successfully for monitoring AFB1 with appropriate recoveries in pasteurized cow milk and human blood plasma as real samples.
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Affiliation(s)
| | | | - Zarrin Es'haghi
- Department of Chemistry, Payame Noor University (PNU), P.O. Box: 19395-4697, Tehran, Iran.
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30
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Rani D, Pachauri V, Madaboosi N, Jolly P, Vu XT, Estrela P, Chu V, Conde JP, Ingebrandt S. Top-Down Fabricated Silicon Nanowire Arrays for Field-Effect Detection of Prostate-Specific Antigen. ACS OMEGA 2018; 3:8471-8482. [PMID: 31458975 PMCID: PMC6644640 DOI: 10.1021/acsomega.8b00990] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/18/2018] [Indexed: 05/16/2023]
Abstract
Highly sensitive electrical detection of biomarkers for the early stage screening of cancer is desired for future, ultrafast diagnostic platforms. In the case of prostate cancer (PCa), the prostate-specific antigen (PSA) is of prime interest and its detection in combination with other PCa-relevant biomarkers in a multiplex approach is advised. Toward this goal, we demonstrate the label-free, potentiometric detection of PSA with silicon nanowire ion-sensitive field-effect transistor (Si NW-ISFET) arrays. To realize the field-effect detection, we utilized the DNA aptamer-receptors specific for PSA, which were covalently and site-specifically immobilized on Si NW-ISFETs. The platform was used for quantitative detection of PSA and the change in threshold voltage of the Si NW-ISEFTs was correlated with the concentration of PSA. Concentration-dependent measurements were done in a wide range of 1 pg/mL to 1 μg/mL, which covers the clinical range of interest. To confirm the PSA-DNA aptamer binding on the Si NW surfaces, a sandwich-immunoassay based on chemiluminescence was implemented. The electrical approach using the Si NW-ISFET platform shows a lower limit of detection and a wide dynamic range of the assay. In future, our platform should be utilized to detect multiple biomarkers in one assay to obtain more reliable information about cancer-related diseases.
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Affiliation(s)
- Dipti Rani
- Department
of Informatics and Microsystem Technology, University of Applied Sciences Kaiserslautern, Amerikastrasse 1, 66482 Zweibrücken, Germany
| | - Vivek Pachauri
- Department
of Informatics and Microsystem Technology, University of Applied Sciences Kaiserslautern, Amerikastrasse 1, 66482 Zweibrücken, Germany
| | - Narayanan Madaboosi
- INESC
Microsistemas e Nanotecnologias, Rua Alves Redol, 91000-029 Lisbon, Portugal
| | - Pawan Jolly
- Department
of Electronic and Electrical Engineering, University of Bath, BA2 7AY Bath, United Kingdom
| | - Xuan-Thang Vu
- Department
of Informatics and Microsystem Technology, University of Applied Sciences Kaiserslautern, Amerikastrasse 1, 66482 Zweibrücken, Germany
- Institute
of Physics I, RWTH Aachen University, Sommerfeldstr. 14, 52074 Aachen, Germany
| | - Pedro Estrela
- Department
of Electronic and Electrical Engineering, University of Bath, BA2 7AY Bath, United Kingdom
| | - Virginia Chu
- INESC
Microsistemas e Nanotecnologias, Rua Alves Redol, 91000-029 Lisbon, Portugal
| | - João Pedro Conde
- INESC
Microsistemas e Nanotecnologias, Rua Alves Redol, 91000-029 Lisbon, Portugal
| | - Sven Ingebrandt
- Department
of Informatics and Microsystem Technology, University of Applied Sciences Kaiserslautern, Amerikastrasse 1, 66482 Zweibrücken, Germany
- E-mail:
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31
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An innovative paradigm of methods in microRNAs detection: highlighting DNAzymes, the illuminators. Biosens Bioelectron 2018; 107:123-144. [DOI: 10.1016/j.bios.2018.02.020] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 01/22/2018] [Accepted: 02/07/2018] [Indexed: 12/15/2022]
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32
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Park KS. Nucleic acid aptamer-based methods for diagnosis of infections. Biosens Bioelectron 2018; 102:179-188. [PMID: 29136589 PMCID: PMC7125563 DOI: 10.1016/j.bios.2017.11.028] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/20/2017] [Accepted: 11/06/2017] [Indexed: 02/07/2023]
Abstract
Infectious diseases are a serious global problem, which not only take an enormous human toll but also incur tremendous economic losses. In combating infectious diseases, rapid and accurate diagnostic tests are required for pathogen identification at the point of care (POC). In this review, investigations of diagnostic strategies for infectious diseases that are based on aptamers, especially nucleic acid aptamers, oligonucleotides that have high affinities and specificities toward their targets, are described. Owing to their unique features including low cost of production, easy chemical modification, high chemical stability, reproducibility, and low levels of immunogenicity and toxicity, aptamers have been widely utilized as bio-recognition elements (bio-receptors) for the development of infection diagnostic systems. We discuss nucleic acid aptamer-based methods that have been developed for diagnosis of infections using a format that organizes discussion according to the target pathogenic analytes including toxins or proteins, whole cells and nucleic acids. Also included is, a summary of recent advances made in the sensitive detection of pathogenic bacteria utilizing the isothermal nucleic acid amplification method. Lastly, a nucleic acid aptamer-based POC system is described and future directions of studies in this area are discussed.
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Affiliation(s)
- Ki Soo Park
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea.
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34
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Nussbaum O, Bar Oz M, Tilayov T, Atiya H, Dagan S. A signal amplification probe enhances sensitivity of antibodies and aptamers based Immuno-diagnostic assays. J Immunol Methods 2017; 448:85-90. [PMID: 28614699 DOI: 10.1016/j.jim.2017.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 06/01/2017] [Accepted: 06/07/2017] [Indexed: 02/07/2023]
Abstract
One major unmet need is improving the sensitivity of immune-diagnostic assays. This is particularly important in the field of biomarker discoveries and monitoring. We have established a novel signal amplification probe system enabling a highly sensitive target detection platform to be used in immuno-assays. The probe consists of a double stranded DNA that can carry a large number of signaling elements such as biotin or fluorescent molecules. The DNA probe anchors to the recognition unit, whether an antibody or an aptamer, by covalent conjugation or by a simple and rapid molecular association process. Binding curves obtained by using the DNA amplification probe are dose dependent and linear over a wide range of antigen concentration. The optimal slopes are characterized by high signals and low background increasing the assay sensitivity and reducing the limit of detection by up to 10-fold compared to biotinylated antibodies commonly used in ELISA systems. When using aptamers in combination with the amplification probe for antigen recognition, the limit of detection is comparable to that obtained by biotinylated antibodies. Biotin labeled aptamers practically cannot be used for detection of low target levels. The DNA amplification probe system enables to expand the range of diagnostic assays including clinical samples and meet research needs.
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35
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Ma X, Gosai A, Balasubramanian G, Shrotriya P. Aptamer based electrostatic-stimuli responsive surfaces for on-demand binding/unbinding of a specific ligand. J Mater Chem B 2017; 5:3675-3685. [DOI: 10.1039/c6tb02386j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report an aptamer functionalized stimuli responsive surface that can controllably switch between binding and releasing its specific ligand α-thrombin under application of electrical stimuli.
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Affiliation(s)
- Xiao Ma
- Department of Mechanical Engineering
- Iowa State University
- Ames
- USA
- Department of Bioinformatics
| | - Agnivo Gosai
- Department of Mechanical Engineering
- Iowa State University
- Ames
- USA
| | - Ganesh Balasubramanian
- Department of Mechanical Engineering
- Iowa State University
- Ames
- USA
- Microelectronics Research Center
| | - Pranav Shrotriya
- Department of Mechanical Engineering
- Iowa State University
- Ames
- USA
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36
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Yu H, Canoura J, Guntupalli B, Lou X, Xiao Y. A cooperative-binding split aptamer assay for rapid, specific and ultra-sensitive fluorescence detection of cocaine in saliva. Chem Sci 2017; 8:131-141. [PMID: 28451157 PMCID: PMC5308383 DOI: 10.1039/c6sc01833e] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/28/2016] [Indexed: 12/25/2022] Open
Abstract
Sensors employing split aptamers that reassemble in the presence of a target can achieve excellent specificity, but the accompanying reduction of target affinity mitigates any overall gains in sensitivity. We for the first time have developed a split aptamer that achieves enhanced target-binding affinity through cooperative binding. We have generated a split cocaine-binding aptamer that incorporates two binding domains, such that target binding at one domain greatly increases the affinity of the second domain. We experimentally demonstrate that the resulting cooperative-binding split aptamer (CBSA) exhibits higher target binding affinity and is far more responsive in terms of target-induced aptamer assembly compared to the single-domain parent split aptamer (PSA) from which it was derived. We further confirm that the target-binding affinity of our CBSA can be affected by the cooperativity of its binding domains and the intrinsic affinity of its PSA. To the best of our knowledge, CBSA-5335 has the highest cocaine affinity of any split aptamer described to date. The CBSA-based assay also demonstrates excellent performance in target detection in complex samples. Using this CBSA, we achieved specific, ultra-sensitive, one-step fluorescence detection of cocaine within fifteen minutes at concentrations as low as 50 nM in 10% saliva without signal amplification. This limit of detection meets the standards recommended by the European Union's Driving under the Influence of Drugs, Alcohol and Medicines program. Our assay also demonstrates excellent reproducibility of results, confirming that this CBSA-platform represents a robust and sensitive means for cocaine detection in actual clinical samples.
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Affiliation(s)
- Haixiang Yu
- 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 .
| | - Bhargav Guntupalli
- Department of Chemistry and Biochemistry , Florida International University , 11200 SW 8th Street , Miami , FL 33199 , USA .
| | - Xinhui Lou
- Department of Chemistry , Capital Normal University , Xisanhuan North Rd. 105 , Beijing , 100048 , China
| | - Yi Xiao
- Department of Chemistry and Biochemistry , Florida International University , 11200 SW 8th Street , Miami , FL 33199 , USA .
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37
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Integrating Deoxyribozymes into Colorimetric Sensing Platforms. SENSORS 2016; 16:s16122061. [PMID: 27918487 PMCID: PMC5191042 DOI: 10.3390/s16122061] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 11/30/2016] [Accepted: 11/30/2016] [Indexed: 01/05/2023]
Abstract
Biosensors are analytical devices that have found a variety of applications in medical diagnostics, food quality control, environmental monitoring and biodefense. In recent years, functional nucleic acids, such as aptamers and nucleic acid enzymes, have shown great potential in biosensor development due to their excellent ability in target recognition and catalysis. Deoxyribozymes (or DNAzymes) are single-stranded DNA molecules with catalytic activity and can be isolated to recognize a wide range of analytes through the process of in vitro selection. By using various signal transduction mechanisms, DNAzymes can be engineered into fluorescent, colorimetric, electrochemical and chemiluminescent biosensors. Among them, colorimetric sensors represent an attractive option as the signal can be easily detected by the naked eye. This reduces reliance on complex and expensive equipment. In this review, we will discuss the recent progress in the development of colorimetric biosensors that make use of DNAzymes and the prospect of employing these sensors in a range of chemical and biological applications.
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38
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Affiliation(s)
- Yan Du
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun 130022, Jilin China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun 130022, Jilin China
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39
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Shamsipur M, Farzin L, Tabrizi MA, Shanehsaz M. CdTe amplification nanoplatforms capped with thioglycolic acid for electrochemical aptasensing of ultra-traces of ATP. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2016; 69:1354-60. [PMID: 27612836 DOI: 10.1016/j.msec.2016.08.038] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/01/2016] [Accepted: 08/14/2016] [Indexed: 12/20/2022]
Abstract
A "signal off" voltammetric aptasensor was developed for the sensitive and selective detection of ultra-low levels of adenosine triphosphate (ATP). For this purpose, a new strategy based on the principle of recognition-induced switching of aptamers from DNA/DNA duplex to DNA/target complex was designed using thioglycolic acid (TGA)-capped CdTe quantum dots (QDs) as the signal amplifying nano-platforms. Owing to the small size, high surface-to-volume ratio and good conductivity, quantum dots were immobilized on the electrode surface for signal amplification. In this work, methylene blue (MB) adsorbed to DNA was used as a sensitive redox reporter. The intensity of voltammetric signal of MB was found to decrease linearly upon ATP addition over a concentration range of 0.1nM to 1.6μM with a correlation coefficient of 0.9924. Under optimized conditions, the aptasensor was able to selectively detect ATP with a limit of detection of 45pM at 3σ. The results also demonstrated that the QDs-based amplification strategy could be feasible for ATP assay and presented a potential universal method for other small biomolecular aptasensors.
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Affiliation(s)
- Mojtaba Shamsipur
- Department of Chemistry, Razi University, P.O. Box 67149-67346, Kermanshah, Iran.
| | - Leila Farzin
- Department of Analytical Chemistry, School of Chemistry, College of Science, University of Tehran, P.O. Box 14174-66191, Tehran, Iran
| | - Mahmoud Amouzadeh Tabrizi
- Research Center for Science and Technology in Medicine,Tehran University of Medical Sciences, P.O. Box 14197-33131, Tehran, Iran
| | - Maryam Shanehsaz
- Analytical Chemistry Research Laboratory, Mobin Shimi Azma Company, P.O. Box 14768-44949, Tehran, Iran
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40
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Coelho L, Marques Martins de Almeida JM, Santos JL, da Silva Jorge PA, Martins MCL, Viegas D, Queirós RB. Aptamer-based fiber sensor for thrombin detection. JOURNAL OF BIOMEDICAL OPTICS 2016; 21:87005. [PMID: 27548775 DOI: 10.1117/1.jbo.21.8.087005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 08/01/2016] [Indexed: 06/06/2023]
Abstract
The detection of thrombin based on aptamer binding is studied using two different optical fiber-based configurations: long period gratings coated with a thin layer of titanium dioxide and surface plasmon resonance devices in optical fibers coated with a multilayer of gold and titanium dioxide. These structures are functionalized and the performance to detect thrombin in the range 10 to 100 nM is compared in transmission mode. The sensitivity to the surrounding refractive index (RI) of the plasmonic device is higher than 3100 nm RIU−1 in the RI range 1.335 to 1.355, a factor of 20 greater than the sensitivity of the coated grating. The detection of 10 nM of thrombin was accomplished with a wavelength shift of 3.5 nm and a resolution of 0.54 nM.
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Affiliation(s)
- Luís Coelho
- University of Porto, CAP/INESC TEC-Technology and Science and FCUP-Faculty of Sciences, Rua do Campo Alegre, 4150-179 Porto, Portugal
| | - José Manuel Marques Martins de Almeida
- University of Porto, CAP/INESC TEC-Technology and Science and FCUP-Faculty of Sciences, Rua do Campo Alegre, 4150-179 Porto, PortugalbUniversidade de Trás-os-Montes e Alto Douro, Department of Physics, School of Sciences and Technology, Apartado 1013, 5001-801 Vila Real, Portugal
| | - José Luís Santos
- University of Porto, CAP/INESC TEC-Technology and Science and FCUP-Faculty of Sciences, Rua do Campo Alegre, 4150-179 Porto, Portugal
| | - Pedro Alberto da Silva Jorge
- University of Porto, CAP/INESC TEC-Technology and Science and FCUP-Faculty of Sciences, Rua do Campo Alegre, 4150-179 Porto, Portugal
| | - Maria Cristina L Martins
- Universidade do Porto, i3S-Instituto de Investigação e Inovação em Saúde, PortugaldUniversidade do Porto, INEB-Instituto de Engenharia Biomédica, Rua Alfredo Allen, 208, 4200-135 Porto, PortugaleUniversidade do Porto, ICBAS-Instituto de Ciências Biomédicas Abel Salazar, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Diana Viegas
- Universidade do Porto, INEB-Instituto de Engenharia Biomédica, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
| | - Raquel B Queirós
- INL-International Iberian Nanotechnology, Avenida Mestre José Veiga s/n, 4715-330 Braga, Portugal
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41
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DNA aptamer selection and aptamer-based fluorometric displacement assay for the hepatotoxin microcystin-RR. Mikrochim Acta 2016. [DOI: 10.1007/s00604-016-1904-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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42
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Wu S, Duan N, Zhang W, Zhao S, Wang Z. Screening and development of DNA aptamers as capture probes for colorimetric detection of patulin. Anal Biochem 2016; 508:58-64. [PMID: 27318239 DOI: 10.1016/j.ab.2016.05.024] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 05/26/2016] [Accepted: 05/28/2016] [Indexed: 12/20/2022]
Abstract
Patulin (PAT) is a kind of mycotoxin that has serious harmful impacts on both food quality and human health. A high-affinity ssDNA aptamer that specifically binds to patulin was generated using systemic evolution of ligands by exponential enrichment (SELEX) assisted by graphene oxide (GO). After 15 rounds of positive and negative selection, a highly enriched ssDNA pool was sequenced and the representative sequences were subjected to binding assays to evaluate their affinity and specificity. Of the eight aptamer candidates tested, the sequence PAT-11 bound to patulin with high affinity and excellent selectivity with a dissociation constant (Kd) of 21.83 ± 5.022 nM. The selected aptamer, PAT-11, was subsequently used as a recognition element to develop a detection method for patulin based on an enzyme-chromogenic substrate system. The colorimetric aptasensor exhibited a linear range from 50 to 2500 pg mL(-1), and the limit of detection was found to be 48 pg mL(-1). The results indicated that GO-SELEX technology was appropriate for the screening of aptamers against small-molecule toxins, offering a promising application for aptamer-based biosensors.
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Affiliation(s)
- Shijia Wu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi 214122, China
| | - Nuo Duan
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi 214122, China
| | - Weixiao Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi 214122, China
| | - Sen Zhao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi 214122, China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi 214122, China.
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43
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Lee DW, Park KM, Gong B, Shetty D, Khedkar JK, Baek K, Kim J, Ryu SH, Kim K. A simple modular aptasensor platform utilizing cucurbit[7]uril and a ferrocene derivative as an ultrastable supramolecular linker. Chem Commun (Camb) 2016; 51:3098-101. [PMID: 25597690 DOI: 10.1039/c4cc08027k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A simple modular aptamer-based sensor (aptasensor) platform was prepared by combining the merits of the rapid and efficient preparation of a self-assembled monolayer of cucurbit[7]uril (CB[7] SAM) and the strong and specific binding affinity of CB[7] to ferrocenemethylammonium (FA), as an ultrastable supramolecular linker, to immobilize aptamers on CB[7] SAM.
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Affiliation(s)
- Don-Wook Lee
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang, 790-784, Republic of Korea
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44
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Lan T, Zhang J, Lu Y. Transforming the blood glucose meter into a general healthcare meter for in vitro diagnostics in mobile health. Biotechnol Adv 2016; 34:331-41. [PMID: 26946282 PMCID: PMC4833671 DOI: 10.1016/j.biotechadv.2016.03.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 02/20/2016] [Accepted: 03/01/2016] [Indexed: 01/08/2023]
Abstract
Recent advances in mobile network and smartphones have provided an enormous opportunity for transforming in vitro diagnostics (IVD) from central labs to home or other points of care (POC). A major challenge to achieving the goal is a long time and high costs associated with developing POC IVD devices in mobile Health (mHealth). Instead of developing a new POC device for every new IVD target, we and others are taking advantage of decades of research, development, engineering and continuous improvement of the blood glucose meter (BGM), including those already integrated with smartphones, and transforming the BGM into a general healthcare meter for POC IVDs of a wide range of biomarkers, therapeutic drugs and other analytical targets. In this review, we summarize methods to transduce and amplify selective binding of targets by antibodies, DNA/RNA aptamers, DNAzyme/ribozymes and protein enzymes into signals such as glucose or NADH that can be measured by commercially available BGM, making it possible to adapt many clinical assays performed in central labs, such as immunoassays, aptamer/DNAzyme assays, molecular diagnostic assays, and enzymatic activity assays onto BGM platform for quantification of non-glucose targets for a wide variety of IVDs in mHealth.
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Affiliation(s)
- Tian Lan
- GlucoSentient, Inc., 60 Hazelwood Drive, Champaign, IL 61820, USA.
| | - Jingjing Zhang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 601 S. Mathews Ave., Urbana, IL 61801, USA
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 601 S. Mathews Ave., Urbana, IL 61801, USA.
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Samanta A, Medintz IL. Nanoparticles and DNA - a powerful and growing functional combination in bionanotechnology. NANOSCALE 2016; 8:9037-95. [PMID: 27080924 DOI: 10.1039/c5nr08465b] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Functionally integrating DNA and other nucleic acids with nanoparticles in all their different physicochemical forms has produced a rich variety of composite nanomaterials which, in many cases, display unique or augmented properties due to the synergistic activity of both components. These capabilities, in turn, are attracting greater attention from various research communities in search of new nanoscale tools for diverse applications that include (bio)sensing, labeling, targeted imaging, cellular delivery, diagnostics, therapeutics, theranostics, bioelectronics, and biocomputing to name just a few amongst many others. Here, we review this vibrant and growing research area from the perspective of the materials themselves and their unique capabilities. Inorganic nanocrystals such as quantum dots or those made from gold or other (noble) metals along with metal oxides and carbon allotropes are desired as participants in these hybrid materials since they can provide distinctive optical, physical, magnetic, and electrochemical properties. Beyond this, synthetic polymer-based and proteinaceous or viral nanoparticulate materials are also useful in the same role since they can provide a predefined and biocompatible cargo-carrying and targeting capability. The DNA component typically provides sequence-based addressability for probes along with, more recently, unique architectural properties that directly originate from the burgeoning structural DNA field. Additionally, DNA aptamers can also provide specific recognition capabilities against many diverse non-nucleic acid targets across a range of size scales from ions to full protein and cells. In addition to appending DNA to inorganic or polymeric nanoparticles, purely DNA-based nanoparticles have recently surfaced as an excellent assembly platform and have started finding application in areas like sensing, imaging and immunotherapy. We focus on selected and representative nanoparticle-DNA materials and highlight their myriad applications using examples from the literature. Overall, it is clear that this unique functional combination of nanomaterials has far more to offer than what we have seen to date and as new capabilities for each of these materials are developed, so, too, will new applications emerge.
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Affiliation(s)
- Anirban Samanta
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA. and College of Science, George Mason University, Fairfax, Virginia 22030, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA.
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Alves Ferreira-Bravo I, Cozens C, Holliger P, DeStefano JJ. Selection of 2'-deoxy-2'-fluoroarabinonucleotide (FANA) aptamers that bind HIV-1 reverse transcriptase with picomolar affinity. Nucleic Acids Res 2015; 43:9587-99. [PMID: 26476448 PMCID: PMC4751925 DOI: 10.1093/nar/gkv1057] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 10/02/2015] [Indexed: 11/17/2022] Open
Abstract
Using a Systematic Evolution of Ligands by Exponential Enrichment (SELEX) protocol capable of selecting xeno-nucleic acid (XNA) aptamers, a 2′-deoxy-2′-fluoroarabinonucleotide (FANA) aptamer (referred to as FA1) to HIV-1 reverse transcriptase (HIV-1 RT) was selected. FA1 bound HIV-1 RT with KD,app values in the low pM range under different ionic conditions. Comparisons to published HIV-1 RT RNA and DNA aptamers indicated that FA1 bound at least as well as these aptamers. FA1 contained a 20 nucleotide 5′ DNA sequence followed by a 57 nucleotide region of FANA nucleotides. Removal of the fourteen 5′ DNA nucleotides did not affect binding. FA1's predicted structure was composed of four stems and four loops. All stem nucleotides could be modified to G-C base pairs (14 total changes) with a small effect on binding. Eliminating or altering most loop sequences reduced or abolished tight binding. Overall, results suggested that the structure and the sequence of FA1 were important for binding. FA1 showed strong inhibition of HIV-1 RT in extension assays while no specific binding to avian myeloblastosis or Moloney murine leukemia RTs was detected. A complete DNA version of FA1 showed low binding to HIV-1 RT, emphasizing the unique properties of FANA in HIV-1 RT binding.
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Affiliation(s)
- Irani Alves Ferreira-Bravo
- Cell Biology and Molecular Genetics, Bioscience Research Building, University of Maryland, College Park, MD 20742, USA Maryland Pathogen Research Institute, College Park, MD 20742, USA
| | - Christopher Cozens
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Jeffrey J DeStefano
- Cell Biology and Molecular Genetics, Bioscience Research Building, University of Maryland, College Park, MD 20742, USA Maryland Pathogen Research Institute, College Park, MD 20742, USA
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Qi P, Yan W, Yang Y, Li Y, Fan Y, Chen J, Yang Z, Tu Q, Huang N. Immobilization of DNA aptamers via plasma polymerized allylamine film to construct an endothelial progenitor cell-capture surface. Colloids Surf B Biointerfaces 2014; 126:70-9. [PMID: 25575347 DOI: 10.1016/j.colsurfb.2014.12.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 11/25/2014] [Accepted: 12/01/2014] [Indexed: 02/06/2023]
Abstract
The endothelial progenitor cells (EPCs) capture stent has drawn increasing attentions and become one of the most promising concepts for the next generation vascular stent. In this regard, it is of great significance to immobilize a molecule with the ability to bind EPC for rapid in vivo endothelialization with high specificity. In this work, a facile two-step method aimed at constructing a coating with specific EPC capturing aptamers is reported. The processes involves as the first-step deposition of plasma polymerized allylamine (PPAam) on a substrate to introduce amine groups, followed by the electrostatic adsorption of a 34 bases single strand DNA sequence to the PPAam surface as a second step (PPAam-DNA). Grazing incidence attenuated total reflection Fourier transform infrared spectroscopy (GATR-FTIR) and X-ray photoelectron spectroscopy (XPS) confirmed the successful immobilization of the aptamers. Quartz crystal microbalance with dissipation (QCM-D) real time monitoring result shows that about 175 ng/cm(2) aptamers were conjugated onto the PPAam surface. The interactions between the modified surfaces and human umbilical vein endothelial cells (ECs), smooth muscle cells (SMCs), and murine induced EPCs derived from mesenchymal stem cells (MSCs) were also investigated. It was demonstrated that PPAam-DNA samples could capture more EPCs, and present a cellular friendly surface for the proliferation of both EPCs and ECs but no effect on the hyperplasia of SMCs. Also, the co-culture results of 3 types of cells confirmed that the aptamer could specifically bond EPCs rather than ECs and SMCs, suggesting the competitive adhesion advantage of EPCs to ECs and SMCs. These data demonstrate that the EPC aptamer has large potential for designing an EPC captured stent and other vascular grafts with targeted in situ endothelialization.
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Affiliation(s)
- Pengkai Qi
- Key Lab of Advanced Technology of Materials of Education Ministry, Southwest Jiaotong University, Chengdu 610031, China; School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Wei Yan
- Key Lab of Advanced Technology of Materials of Education Ministry, Southwest Jiaotong University, Chengdu 610031, China; School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Ying Yang
- Key Lab of Advanced Technology of Materials of Education Ministry, Southwest Jiaotong University, Chengdu 610031, China; School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Yalong Li
- Key Lab of Advanced Technology of Materials of Education Ministry, Southwest Jiaotong University, Chengdu 610031, China; Laboratory of Biosensing and MicroMechatronics, Southwest Jiaotong University, Chengdu 610031, China
| | - Yi Fan
- Key Lab of Advanced Technology of Materials of Education Ministry, Southwest Jiaotong University, Chengdu 610031, China; School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Junying Chen
- Key Lab of Advanced Technology of Materials of Education Ministry, Southwest Jiaotong University, Chengdu 610031, China; School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Zhilu Yang
- Key Lab of Advanced Technology of Materials of Education Ministry, Southwest Jiaotong University, Chengdu 610031, China; School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China.
| | - Qiufen Tu
- Key Lab of Advanced Technology of Materials of Education Ministry, Southwest Jiaotong University, Chengdu 610031, China; Laboratory of Biosensing and MicroMechatronics, Southwest Jiaotong University, Chengdu 610031, China.
| | - Nan Huang
- Key Lab of Advanced Technology of Materials of Education Ministry, Southwest Jiaotong University, Chengdu 610031, China; School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China.
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Gedi V, Kim YP. Detection and characterization of cancer cells and pathogenic bacteria using aptamer-based nano-conjugates. SENSORS (BASEL, SWITZERLAND) 2014; 14:18302-27. [PMID: 25268922 PMCID: PMC4239906 DOI: 10.3390/s141018302] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 08/08/2014] [Accepted: 09/02/2014] [Indexed: 12/30/2022]
Abstract
Detection and characterization of cells using aptamers and aptamer-conjugated nanoprobes has evolved a great deal over the past few decades. This evolution has been driven by the easy selection of aptamers via in vitro cell-SELEX, permitting sensitive discrimination between target and normal cells, which includes pathogenic prokaryotic and cancerous eukaryotic cells. Additionally, when the aptamer-based strategies are used in conjunction with nanomaterials, there is the potential for cell targeting and therapeutic effects with improved specificity and sensitivity. Here we review recent advances in aptamer-based nano-conjugates and their applications for detecting cancer cells and pathogenic bacteria. The multidisciplinary research utilized in this field will play an increasingly significant role in clinical medicine and drug discovery.
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Affiliation(s)
- Vinayakumar Gedi
- Department of Life Science, Hanyang University, Seoul 133-791, Korea.
| | - Young-Pil Kim
- Department of Life Science, Hanyang University, Seoul 133-791, Korea.
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Pollet J, Strych U, Willson RC. A peroxidase-active aptazyme as an isothermally amplifiable label in an aptazyme-linked oligonucleotide assay for low-picomolar IgE detection. Analyst 2013; 137:5710-2. [PMID: 23103946 DOI: 10.1039/c2an36201e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A peroxidase-active hemin-aptamer was clicked onto an immunoglobulin E (IgE) binding aptamer. The resulting bifunctional aptamer was successfully used in a highly sensitive aptazyme-linked oligonucleotide assay (ALONA) for the detection of IgE. The sensitivity of the assay is enhanced by isothermal amplification of the aptazyme followed by colorimetric detection of the aptazyme's peroxidase activity, which can easily be evaluated even without advanced lab instruments.
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Affiliation(s)
- Jeroen Pollet
- Department of Chemical & Biomolecular Engineering, University of Houston, TX 77204, USA
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Grozio A, Gonzalez VM, Millo E, Sturla L, Vigliarolo T, Bagnasco L, Guida L, D'Arrigo C, De Flora A, Salis A, Martin EM, Bellotti M, Zocchi E. Selection and characterization of single stranded DNA aptamers for the hormone abscisic Acid. Nucleic Acid Ther 2013; 23:322-31. [PMID: 23971905 PMCID: PMC3760064 DOI: 10.1089/nat.2013.0418] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The hormone abscisic acid (ABA) is a small molecule involved in pivotal physiological functions in higher plants. Recently, ABA has been also identified as an endogenous hormone in mammals, regulating different cell functions including inflammatory processes, stem cell expansion, insulin release, and glucose uptake. Aptamers are short, single-stranded (ss) oligonucleotidesable to recognize target molecules with high affinity. The small size of the ABA molecule represented a challenge for aptamer development and the aim of this study was to develop specific anti-ABA DNA aptamers. Biotinylated abscisic acid (bio-ABA) was immobilized on streptavidin-coated magnetic beads. DNA aptamers against bio-ABA were selected with 7 iterative rounds of the systematic evolution of ligands by exponential enrichment method (SELEX), each round comprising incubation of the ABA-binding beads with the ssDNA sequences, DNA elution, electrophoresis, and polymerase chain reaction (PCR) amplification. The PCR product was cloned and sequenced. The binding affinity of several clones was determined using bio-ABA immobilized on streptavidin-coated plates. Aptamer 2 and aptamer 9 showed the highest binding affinity, with dissociation constants values of 0.98 ± 0.14 μM and 0.80 ± 0.07 μM, respectively. Aptamers 2 and 9 were also able to bind free, unmodified ABA and to discriminate between different ABA enantiomers and isomers. Our findings indicate that ssDNA aptamers can selectively bind ABA and could be used for the development of ABA quantitation assays.
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Affiliation(s)
- Alessia Grozio
- Department of Experimental Medicine, Section of Biochemistry, University of Genova, Genova, Italy
| | - Victor M. Gonzalez
- Departamento de Bioquímica-Investigación, IRYCIS-Hospital Ramón y Cajal, Madrid, Spain
| | - Enrico Millo
- Center of Excellence for Biomedical Research (CEBR), University of Genova, Genova, Italy
| | - Laura Sturla
- Center of Excellence for Biomedical Research (CEBR), University of Genova, Genova, Italy
| | - Tiziana Vigliarolo
- Department of Experimental Medicine, Section of Biochemistry, University of Genova, Genova, Italy
| | - Luca Bagnasco
- Department of Internal Medicine, University of Genova, Genova, Italy
| | - Lucrezia Guida
- Center of Excellence for Biomedical Research (CEBR), University of Genova, Genova, Italy
| | - Cristina D'Arrigo
- Institute for Macromolecular Studies, National Research Council, Genova, Italy
| | - Antonio De Flora
- Center of Excellence for Biomedical Research (CEBR), University of Genova, Genova, Italy
| | - Annalisa Salis
- Center of Excellence for Biomedical Research (CEBR), University of Genova, Genova, Italy
| | - Elena M. Martin
- Departamento de Bioquímica-Investigación, IRYCIS-Hospital Ramón y Cajal, Madrid, Spain
| | - Marta Bellotti
- Center of Excellence for Biomedical Research (CEBR), University of Genova, Genova, Italy
| | - Elena Zocchi
- Center of Excellence for Biomedical Research (CEBR), University of Genova, Genova, Italy
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