51
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Bauer M, Strom M, Hammond DS, Shigdar S. Anything You Can Do, I Can Do Better: Can Aptamers Replace Antibodies in Clinical Diagnostic Applications? Molecules 2019; 24:molecules24234377. [PMID: 31801185 PMCID: PMC6930532 DOI: 10.3390/molecules24234377] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 11/28/2019] [Accepted: 11/28/2019] [Indexed: 02/07/2023] Open
Abstract
The mainstay of clinical diagnostics is the use of specialised ligands that can recognise specific biomarkers relating to pathological changes. While protein antibodies have been utilised in these assays for the last 40 years, they have proven to be unreliable due to a number of reasons. The search for the 'perfect' targeting ligand or molecular probe has been slow, though the description of chemical antibodies, also known as aptamers, nearly 30 years ago suggested a replacement reagent. However, uptake has been slow to progress into the clinical environment. In this review, we discuss the issues associated with antibodies and describe some of the applications of aptamers that have relevancy to the clinical diagnostic environment.
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Affiliation(s)
- Michelle Bauer
- School of Medicine Deakin University, Geelong, Victoria 3128, Australia; (M.B.); (M.S.); (D.S.H.)
| | - Mia Strom
- School of Medicine Deakin University, Geelong, Victoria 3128, Australia; (M.B.); (M.S.); (D.S.H.)
| | - David S Hammond
- School of Medicine Deakin University, Geelong, Victoria 3128, Australia; (M.B.); (M.S.); (D.S.H.)
- Centre for Molecular and Medical Research, Deakin University, Geelong, Victoria 3128, Australia
| | - Sarah Shigdar
- School of Medicine Deakin University, Geelong, Victoria 3128, Australia; (M.B.); (M.S.); (D.S.H.)
- Centre for Molecular and Medical Research, Deakin University, Geelong, Victoria 3128, Australia
- Correspondence:
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52
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Godri Pollitt KJ, Kim JH, Peccia J, Elimelech M, Zhang Y, Charkoftaki G, Hodges B, Zucker I, Huang H, Deziel NC, Murphy K, Ishii M, Johnson CH, Boissevain A, O'Keefe E, Anastas PT, Orlicky D, Thompson DC, Vasiliou V. 1,4-Dioxane as an emerging water contaminant: State of the science and evaluation of research needs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 690:853-866. [PMID: 31302550 DOI: 10.1016/j.scitotenv.2019.06.443] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/26/2019] [Accepted: 06/26/2019] [Indexed: 06/10/2023]
Abstract
1,4-Dioxane has historically been used to stabilize chlorinated solvents and more recently has been found as a contaminant of numerous consumer and food products. Once discharged into the environment, its physical and chemical characteristics facilitate migration in groundwater, resulting in widespread contamination of drinking water supplies. Over one-fifth of U.S. public drinking water supplies contain detectable levels of 1,4-dioxane. Remediation efforts using common adsorption and membrane filtration techniques have been ineffective, highlighting the need for alternative removal approaches. While the data evaluating human exposure and health effects are limited, animal studies have shown chronic exposure to cause carcinogenic responses in the liver across multiple species and routes of exposure. Based on this experimental evidence, the U.S. Environmental Protection Agency has listed 1,4-dioxane as a high priority chemical and classified it as a probable human carcinogen. Despite these health concerns, there are no federal or state maximum contaminant levels for 1,4-dioxane. Effective public health policy for this emerging contaminant requires additional information about human health effects, chemical interactions, environmental fate, analytical detection, and treatment technologies. This review highlights the current state of knowledge, key uncertainties, and data needs for future research on 1,4-dioxane.
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Affiliation(s)
- Krystal J Godri Pollitt
- Department of Environmental Health Sciences, School of Public Health, Yale University, New Haven, CT 06510, United States.
| | - Jae-Hong Kim
- Department of Chemical & Environmental Engineering, School of Engineering & Applied Science, Yale University, New Haven, CT 06520, United States
| | - Jordan Peccia
- Department of Chemical & Environmental Engineering, School of Engineering & Applied Science, Yale University, New Haven, CT 06520, United States
| | - Menachem Elimelech
- Department of Chemical & Environmental Engineering, School of Engineering & Applied Science, Yale University, New Haven, CT 06520, United States
| | - Yawei Zhang
- Department of Environmental Health Sciences, School of Public Health, Yale University, New Haven, CT 06510, United States; Department of Surgery, School of Medicine, Yale University, New Haven, CT 06520, United States
| | - Georgia Charkoftaki
- Department of Environmental Health Sciences, School of Public Health, Yale University, New Haven, CT 06510, United States
| | - Brenna Hodges
- Department of Chemical & Environmental Engineering, School of Engineering & Applied Science, Yale University, New Haven, CT 06520, United States
| | - Ines Zucker
- Department of Chemical & Environmental Engineering, School of Engineering & Applied Science, Yale University, New Haven, CT 06520, United States
| | - Huang Huang
- Department of Environmental Health Sciences, School of Public Health, Yale University, New Haven, CT 06510, United States
| | - Nicole C Deziel
- Department of Environmental Health Sciences, School of Public Health, Yale University, New Haven, CT 06510, United States
| | - Kara Murphy
- Northeast States for Coordinated Air Use Management (NESCAUM), Boston, MA 02111, United States
| | - Momoko Ishii
- Department of Environmental Health Sciences, School of Public Health, Yale University, New Haven, CT 06510, United States
| | - Caroline H Johnson
- Department of Environmental Health Sciences, School of Public Health, Yale University, New Haven, CT 06510, United States
| | | | - Elaine O'Keefe
- Office of Public Health Practice, School of Public Health, Yale University, New Haven, CT 06510, United States
| | - Paul T Anastas
- Department of Environmental Health Sciences, School of Public Health, Yale University, New Haven, CT 06510, United States; Center for Green Chemistry and Green Engineering, Department of Chemistry, Yale School of Forestry & Environmental Studies, New Haven, CT 06511, United States
| | - David Orlicky
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO 80045, United States
| | - David C Thompson
- Department of Clinical Pharmacy, University of Colorado School of Pharmacy, Aurora, CO 80045, United States
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, School of Public Health, Yale University, New Haven, CT 06510, United States.
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53
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Wilson BD, Hariri AA, Thompson IAP, Eisenstein M, Soh HT. Independent control of the thermodynamic and kinetic properties of aptamer switches. Nat Commun 2019; 10:5079. [PMID: 31699984 PMCID: PMC6838323 DOI: 10.1038/s41467-019-13137-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 10/21/2019] [Indexed: 12/15/2022] Open
Abstract
Molecular switches that change their conformation upon target binding offer powerful capabilities for biotechnology and synthetic biology. Aptamers are useful as molecular switches because they offer excellent binding properties, undergo reversible folding, and can be engineered into many nanostructures. Unfortunately, the thermodynamic and kinetic properties of the aptamer switches developed to date are intrinsically coupled, such that high temporal resolution can only be achieved at the cost of lower sensitivity or high background. Here, we describe a design strategy that decouples and enables independent control over the thermodynamics and kinetics of aptamer switches. Starting from a single aptamer, we create an array of aptamer switches with effective dissociation constants ranging from 10 μM to 40 mM and binding kinetics ranging from 170 ms to 3 s. Our strategy is broadly applicable to other aptamers, enabling the development of switches suitable for a diverse range of biotechnology applications. Aptamer switches are promising biotechnological tools but coupling of their affinity and temporal response limits their versatility. Here, the authors developed an intramolecular strand-displacement strategy that allows for independent fine-tuning of thermodynamics and kinetics of aptamer switches.
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Affiliation(s)
- Brandon D Wilson
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Amani A Hariri
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Ian A P Thompson
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Michael Eisenstein
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA.,Department of Radiology, Stanford University, Stanford, CA, 94305, USA
| | - H Tom Soh
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA. .,Department of Radiology, Stanford University, Stanford, CA, 94305, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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54
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An aptamer cocktail-based electrochemical aptasensor for direct capture and rapid detection of tetracycline in honey. Microchem J 2019. [DOI: 10.1016/j.microc.2019.104179] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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55
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Gao H, Zhao J, Huang Y, Cheng X, Wang S, Han Y, Xiao Y, Lou X. Universal Design of Structure-Switching Aptamers with Signal Reporting Functionality. Anal Chem 2019; 91:14514-14521. [PMID: 31614078 DOI: 10.1021/acs.analchem.9b03368] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Structure-switching aptamers (SSAs) offer a promising recognition element for sensor development. However, the generation of SSAs via in vitro aptamer selection technologies or postselection engineering is challenging. Inspired by the two-domain structure of antibodies, we have devised a simple, universal strategy for engineering aptamers into SSAs with signal reporting functionality. These constructs consist of a "constant" domain, comprising a split DNAzyme G-quadruplex (G4) region for signal transduction, and a "variable" domain, comprising an aptamer sequence capable of specific target binding. In the absence of target, the G4-SSA construct folds into a parallel G4 structure with high peroxidase catalytic activity. Target binding disrupts the G4 structure, resulting in low enzymatic activity. We demonstrate that this change in DNAzyme activity enables sensitive and specific colorimetric detection of diverse targets including Hg2+, thrombin, sulfadimethoxine, cocaine, and 17β-estradiol. G4-SSAs can also achieve label-free fluorescence detection of various targets using a specific G4-binding dye. We demonstrate that diverse aptamers can be readily engineered into G4-SSA constructs independent of target class, binding affinity, aptamer length, or structure. This design strategy could broadly extend the power, accessibility, and utility of numerous SSA-based biosensors.
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Affiliation(s)
- Hualong Gao
- Department of Chemistry , Capital Normal University , Xisanhuan North Road, 105 , Beijing 100048 , China
| | - Jiaoxing Zhao
- Department of Chemistry , Capital Normal University , Xisanhuan North Road, 105 , Beijing 100048 , China
| | - Yang Huang
- Department of Chemistry , Capital Normal University , Xisanhuan North Road, 105 , Beijing 100048 , China
| | - Xiao Cheng
- Department of Chemistry , Capital Normal University , Xisanhuan North Road, 105 , Beijing 100048 , China
| | - Shuo Wang
- Department of Chemistry , Capital Normal University , Xisanhuan North Road, 105 , Beijing 100048 , China
| | - Yu Han
- Department of Chemistry , Capital Normal University , Xisanhuan North Road, 105 , Beijing 100048 , China
| | - Yi Xiao
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - Xinhui Lou
- Department of Chemistry , Capital Normal University , Xisanhuan North Road, 105 , Beijing 100048 , China.,Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
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56
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Roxo C, Kotkowiak W, Pasternak A. G-Quadruplex-Forming Aptamers-Characteristics, Applications, and Perspectives. Molecules 2019; 24:E3781. [PMID: 31640176 PMCID: PMC6832456 DOI: 10.3390/molecules24203781] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/16/2019] [Accepted: 10/18/2019] [Indexed: 12/31/2022] Open
Abstract
G-quadruplexes constitute a unique class of nucleic acid structures formed by G-rich oligonucleotides of DNA- or RNA-type. Depending on their chemical nature, loops length, and localization in the sequence or structure molecularity, G-quadruplexes are highly polymorphic structures showing various folding topologies. They may be formed in the human genome where they are believed to play a pivotal role in the regulation of multiple biological processes such as replication, transcription, and translation. Thus, natural G-quadruplex structures became prospective targets for disease treatment. The fast development of systematic evolution of ligands by exponential enrichment (SELEX) technologies provided a number of G-rich aptamers revealing the potential of G-quadruplex structures as a promising molecular tool targeted toward various biologically important ligands. Because of their high stability, increased cellular uptake, ease of chemical modification, minor production costs, and convenient storage, G-rich aptamers became interesting therapeutic and diagnostic alternatives to antibodies. In this review, we describe the recent advances in the development of G-quadruplex based aptamers by focusing on the therapeutic and diagnostic potential of this exceptional class of nucleic acid structures.
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Affiliation(s)
- Carolina Roxo
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Weronika Kotkowiak
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Anna Pasternak
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
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57
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Ebrahimi SB, Samanta D, Cheng HF, Nathan LI, Mirkin CA. Forced Intercalation (FIT)-Aptamers. J Am Chem Soc 2019; 141:13744-13748. [PMID: 31441661 DOI: 10.1021/jacs.9b06450] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Aptamers are oligonucleotide sequences that can be evolved to bind to various analytes of interest. Here, we present a general design strategy that transduces an aptamer-target binding event into a fluorescence readout via the use of a viscosity-sensitive dye. Target binding to the aptamer leads to forced intercalation (FIT) of the dye between oligonucleotide base pairs, increasing its fluorescence by up to 20-fold. Specifically, we demonstrate that FIT-aptamers can report target presence through intramolecular conformational changes, sandwich assays, and target-templated reassociation of split-aptamers, showing that the most common aptamer-target binding modes can be coupled to a FIT-based readout. This strategy also can be used to detect the formation of a metallo-base pair within a duplexed strand and is therefore attractive for screening for metal-mediated base pairing events. Importantly, FIT-aptamers reduce false-positive signals typically associated with fluorophore-quencher based systems, quantitatively outperform FRET-based probes by providing up to 15-fold higher signal to background ratios, and allow rapid and highly sensitive target detection (nanomolar range) in complex media such as human serum. Taken together, FIT-aptamers are a new class of signaling aptamers which contain a single modification, yet can be used to detect a broad range of targets.
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58
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Iqbal A, Liu J, Dixon B, Zargar B, Sattar SA. Development and application of DNA-aptamer-coupled magnetic beads and aptasensors for the detection of Cryptosporidium parvum oocysts in drinking and recreational water resources. Can J Microbiol 2019; 65:851-857. [PMID: 31404505 DOI: 10.1139/cjm-2019-0153] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Environmentally stable and disinfectant-resistant oocysts of Cryptosporidium spp. shed in the feces of infected humans and animals frequently contaminate water resources and are subsequently spread via potable and recreational waters. The current monoclonal-antibody-based methods for detecting them in water are slow, labor-intensive, and demand skills to interpret the results. We have developed DNA-aptamer-based aptasensors, coupled with magnetic beads, to detect and identify the oocysts of C. parvum for monitoring recreational and drinking water sources. A sensitive and specific electrochemical aptasensor (3'-biotinylated R4-6 aptamer) was used as a secondary ligand to bind the streptavidin-coated magnetic beads. This was incorporated into a probe using gold nanoparticle modified screen-printed carbon electrodes. Square wave voltammetry allowed for specific recognition of C. parvum oocysts. The aptamer-coated probes had an oocyst detection limit of 50. It did not bind to the cysts of Giardia duodenalis, another common waterborne pathogen, thus indicating its high specificity for the target pathogen. The system could successfully detect C. parvum oocysts in spiked samples of the raw lake and river waters. Therefore, the combined use of the aptasensor and magnetic beads has the potential to monitor water quality for C. parvum oocysts in field samples without relying on monoclonal antibodies and skill-demanding microscopy.
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Affiliation(s)
- Asma Iqbal
- CREM Co Labs, Units 1-2, 3403 American Drive, Mississauga, ON L4V 1T4, Canada
| | - Juewen Liu
- Department of Chemistry, Faculty of Science, University of Waterloo, 200 University Avenue W, Waterloo, ON N2L 3G1, Canada
| | - Brent Dixon
- Bureau of Microbial Hazards, Food Directorate, Health Canada, 251 Sir Frederick Banting, Ottawa, ON K1Y 0M1, Canada
| | - Bahram Zargar
- CREM Co Labs, Units 1-2, 3403 American Drive, Mississauga, ON L4V 1T4, Canada
| | - Syed A Sattar
- CREM Co Labs, Units 1-2, 3403 American Drive, Mississauga, ON L4V 1T4, Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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59
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A DNA-Based Biosensor Assay for the Kinetic Characterization of Ion-Dependent Aptamer Folding and Protein Binding. Molecules 2019; 24:molecules24162877. [PMID: 31398834 PMCID: PMC6718989 DOI: 10.3390/molecules24162877] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/02/2019] [Accepted: 08/05/2019] [Indexed: 11/16/2022] Open
Abstract
Therapeutic and diagnostic nucleic acid aptamers are designed to bind tightly and specifically to their target. The combination of structural and kinetic analyses of aptamer interactions has gained increasing importance. Here, we present a fluorescence-based switchSENSE aptasensor for the detailed kinetic characterization of aptamer-analyte interaction and aptamer folding, employing the thrombin-binding aptamer (TBA) as a model system. Thrombin-binding aptamer folding into a G-quadruplex and its binding to thrombin strongly depend on the type and concentration of ions present in solution. We observed conformational changes induced by cations in real-time and determined the folding and unfolding kinetics of the aptamer. The aptamer's affinity for K+ was found to be more than one order of magnitude higher than for other cations (K+ > NH4+ >> Na+ > Li+). The aptamer's affinity to its protein target thrombin in the presence of different cations followed the same trend but differed by more than three orders of magnitude (KD = 0.15 nM to 250 nM). While the stability (kOFF) of the thrombin-TBA complex was similar in all conditions, the cation type strongly influenced the association rate (kON). These results demonstrated that protein-aptamer binding is intrinsically related to the correct aptamer fold and, hence, to the presence of stabilizing ions. Because fast binding kinetics with on-rates exceeding 108 M-1s-1 can be quantified, and folding-related phenomena can be directly resolved, switchSENSE is a useful analytical tool for in-depth characterization of aptamer-ion and aptamer-protein interactions.
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60
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Moutsiopoulou A, Broyles D, Dikici E, Daunert S, Deo SK. Molecular Aptamer Beacons and Their Applications in Sensing, Imaging, and Diagnostics. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1902248. [PMID: 31313884 PMCID: PMC6715520 DOI: 10.1002/smll.201902248] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 05/31/2019] [Indexed: 05/07/2023]
Abstract
The ability to monitor types, concentrations, and activities of different biomolecules is essential to obtain information about the molecular processes within cells. Successful monitoring requires a sensitive and selective tool that can respond to these molecular changes. Molecular aptamer beacon (MAB) is a molecular imaging and detection tool that enables visualization of small or large molecules by combining the selectivity and sensitivity of molecular beacon and aptamer technologies. MAB design leverages structure switching and specific recognition to yield an optical on/off switch in the presence of the target. Various donor-quencher pairs such as fluorescent dyes, quantum dots, carbon-based materials, and metallic nanoparticles have been employed in the design of MABs. In this work, the diverse biomedical applications of MAB technology are focused on. Different conjugation strategies for the energy donor-acceptor pairs are addressed, and the overall sensitivities of each detection system are discussed. The future potential of this technology in the fields of biomedical research and diagnostics is also highlighted.
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Affiliation(s)
- Angeliki Moutsiopoulou
- Leonard M. Miller School of Medicine, Department of Biochemistry and Molecular Biology, University of Miami, Miami, FL, 33136, USA
- Dr. J. T. Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, FL, 33136, USA
- Department of Chemistry Coral Gables, University of Miami, FL, 33146, USA
| | - David Broyles
- Leonard M. Miller School of Medicine, Department of Biochemistry and Molecular Biology, University of Miami, Miami, FL, 33136, USA
- Dr. J. T. Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, FL, 33136, USA
| | - Emre Dikici
- Leonard M. Miller School of Medicine, Department of Biochemistry and Molecular Biology, University of Miami, Miami, FL, 33136, USA
- Dr. J. T. Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, FL, 33136, USA
| | - Sylvia Daunert
- Leonard M. Miller School of Medicine, Department of Biochemistry and Molecular Biology, University of Miami, Miami, FL, 33136, USA
- Dr. J. T. Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, FL, 33136, USA
- University of Miami Clinical and Translational Science Institute, Miami, FL, 33136, USA
| | - Sapna K Deo
- Leonard M. Miller School of Medicine, Department of Biochemistry and Molecular Biology, University of Miami, Miami, FL, 33136, USA
- Dr. J. T. Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, FL, 33136, USA
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61
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Mahmoud M, Laufer S, Deigner HP. Data for homogeneous thermofluorimetric assays for ethanolamine using aptamers and a PCR instrument. Data Brief 2019; 24:103946. [PMID: 31080860 PMCID: PMC6506705 DOI: 10.1016/j.dib.2019.103946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 03/20/2019] [Accepted: 04/15/2019] [Indexed: 11/04/2022] Open
Abstract
The data presented in this article describe the quantitative detection of small molecules e.g. ethanolamine through the shifts in the melting temperatures of aptamer beacons presented in the research article entitled “An aptamer based thermofluorimetric assay for ethanolamine” [1]. The data include prediction and optimization of the folding structure of the aptamers. Moreover, the data from using intercalating dyes such as SYBR green is included for comparison. The presented data could be used for the design of other small molecules sensing platforms using aptamers.
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Affiliation(s)
- Mostafa Mahmoud
- Furtwangen University, Institute of Precision Medicine, Jakob-Kienzle-Straße 17, 78054, Villingen-Schwenningen, Germany.,Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Stefan Laufer
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Hans-Peter Deigner
- Furtwangen University, Institute of Precision Medicine, Jakob-Kienzle-Straße 17, 78054, Villingen-Schwenningen, Germany.,Fraunhofer Institute IZI, Leipzig, EXIM Department, Schillingallee 68, D-18057, Rostock, Germany
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62
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Double Magnetic Separation-assisted Fluorescence Method for Sensitive Detection of Ochratoxin A. Chem Res Chin Univ 2019. [DOI: 10.1007/s40242-019-8322-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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63
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Shin S, Kim B, Kim YJ, Choi S. Integrated microfluidic pneumatic circuit for point-of-care molecular diagnostics. Biosens Bioelectron 2019; 133:169-176. [DOI: 10.1016/j.bios.2019.03.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/09/2019] [Accepted: 03/11/2019] [Indexed: 02/06/2023]
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64
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Wang C, Sun L, Zhao Q. A simple aptamer molecular beacon assay for rapid detection of aflatoxin B1. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2019.01.029] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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65
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Small molecule electro-optical binding assay using nanopores. Nat Commun 2019; 10:1797. [PMID: 30996223 PMCID: PMC6470146 DOI: 10.1038/s41467-019-09476-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 03/12/2019] [Indexed: 01/12/2023] Open
Abstract
The identification of short nucleic acids and proteins at the single molecule level is a major driving force for the development of novel detection strategies. Nanopore sensing has been gaining in prominence due to its label-free operation and single molecule sensitivity. However, it remains challenging to detect small molecules selectively. Here we propose to combine the electrical sensing modality of a nanopore with fluorescence-based detection. Selectivity is achieved by grafting either molecular beacons, complementary DNA, or proteins to a DNA molecular carrier. We show that the fraction of synchronised events between the electrical and optical channels, can be used to perform single molecule binding assays without the need to directly label the analyte. Such a strategy can be used to detect targets in complex biological fluids such as human serum and urine. Future optimisation of this technology may enable novel assays for quantitative protein detection as well as gene mutation analysis with applications in next-generation clinical sample analysis. Nanopore detection of small molecules can be improved using molecular carriers, but separating a small analyte from the carrier signal can be challenging. Here the authors address this challenge using simultaneous electrical and optical readout in nanopore sensing to detect small molecules and quantify binding affinities.
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66
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DNA aptamers for the recognition of HMGB1 from Plasmodium falciparum. PLoS One 2019; 14:e0211756. [PMID: 30964875 PMCID: PMC6456224 DOI: 10.1371/journal.pone.0211756] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 03/24/2019] [Indexed: 12/21/2022] Open
Abstract
Rapid Diagnostic Tests (RDTs) for malaria are restricted to a few biomarkers and antibody-mediated detection. However, the expression of commonly used biomarkers varies geographically and the sensibility of immunodetection can be affected by batch-to-batch differences or limited thermal stability. In this study we aimed to overcome these limitations by identifying a potential biomarker and by developing molecular sensors based on aptamer technology. Using gene expression databases, ribosome profiling analysis, and structural modeling, we find that the High Mobility Group Box 1 protein (HMGB1) of Plasmodium falciparum is highly expressed, structurally stable, and present along all blood-stages of P. falciparum infection. To develop biosensors, we used in vitro evolution techniques to produce DNA aptamers for the recombinantly expressed HMG-box, the conserved domain of HMGB1. An evolutionary approach for evaluating the dynamics of aptamer populations suggested three predominant aptamer motifs. Representatives of the aptamer families were tested for binding parameters to the HMG-box domain using microscale thermophoresis and rapid kinetics. Dissociation constants of the aptamers varied over two orders of magnitude between nano- and micromolar ranges while the aptamer-HMG-box interaction occurred in a few seconds. The specificity of aptamer binding to the HMG-box of P. falciparum compared to its human homolog depended on pH conditions. Altogether, our study proposes HMGB1 as a candidate biomarker and a set of sensing aptamers that can be further developed into rapid diagnostic tests for P. falciparum detection.
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67
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Munzar JD, Ng A, Juncker D. Duplexed aptamers: history, design, theory, and application to biosensing. Chem Soc Rev 2019; 48:1390-1419. [PMID: 30707214 DOI: 10.1039/c8cs00880a] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nucleic acid aptamers are single stranded DNA or RNA sequences that specifically bind a cognate ligand. In addition to their widespread use as stand-alone affinity binding reagents in analytical chemistry, aptamers have been engineered into a variety of ligand-specific biosensors, termed aptasensors. One of the most common aptasensor formats is the duplexed aptamer (DA). As defined herein, DAs are aptasensors containing two nucleic acid elements coupled via Watson-Crick base pairing: (i) an aptamer sequence, which serves as a ligand-specific receptor, and (ii) an aptamer-complementary element (ACE), such as a short DNA oligonucleotide, which is designed to hybridize to the aptamer. The ACE competes with ligand binding, such that DAs generate a signal upon ligand-dependent ACE-aptamer dehybridization. DAs possess intrinsic advantages over other aptasensor designs. For example, DA biosensing designs generalize across DNA and RNA aptamers, DAs are compatible with many readout methods, and DAs are inherently tunable on the basis of nucleic acid hybridization. However, despite their utility and popularity, DAs have not been well defined in the literature, leading to confusion over the differences between DAs and other aptasensor formats. In this review, we introduce a framework for DAs based on ACEs, and use this framework to distinguish DAs from other aptasensor formats and to categorize cis- and trans-DA designs. We then explore the ligand binding dynamics and chemical properties that underpin DA systems, which fall under conformational selection and induced fit models, and which mirror classical SN1 and SN2 models of nucleophilic substitution reactions. We further review a variety of in vitro and in vivo applications of DAs in the chemical and biological sciences, including riboswitches and riboregulators. Finally, we present future directions of DAs as ligand-responsive nucleic acids. Owing to their tractability, versatility and ease of engineering, DA biosensors bear a great potential for the development of new applications and technologies in fields ranging from analytical chemistry and mechanistic modeling to medicine and synthetic biology.
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Affiliation(s)
- Jeffrey D Munzar
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
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68
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Mahmoud M, Laufer S, Deigner HP. An aptamer based thermofluorimetric assay for ethanolamine. Biochimie 2019; 158:233-237. [PMID: 30685448 DOI: 10.1016/j.biochi.2019.01.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 01/21/2019] [Indexed: 12/26/2022]
Abstract
There is a great need for fast, simple and precise diagnostic assays capable of direct quantification of biomarkers in complex biological matrices. Yet, the commonly used techniques such as ELISA/Immunoassays are tedious and involve various steps e.g. blocking, washing and signal development. Moreover, most of these assays have very limited ability of detecting small molecules and have hardly any multiplexing capabilities. The gold standard and alternative, mass-spectrometry, however, depends upon expensive hardware and is incompatible with point of care (POC) diagnostics. As opposed to POC assays for proteins or larger targets where variable formats are readily available. Here, we present a simple, versatile and fast one-step assay for detecting a small molecule, ethanolamine as example. The assay makes use of commonly available qPCR machines to detect target-concentration dependent shifts in the melting temperatures of aptamer beacons. The method allows detection of ethanolamine in the low nM range without requiring tedious elaboration of assay conditions as required for molecular beacons at room temperature. If generalizable, it may change the situation of small molecule assays significantly.
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Affiliation(s)
- Mostafa Mahmoud
- Furtwangen University, Institute of Precision Medicine, Jakob-Kienzle-Straße 17, 78054, Villingen-Schwenningen, Germany; Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Stefan Laufer
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Hans-Peter Deigner
- Furtwangen University, Institute of Precision Medicine, Jakob-Kienzle-Straße 17, 78054, Villingen-Schwenningen, Germany; Fraunhofer Institute IZI, Leipzig, EXIM Department, Schillingallee 68, D-18057, Rostock, Germany.
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69
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Jung Y, Lee CY, Park KS, Park HG. Sensitive and specific detection of proteins based on target-responsive DNA polymerase activity. Anal Chim Acta 2019; 1059:80-85. [PMID: 30876635 DOI: 10.1016/j.aca.2019.01.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 11/09/2018] [Accepted: 01/15/2019] [Indexed: 10/27/2022]
Abstract
We herein describe a novel method for the detection of target protein based on the target-responsive DNA polymerase activity. In the sensor, two different types of DNA aptamers with the respective functions: one binds to the target protein and the other binds to DNA polymerase, are rationally engineered and combined to form the detection probe that regulates DNA polymerase activity in response to the target protein. In the presence of target protein, the detection probe becomes destabilized and stops the inhibition of DNA polymerase activity. Consequently, the active DNA polymerase initiates the primer extension reaction on the target-specific DNA aptamer, which recycles the target protein to promote another activation cycle of DNA polymerase. In addition, DNA polymerase also catalyzes the primer extension reaction on the primer/template complex in conjugation with TaqMan probe, leading to the significantly enhanced fluorescence intensities. With this novel strategy, we detected a model target protein, lysozyme with a limit of detection as low as 0.80 nM. In addition, the practical applicability of this system was successfully demonstrated by determining lysozyme in human serum.
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Affiliation(s)
- Yujin Jung
- Department of Chemical and Biomolecular Engineering (BK21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Chang Yeol Lee
- Department of Chemical and Biomolecular Engineering (BK21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Ki Soo Park
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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70
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Comparison of turn-on and ratiometric fluorescent G-quadruplex aptasensor approaches for the detection of ATP. Anal Bioanal Chem 2019; 411:1319-1330. [PMID: 30612178 DOI: 10.1007/s00216-018-1484-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 10/19/2018] [Accepted: 11/07/2018] [Indexed: 12/31/2022]
Abstract
Two fluorescent aptasensor methods were developed for the detection of ATP in biochemical systems. The first method consisted of a label-free fluorescent "turn-on" approach using a guanine-rich ATP aptamer sequence and the DNA-binding agent berberine complex. In the presence of ATP, the ATP preferentially binds with its aptamer and conformationally changes into a G-quadruplex structure. The association of berberine with the G-quadruplex results in the enhancement of the fluorescence signal of the former. The detection limit of ATP was found to be 3.5 μM. Fluorescence, circular dichroism and melting temperature (Tm) experiments were carried out to confirm the binding specificity and structural changes. The second method employs the ratiometric fluorescent approach based on the Forster resonance energy transfer (FRET) for the detection of ATP using berberine along with a quencher (AuNRs, AgNPs) and a fluorophore (red quantum dots (RQDs), carbon dots (CDs)) labeled at 5' and 3' termini of the ATP-binding aptamer sequence. Upon addition of ATP and berberine, ATP specifically binds with its aptamer leading to the formation of G-quadruplex, and similarly, berberine also binds to the G-quadruplex. This leads to an enhancement of fluorescence of berberine while that of RQD and CDs were significantly quenched via FRET. The respective detection limits calculated were 3.6 μM and 3.8 μM, indicating these fluorescent aptasensor methods may be used for a wide variety of small molecules. Graphical abstract.
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71
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Tachallait H, Safir Filho M, Marzag H, Bougrin K, Demange L, Martin AR, Benhida R. A straightforward and versatile FeCl3 catalyzed Friedel–Crafts C-glycosylation process. Application to the synthesis of new functionalized C-nucleosides. NEW J CHEM 2019. [DOI: 10.1039/c8nj06300a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Rapid and straightforward access to C-nucleosides using an inexpensive FeCl3 catalyst.
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Affiliation(s)
- Hamza Tachallait
- Laboratoire de Chimie des Plantes et de Synthèse Organique et Bioorganique
- URAC23
- Faculté des Sciences
- 1014 Rabat
- Morocco
| | - Mauro Safir Filho
- Université Côte d’Azur
- CNRS
- Institut de Chimie de Nice UMR 7272
- 06108 Nice
- France
| | - Hamid Marzag
- Université Côte d’Azur
- CNRS
- Institut de Chimie de Nice UMR 7272
- 06108 Nice
- France
| | - Khalid Bougrin
- Laboratoire de Chimie des Plantes et de Synthèse Organique et Bioorganique
- URAC23
- Faculté des Sciences
- 1014 Rabat
- Morocco
| | - Luc Demange
- Université Côte d’Azur
- CNRS
- Institut de Chimie de Nice UMR 7272
- 06108 Nice
- France
| | - Anthony R. Martin
- Université Côte d’Azur
- CNRS
- Institut de Chimie de Nice UMR 7272
- 06108 Nice
- France
| | - Rachid Benhida
- Université Côte d’Azur
- CNRS
- Institut de Chimie de Nice UMR 7272
- 06108 Nice
- France
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72
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Lin KC, Jagannath B, Muthukumar S, Prasad S. Sub-picomolar label-free detection of thrombin using electrochemical impedance spectroscopy of aptamer-functionalized MoS 2. Analyst 2018. [PMID: 28650005 DOI: 10.1039/c7an00548b] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
An ultrasensitive aptasensor for the label free non-faradaic detection of thrombin has been demonstrated on molybdenum disulphide (MoS2) nanosheets. These nanosheets were physiochemically immobilized onto a silicon micro-electrode platform. Thrombin detection was achieved through the charge modulation of the electrical double layer due to the specific and dose dependent binding of thrombin to the surface of thiol terminated ssDNA aptamer functionalized MoS2 nanosheets. Electrical double layer charge modulation associated with thrombin binding was characterized using electrochemical impedance spectroscopy. Dynamic light scattering was also used to confirm the dose dependent behavior. ATR-FTIR spectroscopy and XPS analysis were independently used to validate the functionalization of the ssDNA aptamer onto MoS2 nanosheets. ssDNA aptamer functionalized molybdenum disulfide (MoS2) for selective and specific capture of thrombin was demonstrated both in phosphate buffered saline (PBS) and human serum. The optimized immunoassay enabled the detection of thrombin ranging from 267 fM to 267 pM in phosphate buffer. The limit of detection of 53 pM and the linear dynamic range of detection of thrombin ranged from 53 to 854 pM in human serum. The rapid response time for the electrochemical impedance spectroscopy signal makes it an attractive option for the real-time detection of thrombin based point-of-care diagnostic devices.
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Affiliation(s)
- Kai-Chun Lin
- Department of Bioengineering, University of Texas, Dallas, Richardson, TX 75080, USA.
| | - Badrinath Jagannath
- Department of Bioengineering, University of Texas, Dallas, Richardson, TX 75080, USA.
| | | | - Shalini Prasad
- Department of Bioengineering, University of Texas, Dallas, Richardson, TX 75080, USA.
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73
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Fan TW, Hsing IM. Kinetically modulated specificity against single-base mutants in nucleic acid recycling circuitry using the destabilization motif. Analyst 2018; 142:2786-2795. [PMID: 28671226 DOI: 10.1039/c6an02731h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Signal amplification in nucleic acid sensing improves detection sensitivity, but difficulties remain in sustaining specificity over time, particularly under excess amounts of single-base mutants. Here, we report simple, self-refining target recycling circuitry, which cumulates differentiation between on and off targets by 2-step cyclic interaction with the sensing probe. In the reaction, the analyte recycles only if the protective strand of the sensing probe is removed. The dissociation kinetics of such interaction was modulated by reacting it with different lengths of assistant strands. When shorter assistant strands are used, the destabilization motif of the sensing probe has to spontaneously dissociate before another assistant strand approaches and fully displaces it. This sets up a high kinetic barrier sensitive to the subtle reaction energy differences imposed by the single-base mutants, and substantially improved specificity. As a proof of concept, a microRNA 21 DNA analogue was chosen as our target analyte together with its 14 point mutants (substitution, insertion, or deletion) for specificity measurements. The experimental results corroborate that our system amplifies signals in a comparable manner to the traditional one-layer recycling approach but with negligible system leakage. With the use of shortened assistant strands, up to 100 fold increase in the discrimination factor against the single-base mutants is observed. Specificity is sustainable or even increased over long period measurements (i.e. 4 days). More importantly, target differentiation is successfully demonstrated even in excess amounts of spurious analogs (100×) and low target frequency mixtures (i.e. 0.1%), which mimic the lean conditions practically encountered. Explicit mechanisms of the system specificity are elucidated through analytical calculations and free energy level diagrams. The modularity of the destabilization motif herein promises detection of different nucleic acid based targets and integration into other signal amplification approaches for specificity enhancement.
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Affiliation(s)
- Tsz Wing Fan
- Department of Chemical and Biomolecular Engineering, Clear Water Bay, Kowloon, Hong Kong.
| | - I-Ming Hsing
- Department of Chemical and Biomolecular Engineering, Clear Water Bay, Kowloon, Hong Kong. and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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74
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Deng R, Dong Y, Xia X, Dai Y, Zhang K, He Q, Zeng WC, Ren X, Li J. Recognition-Enhanced Metastably Shielded Aptamer for Digital Quantification of Small Molecules. Anal Chem 2018; 90:14347-14354. [PMID: 30411873 DOI: 10.1021/acs.analchem.8b03763] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Aptamers are recognized as competitive affinity reagents; their application, however, often suffers from their relatively low target binding affinity, especially for small molecules. We herein introduce the concept of a recognition-enhanced metastably shielded aptamer probe (RMSApt) and explore its performance for digital quantification of low-affinity small molecules. The RMSApt design employs the idea of constructing an allosteric aptamer probe conferring a minor energy gap in the recognition switch process to facilitate target binding and probe response, in turn significantly improving the recognition efficiency for low-affinity targets. The probe design strategy boosts the application of aptamers for precisely quantifying targets with a dissociation constant Kd ranging from 10-4 to 10-9 M, which would cover most of the small-molecule species that exist binding aptamers. Thus, RMSApt would facilitate the translation of aptamers for medical diagnosis, food safety, and environmental screening.
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Affiliation(s)
- Ruijie Deng
- College of Light Industry, Textile and Food Engineering and Healthy Food Evaluation Research Center , Sichuan University , Chengdu 610065 , China.,Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | - Yi Dong
- College of Light Industry, Textile and Food Engineering and Healthy Food Evaluation Research Center , Sichuan University , Chengdu 610065 , China
| | - Xuhan Xia
- College of Light Industry, Textile and Food Engineering and Healthy Food Evaluation Research Center , Sichuan University , Chengdu 610065 , China
| | - Yicong Dai
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | - Kaixiang Zhang
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | - Qiang He
- College of Light Industry, Textile and Food Engineering and Healthy Food Evaluation Research Center , Sichuan University , Chengdu 610065 , China
| | - Wei-Cai Zeng
- College of Light Industry, Textile and Food Engineering and Healthy Food Evaluation Research Center , Sichuan University , Chengdu 610065 , China
| | - Xiaojun Ren
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | - Jinghong Li
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry , Tsinghua University , Beijing 100084 , China
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75
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Xia X, Wang H, Yang H, Deng S, Deng R, Dong Y, He Q. Dual-Terminal Stemmed Aptamer Beacon for Label-Free Detection of Aflatoxin B 1 in Broad Bean Paste and Peanut Oil via Aggregation-Induced Emission. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:12431-12438. [PMID: 30387615 DOI: 10.1021/acs.jafc.8b05217] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Aflatoxin B1 (AFB1) contamination ranks as one of the most critical food safety issues, and assays for its on-site monitoring are highly demanded. Herein, we propose a label-free, one-tube, homogeneous, and cheap AFB1 assay based on a finely tunable dual-terminal stemmed aptamer beacon (DS aptamer beacon) and aggregation-induced emission (AIE) effects. The DS aptamer beacon structure could provide terminal protection of the aptamer probe against exonuclease I and confer specific and quick response to target AFB1. In comparison to the conventional molecule beacon structure, the stability of the DS aptamer beacon could be finely tuned by adjusting its two terminal stems, allowing for elaborately optimizing probe affinity and selectivity. By the utilization of an AIE-active fluorophore, which would be lighted up by aggregating to negatively charged DNA, AFB1 could be determined in a label-free manner. The proposed method could quantify AFB1 in one test tube using two unlabeled DNA strands. It has been successfully applied for analyzing AFB1 in peanut oil and broad bean sauce, with total recoveries ranging from 92.75 to 118.70%. Thus, the DS aptamer beacon-based assay could potentially facilitate real-time monitoring and controlling of AFB1 pollution.
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Affiliation(s)
- Xuhan Xia
- College of Light Industry, Textile and Food Engineering, Healthy Food Evaluation Research Center, and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province , Sichuan University , Chengdu , Sichuan 610065 , People's Republic of China
| | - Haibo Wang
- College of Light Industry, Textile and Food Engineering, Healthy Food Evaluation Research Center, and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province , Sichuan University , Chengdu , Sichuan 610065 , People's Republic of China
| | - Hao Yang
- College of Light Industry, Textile and Food Engineering, Healthy Food Evaluation Research Center, and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province , Sichuan University , Chengdu , Sichuan 610065 , People's Republic of China
| | - Sha Deng
- College of Light Industry, Textile and Food Engineering, Healthy Food Evaluation Research Center, and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province , Sichuan University , Chengdu , Sichuan 610065 , People's Republic of China
| | - Ruijie Deng
- College of Light Industry, Textile and Food Engineering, Healthy Food Evaluation Research Center, and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province , Sichuan University , Chengdu , Sichuan 610065 , People's Republic of China
| | - Yi Dong
- College of Light Industry, Textile and Food Engineering, Healthy Food Evaluation Research Center, and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province , Sichuan University , Chengdu , Sichuan 610065 , People's Republic of China
| | - Qiang He
- College of Light Industry, Textile and Food Engineering, Healthy Food Evaluation Research Center, and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province , Sichuan University , Chengdu , Sichuan 610065 , People's Republic of China
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76
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Wiraja C, Yeo DC, Lio DCS, Zheng M, Xu C. Functional Imaging with Nucleic-Acid-Based Sensors: Technology, Application and Future Healthcare Prospects. Chembiochem 2018; 20:437-450. [PMID: 30230165 DOI: 10.1002/cbic.201800430] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Indexed: 12/11/2022]
Abstract
Timely monitoring and assessment of human health plays a crucial role in maintaining the wellbeing of our advancing society. In addition to medical tools and devices, suitable probe agents are crucial to assist such monitoring, either in passive or active ways (i.e., sensors) through inducible signals. In this review we highlight recent developments in activatable optical sensors based on nucleic acids. Sensing mechanisms and bio-applications of these nucleic acid sensors in ex vivo assays, intracellular or in vivo settings are described. In addition, we discuss the limitations of these sensors and how nanotechnology can complement/enhance sensor properties to promote translation into clinical applications.
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Affiliation(s)
- Christian Wiraja
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459, Singapore
| | - David C Yeo
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459, Singapore
| | - Daniel Chin Shiuan Lio
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459, Singapore
| | - Mengjia Zheng
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459, Singapore
| | - Chenjie Xu
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459, Singapore.,NTU-Northwestern Institute for Nanomedicine, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
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77
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Saha S, Hetzke T, Prisner TF, Sigurdsson ST. Noncovalent spin-labeling of RNA: the aptamer approach. Chem Commun (Camb) 2018; 54:11749-11752. [PMID: 30276367 DOI: 10.1039/c8cc05597a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the first example of site-directed spin-labeling of unmodified RNA, a pyrrolidine-nitroxide derivative of tetramethylrosamine (TMR) was shown to bind with high affinity to the malachite green (MG) aptamer, as determined by continuous-wave (CW) electron paramagnetic resonance (EPR), pulsed electron-electron double resonance (PELDOR) and fluorescence spectroscopies.
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Affiliation(s)
- Subham Saha
- Department of Chemistry, Science Institute, Dunhaga 3, 107 Reykjavik, Iceland.
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78
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Switchable DNA-origami nanostructures that respond to their environment and their applications. Biophys Rev 2018; 10:1283-1293. [PMID: 30280371 DOI: 10.1007/s12551-018-0462-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 09/18/2018] [Indexed: 12/22/2022] Open
Abstract
Structural DNA nanotechnology, in which Watson-Crick base pairing drives the formation of self-assembling nanostructures, has rapidly expanded in complexity and functionality since its inception in 1981. DNA nanostructures can now be made in arbitrary three-dimensional shapes and used to scaffold many other functional molecules such as proteins, metallic nanoparticles, polymers, fluorescent dyes and small molecules. In parallel, the field of dynamic DNA nanotechnology has built DNA circuits, motors and switches. More recently, these two areas have begun to merge-to produce switchable DNA nanostructures, which change state in response to their environment. In this review, we summarise switchable DNA nanostructures into two major classes based on response type: molecular actuation triggered by local chemical changes such as pH or concentration and external actuation driven by light, electric or magnetic fields. While molecular actuation has been well explored, external actuation of DNA nanostructures is a relatively new area that allows for the remote control of nanoscale devices. We discuss recent applications for DNA nanostructures where switching is used to perform specific functions-such as opening a capsule to deliver a molecular payload to a target cell. We then discuss challenges and future directions towards achieving synthetic nanomachines with complexity on the level of the protein machinery in living cells.
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79
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Abstract
Aptamer biosensor that can switch its structure upon target binding offers a powerful strategy for molecular detection. However, the process of converting an aptamer into a "structure-switching" biosensor is challenging and often relies on trial-and-error without established design principles. In this Sensor Issues, we examine a variety of design approaches for incorporating structure-switching functionality into existing aptamers, and provide thermodynamic analyses to highlight the variables that most strongly influence their performance. Finally, we also describe emerging efforts for incorporating the structure-switching functionality directly into the aptamer selection process.
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Affiliation(s)
- Trevor A. Feagin
- Department of Electrical Engineering, Stanford University,350 Serra Mall, Stanford, California 94305, United States
- Department of Radiology, Stanford University School of Medicine,300 Pasteur Drive, Stanford, California 94305, United States
| | - Nicolò Maganzini
- Department of Electrical Engineering, Stanford University,350 Serra Mall, Stanford, California 94305, United States
| | - Hyongsok Tom Soh
- Department of Electrical Engineering, Stanford University,350 Serra Mall, Stanford, California 94305, United States
- Department of Radiology, Stanford University School of Medicine,300 Pasteur Drive, Stanford, California 94305, United States
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80
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A facile electrochemical aptasensor for lysozyme detection based on target-induced turn-off of photosensitization. Biosens Bioelectron 2018; 126:412-417. [PMID: 30471566 DOI: 10.1016/j.bios.2018.09.074] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 09/09/2018] [Accepted: 09/20/2018] [Indexed: 12/28/2022]
Abstract
The quantification of proteins is essential in fundamental research or clinical applications. Here, we developed a facile electrochemical aptasensor based on target-induced turn-off of photosensitization for label-free and ultrasensitive detection of protein (exemplified by lysozyme). EB (ethidium bromide) molecules that were embedded in dsDNA between lysozyme binding aptamer and complementary DNA immobilized on the electrode, could photo-cleave the dsDNA via singlet oxygen (O21) during photosensitization, resulting in a high voltammetry current of the [Fe(CN)6]3-/4-. Upon recognition of the lysozyme by aptamer, the EB molecules were released from dsDNA, and its photosensitization activity was turned off. As a result, more amount of complementary DNA was retained on the Au nanoparticles modified carbon nanotube paste electrode (AuNPs-CNPE), leading to a declined voltammetry current. Such a sensing strategy allowed detection of 10 pM-1 µM lysozyme with a low detection limit (about 2 pM). Besides, the sensor was free of labeling procedure as well as extra signal amplification step, and the CNPE modification was quite simple, only with AuNPs. The sensor also showed excellent selectivity toward lysozyme in the presence of interfering proteins, such as thrombin, bovine serum albumin, myoglobin, etc. The proposed sensor was applied to the determination of lysozyme in urine samples with the recoveries ranging from 96.6% to 101%. The proposed biosensor holds a great promise in developing other electrochemical sensors based on photosensitization.
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81
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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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82
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Stewart MP, Langer R, Jensen KF. Intracellular Delivery by Membrane Disruption: Mechanisms, Strategies, and Concepts. Chem Rev 2018; 118:7409-7531. [PMID: 30052023 PMCID: PMC6763210 DOI: 10.1021/acs.chemrev.7b00678] [Citation(s) in RCA: 399] [Impact Index Per Article: 66.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Intracellular delivery is a key step in biological research and has enabled decades of biomedical discoveries. It is also becoming increasingly important in industrial and medical applications ranging from biomanufacture to cell-based therapies. Here, we review techniques for membrane disruption-based intracellular delivery from 1911 until the present. These methods achieve rapid, direct, and universal delivery of almost any cargo molecule or material that can be dispersed in solution. We start by covering the motivations for intracellular delivery and the challenges associated with the different cargo types-small molecules, proteins/peptides, nucleic acids, synthetic nanomaterials, and large cargo. The review then presents a broad comparison of delivery strategies followed by an analysis of membrane disruption mechanisms and the biology of the cell response. We cover mechanical, electrical, thermal, optical, and chemical strategies of membrane disruption with a particular emphasis on their applications and challenges to implementation. Throughout, we highlight specific mechanisms of membrane disruption and suggest areas in need of further experimentation. We hope the concepts discussed in our review inspire scientists and engineers with further ideas to improve intracellular delivery.
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Affiliation(s)
- Martin P. Stewart
- Department of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, USA
- The Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, USA
| | - Robert Langer
- Department of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, USA
- The Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, USA
| | - Klavs F. Jensen
- Department of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, USA
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83
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Xu X, Clément P, Eklöf-Österberg J, Kelley-Loughnane N, Moth-Poulsen K, Chávez JL, Palma M. Reconfigurable Carbon Nanotube Multiplexed Sensing Devices. NANO LETTERS 2018; 18:4130-4135. [PMID: 29923734 DOI: 10.1021/acs.nanolett.8b00856] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Here we report on the fabrication of reconfigurable and solution processable nanoscale biosensors with multisensing capability, based on single-walled carbon nanotubes (SWCNTs). Distinct DNA-wrapped (hence water-soluble) CNTs were immobilized from solution onto different prepatterned electrodes on the same chip, via a low-cost dielectrophoresis (DEP) methodology. The CNTs were functionalized with specific, and different, aptamer sequences that were employed as selective recognition elements for biomarkers indicative of stress and neuro-trauma conditions. Multiplexed detection of three different biomarkers was successfully performed, and real-time detection was achieved in serum down to physiologically relevant concentrations of 50 nM, 10 nM, and 500 pM for cortisol, dehydroepiandrosterone-sulfate (DHEAS), and neuropeptide Y (NPY), respectively. Additionally, the fabricated nanoscale devices were shown to be reconfigurable and reusable via a simple cleaning procedure. The general applicability of the strategy presented, and the facile device fabrication from aqueous solution, hold great potential for the development of the next generation of low power consumption portable diagnostic assays for the simultaneous monitoring of different health parameters.
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Affiliation(s)
- Xinzhao Xu
- School of Biological and Chemical Sciences, Institute of Bioengineering, and Materials Research Institute , Queen Mary University of London , Mile End Road , London , E1 4NS , United Kingdom
| | - Pierrick Clément
- School of Biological and Chemical Sciences, Institute of Bioengineering, and Materials Research Institute , Queen Mary University of London , Mile End Road , London , E1 4NS , United Kingdom
| | - Johnas Eklöf-Österberg
- Department of Chemistry and Chemical Engineering , Chalmers University of Technology , Gothenburg , 412 96 , Sweden
| | - Nancy Kelley-Loughnane
- Air Force Research Laboratory, 711th Human Performance Wing , Wright-Patterson Air Force Base , Dayton , Ohio 45433 , United States
| | - Kasper Moth-Poulsen
- Department of Chemistry and Chemical Engineering , Chalmers University of Technology , Gothenburg , 412 96 , Sweden
| | - Jorge L Chávez
- Air Force Research Laboratory, 711th Human Performance Wing , Wright-Patterson Air Force Base , Dayton , Ohio 45433 , United States
| | - Matteo Palma
- School of Biological and Chemical Sciences, Institute of Bioengineering, and Materials Research Institute , Queen Mary University of London , Mile End Road , London , E1 4NS , United Kingdom
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84
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Affinity capture of aflatoxin B 1 and B 2 by aptamer-functionalized magnetic agarose microspheres prior to their determination by HPLC. Mikrochim Acta 2018; 185:326. [PMID: 29896649 DOI: 10.1007/s00604-018-2849-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 05/22/2018] [Indexed: 10/14/2022]
Abstract
A novel adsorbent is described for magnetic solid-phase extraction (MSPE) of the aflatoxins AFB1 and AFB2 (AFBs). Magnetic agarose microspheres (MAMs) were functionalized with an aptamer to bind the AFBs which then were quantified by HPLC and on-line post-column photochemical derivatization with fluorescence detection. Streptavidin-conjugated MAMs were synthesized first by a highly reproducible strategy. They possess strong magnetism and high surface area. The MAMs were characterized by transmission electron microscopy, scanning electron microscopy, optical microscopy, laser diffraction particle size analyzer, Fourier transform infrared spectrometry, vibrating sample magnetometry and laser scanning confocal microscopy. Then, the AFB-aptamers were immobilized on MAMs through biotin-streptavidin interaction. Finally, the MSPE is performed by suspending the aptamer-modified MAMs in the sample. They are then collected by an external magnetic field and the AFBs are eluted with methanol/buffer (20:80). Several parameters affecting the coupling, capturing and eluting efficiency were optimized. Under the optimized conditions, the method is fast, has good linearity, high selectivity, and sensitivity. The LODs are 25 pg·mL-1 for AFB1 and 10 pg·mL-1 for AFB2. The binding capacity is 350 ± 8 ng·g-1 for AFB1 and 384 ± 8 ng·g-1 for AFB2, and the precision of the assay is <8%. The method was successfully applied to the analysis of AFBs in spiked maize samples. Graphical abstract Schematic of novel aptamer functionalized magnetic agarose microspheres (Apt-MAM) as magnetic adsorbents for simultaneous and specific affinity capture of aflatoxins B1 and B2 (AFBs).
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85
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Golichenari B, Nosrati R, Farokhi-Fard A, Abnous K, Vaziri F, Behravan J. Nano-biosensing approaches on tuberculosis: Defy of aptamers. Biosens Bioelectron 2018; 117:319-331. [PMID: 29933223 DOI: 10.1016/j.bios.2018.06.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/04/2018] [Accepted: 06/10/2018] [Indexed: 12/12/2022]
Abstract
Tuberculosis is a major global health problem caused by the bacterium Mycobacterium tuberculosis (Mtb) complex. According to WHO reports, 53 million TB patients died from 2000 to 2016. Therefore, early diagnosis of the disease is of great importance for global health care programs. The restrictions of traditional methods have encouraged the development of innovative methods for rapid, reliable, and cost-effective diagnosis of tuberculosis. In recent years, aptamer-based biosensors or aptasensors have drawn great attention to sensitive and accessible detection of tuberculosis. Aptamers are small short single-stranded molecules of DNA or RNA that fold to a unique form and bind to targets. Once combined with nanomaterials, nano-scale aptasensors provide powerful analytical platforms for diagnosing of tuberculosis. Various groups designed and studied aptamers specific for the whole cells of M. tuberculosis, mycobacterial proteins and IFN-γ for early diagnosis of TB. Advantages such as high specificity and strong affinity, potential for binding to a larger variety of targets, increased stability, lower costs of synthesis and storage requirements, and lower probability of contamination make aptasensors pivotal alternatives for future TB diagnostics. In recent years, the concept of SOMAmer has opened new horizons in high precision detection of tuberculosis biomarkers. This review article provides a description of the research progresses of aptamer-based and SOMAmer-based biosensors and nanobiosensors for the detection of tuberculosis.
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Affiliation(s)
- Behrouz Golichenari
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Rahim Nosrati
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Molecular Microbiology Research Center (MMRC), Shahed University, Tehran, Iran
| | - Aref Farokhi-Fard
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
| | - Javad Behravan
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Mediphage Bioceuticals, Inc., 661 University Avenue, Suite 1300, MaRS Centre, West Tower, Toronto, Canada.
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86
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Bagheri E, Abnous K, Alibolandi M, Ramezani M, Taghdisi SM. Triple-helix molecular switch-based aptasensors and DNA sensors. Biosens Bioelectron 2018; 111:1-9. [PMID: 29627731 DOI: 10.1016/j.bios.2018.03.070] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 03/28/2018] [Accepted: 03/29/2018] [Indexed: 12/31/2022]
Abstract
Utilization of traditional analytical techniques is limited because they are generally time-consuming and require high consumption of reagents, complicated sample preparation and expensive equipment. Therefore, it is of great interest to achieve sensitive, rapid and simple detection methods. It is believed that nucleic acids assays, especially aptamers, are very important in modern life sciences for target detection and biological analysis. Aptamers and DNA-based sensors have been widely used for the design of various sensors owing to their unique features. In recent years, triple-helix molecular switch (THMS)-based aptasensors and DNA sensors have been broadly utilized for the detection and analysis of different targets. The THMS relies on the formation of DNA triplex via Watson-Crick and Hoogsteen base pairings under optimal conditions. This review focuses on recent progresses in the development and applications of electrochemical, colorimetric, fluorescence and SERS aptasensors and DNA sensors, which are based on THMS. Also, the advantages and drawbacks of these methods are discussed.
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Affiliation(s)
- Elnaz Bagheri
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
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87
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Zhang D, Ma F, Zhang Q, Zhang CY. Highly sensitive detection of epidermal growth factor receptor in lung cancer cells by aptamer-based target-/probe-mediated cyclic signal amplification. Chem Commun (Camb) 2018; 53:11496-11499. [PMID: 28990029 DOI: 10.1039/c7cc06823a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We develop an antibody-free fluorescence method for the epidermal growth factor receptor (EGFR) assay using aptamer-based target-/probe-mediated cyclic signal amplification. The method is highly sensitive with a detection limit of 0.16 fM, and it can be applied to detect EGFR in lung cancer cells, holding great potential in clinical diagnosis.
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Affiliation(s)
- Dandan Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China.
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88
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Perrier S, Guieu V, Chovelon B, Ravelet C, Peyrin E. Panoply of Fluorescence Polarization/Anisotropy Signaling Mechanisms for Functional Nucleic Acid-Based Sensing Platforms. Anal Chem 2018. [PMID: 29513518 DOI: 10.1021/acs.analchem.7b04593] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Fluorescence polarization/anisotropy is a very popular technique that is widely used in homogeneous-phase immunoassays for the small molecule quantification. In the present Feature, we discuss how the potential of this signaling approach considerably expanded during the last 2 decades through the implementation of a myriad of original transducing strategies that use functional nucleic acid recognition elements as a promising alternative to antibodies.
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Affiliation(s)
- Sandrine Perrier
- University Grenoble Alpes , DPM UMR 5063, F-38041 Grenoble , France.,CNRS , DPM UMR 5063, F-38041 Grenoble , France
| | - Valérie Guieu
- University Grenoble Alpes , DPM UMR 5063, F-38041 Grenoble , France.,CNRS , DPM UMR 5063, F-38041 Grenoble , France
| | - Benoit Chovelon
- University Grenoble Alpes , DPM UMR 5063, F-38041 Grenoble , France.,CNRS , DPM UMR 5063, F-38041 Grenoble , France.,Département de Biochimie, Toxicologie et Pharmacologie , CHU de Grenoble Site Nord-Institut de Biologie et de Pathologie , F-38041 Grenoble , France
| | - Corinne Ravelet
- University Grenoble Alpes , DPM UMR 5063, F-38041 Grenoble , France.,CNRS , DPM UMR 5063, F-38041 Grenoble , France
| | - Eric Peyrin
- University Grenoble Alpes , DPM UMR 5063, F-38041 Grenoble , France.,CNRS , DPM UMR 5063, F-38041 Grenoble , France
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89
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Harroun SG, Prévost-Tremblay C, Lauzon D, Desrosiers A, Wang X, Pedro L, Vallée-Bélisle A. Programmable DNA switches and their applications. NANOSCALE 2018; 10:4607-4641. [PMID: 29465723 DOI: 10.1039/c7nr07348h] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
DNA switches are ideally suited for numerous nanotechnological applications, and increasing efforts are being directed toward their engineering. In this review, we discuss how to engineer these switches starting from the selection of a specific DNA-based recognition element, to its adaptation and optimisation into a switch, with applications ranging from sensing to drug delivery, smart materials, molecular transporters, logic gates and others. We provide many examples showcasing their high programmability and recent advances towards their real life applications. We conclude with a short perspective on this exciting emerging field.
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Affiliation(s)
- Scott G Harroun
- Laboratory of Biosensors & Nanomachines, Département de Chimie, Université de Montréal, Montréal, Québec H3C 3J7, Canada.
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90
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Lorenz JS, Schnauß J, Glaser M, Sajfutdinow M, Schuldt C, Käs JA, Smith DM. Synthetic Transient Crosslinks Program the Mechanics of Soft, Biopolymer-Based Materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1706092. [PMID: 29446165 PMCID: PMC5878933 DOI: 10.1002/adma.201706092] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 12/20/2017] [Indexed: 05/21/2023]
Abstract
Actin networks are adaptive materials enabling dynamic and static functions of living cells. A central element for tuning their underlying structural and mechanical properties is the ability to reversibly connect, i.e., transiently crosslink, filaments within the networks. Natural crosslinkers, however, vary across many parameters. Therefore, systematically studying the impact of their fundamental properties like size and binding strength is unfeasible since their structural parameters cannot be independently tuned. Herein, this problem is circumvented by employing a modular strategy to construct purely synthetic actin crosslinkers from DNA and peptides. These crosslinkers mimic both intuitive and noncanonical mechanical properties of their natural counterparts. By isolating binding affinity as the primary control parameter, effects on structural and dynamic behaviors of actin networks are characterized. A concentration-dependent triphasic behavior arises from both strong and weak crosslinkers due to emergent structural polymorphism. Beyond a certain threshold, strong binding leads to a nonmonotonic elastic pulse, which is a consequence of self-destruction of the mechanical structure of the underlying network. The modular design also facilitates an orthogonal regulatory mechanism based on enzymatic cleaving. This approach can be used to guide the rational design of further biomimetic components for programmable modulation of the properties of biomaterials and cells.
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Affiliation(s)
- Jessica S Lorenz
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), 04103, Leipzig, Germany
| | - Jörg Schnauß
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), 04103, Leipzig, Germany
- Peter Debye Institute for Soft Matter Physics, Leipzig University, 04103, Leipzig, Germany
| | - Martin Glaser
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), 04103, Leipzig, Germany
- Peter Debye Institute for Soft Matter Physics, Leipzig University, 04103, Leipzig, Germany
| | - Martin Sajfutdinow
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), 04103, Leipzig, Germany
| | - Carsten Schuldt
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), 04103, Leipzig, Germany
- Peter Debye Institute for Soft Matter Physics, Leipzig University, 04103, Leipzig, Germany
| | - Josef A Käs
- Peter Debye Institute for Soft Matter Physics, Leipzig University, 04103, Leipzig, Germany
| | - David M Smith
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), 04103, Leipzig, Germany
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91
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Hasan MR, Hassan N, Khan R, Kim YT, Iqbal SM. Classification of cancer cells using computational analysis of dynamic morphology. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2018; 156:105-112. [PMID: 29428061 DOI: 10.1016/j.cmpb.2017.12.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 11/09/2017] [Accepted: 12/05/2017] [Indexed: 06/08/2023]
Abstract
BACKGROUND AND OBJECTIVE Detection of metastatic tumor cells is important for early diagnosis and staging of cancer. However, such cells are exceedingly difficult to detect from blood or biopsy samples at the disease onset. It is reported that cancer cells, and especially metastatic tumor cells, show very distinctive morphological behavior compared to their healthy counterparts on aptamer functionalized substrates. The ability to quickly analyze the data and quantify the cell morphology for an instant real-time feedback can certainly contribute to early cancer diagnosis. A supervised machine learning approach is presented for identification and classification of cancer cell gestures for early diagnosis. METHODS We quantified the morphologically distinct behavior of metastatic cells and their healthy counterparts captured on aptamer-functionalized glass substrates from time-lapse optical micrographs. As a proof of concept, the morphologies of human glioblastoma (hGBM) and astrocyte cells were used. The cells were captured and imaged with an optical microscope. Multiple feature vectors were extracted to quantify and differentiate the complex physical gestures of cancerous and non-cancerous cells. Three different classifier models, Support Vector Machine (SVM), Random Forest Tree (RFT), and Naïve Bayes Classifier (NBC) were trained with the known dataset using machine learning algorithms. The performances of the classifiers were compared for accuracy, precision, and recall measurements using five-fold cross-validation technique. RESULTS All the classifier models detected the cancer cells with an average accuracy of at least 82%. The NBC performed the best among the three classifiers in terms of Precision (0.91), Recall (0.9), and F1-score (0.89) for the existing dataset. CONCLUSIONS This paper presents a standalone system built on machine learning techniques for cancer screening based on cell gestures. The system offers rapid, efficient, and novel identification of hGBM brain tumor cells and can be extended to define single cell analysis metrics for many other types of tumor cells.
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Affiliation(s)
- Mohammad R Hasan
- Nano-Bio Lab, University of Texas at Arlington, Arlington, TX 76019, USA; Nanotechnology Research Center, University of Texas at Arlington, Arlington, TX 76019, USA; Department of Electrical Engineering, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Naeemul Hassan
- Department of Computer and Information Science, University of Mississippi, University, MS 38677, USA
| | - Rayan Khan
- Nano-Bio Lab, University of Texas at Arlington, Arlington, TX 76019, USA; Nanotechnology Research Center, University of Texas at Arlington, Arlington, TX 76019, USA; Department of Electrical Engineering, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Young-Tae Kim
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX 76019, USA; Department of Urology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75235, USA
| | - Samir M Iqbal
- Nano-Bio Lab, University of Texas at Arlington, Arlington, TX 76019, USA; Department of Electrical Engineering, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA; School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA.
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92
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Vega-Figueroa K, Santillán J, Ortiz-Gómez V, Ortiz-Quiles EO, Quiñones-Colón BA, Castilla-Casadiego DA, Almodóvar J, Bayro MJ, Rodríguez-Martínez JA, Nicolau E. Aptamer-Based Impedimetric Assay of Arsenite in Water: Interfacial Properties and Performance. ACS OMEGA 2018; 3:1437-1444. [PMID: 29503970 PMCID: PMC5830693 DOI: 10.1021/acsomega.7b01710] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/23/2018] [Indexed: 06/08/2023]
Abstract
In this work, we explore the use of electrochemical methods (i.e., impedance) along with the arsenic-specific aptamer (ArsSApt) to fabricate and study the interfacial properties of an arsenic (As(III)) sensor. The ArsSApt layer was self-assembled on a gold substrate, and upon binding of As(III), a detectable change in the impedimetric signal was recorded because of conformational changes at the interfacial layer. These interfacial changes are linearly correlated with the concentration of arsenic present in the system. This target-induced signal was utilized for the selective detection of As(III) with a linear dynamic range of 0.05-10 ppm and minimum detectable concentrations of ca. 0.8 μM. The proposed system proved to be successful mainly because of the combination of a highly sensitive electrochemical platform and the recognized specificity of the ArsSApt toward its target molecule. Also, the interaction between the ArsSApt and the target molecule (i.e., arsenic) was explored in depth. The obtained results in this work are aimed at proving the development of a simple and environmentally benign sensor for the detection of As(III) as well as in elucidating the possible interactions between the ArsSApt and arsenic molecules.
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Affiliation(s)
- Karlene Vega-Figueroa
- Department
of Biology and Department of Physics, University of Puerto
Rico, Rio Piedras Campus, P.O. Box 23346, San Juan, Puerto Rico 00931-3346, United States
- Molecular
Sciences Research Center, University of
Puerto Rico, 1390 Ponce
De Leon Avenue, Suite 2, San Juan, Puerto Rico 00931-3346, United States
| | - Jaime Santillán
- Department
of Biology and Department of Physics, University of Puerto
Rico, Rio Piedras Campus, P.O. Box 23346, San Juan, Puerto Rico 00931-3346, United States
- Molecular
Sciences Research Center, University of
Puerto Rico, 1390 Ponce
De Leon Avenue, Suite 2, San Juan, Puerto Rico 00931-3346, United States
| | - Valerie Ortiz-Gómez
- Department
of Biology and Department of Physics, University of Puerto
Rico, Rio Piedras Campus, P.O. Box 23346, San Juan, Puerto Rico 00931-3346, United States
- Molecular
Sciences Research Center, University of
Puerto Rico, 1390 Ponce
De Leon Avenue, Suite 2, San Juan, Puerto Rico 00931-3346, United States
| | - Edwin O. Ortiz-Quiles
- Department
of Chemistry, University of Puerto Rico, Rio Piedras Campus, 17 Ave. Universidad
Ste. 1701, San Juan, Puerto
Rico 00925-2537, United
States
- Molecular
Sciences Research Center, University of
Puerto Rico, 1390 Ponce
De Leon Avenue, Suite 2, San Juan, Puerto Rico 00931-3346, United States
| | - Beatriz A. Quiñones-Colón
- Department
of Chemical Engineering, University of Puerto
Rico Mayaguez, Call Box 9000, Mayaguez, Puerto Rico 00681-9000, United States
| | - David A. Castilla-Casadiego
- Department
of Chemical Engineering, University of Puerto
Rico Mayaguez, Call Box 9000, Mayaguez, Puerto Rico 00681-9000, United States
| | - Jorge Almodóvar
- Department
of Chemical Engineering, University of Puerto
Rico Mayaguez, Call Box 9000, Mayaguez, Puerto Rico 00681-9000, United States
| | - Marvin J. Bayro
- Department
of Chemistry, University of Puerto Rico, Rio Piedras Campus, 17 Ave. Universidad
Ste. 1701, San Juan, Puerto
Rico 00925-2537, United
States
- Molecular
Sciences Research Center, University of
Puerto Rico, 1390 Ponce
De Leon Avenue, Suite 2, San Juan, Puerto Rico 00931-3346, United States
| | - José A. Rodríguez-Martínez
- Department
of Biology and Department of Physics, University of Puerto
Rico, Rio Piedras Campus, P.O. Box 23346, San Juan, Puerto Rico 00931-3346, United States
- Molecular
Sciences Research Center, University of
Puerto Rico, 1390 Ponce
De Leon Avenue, Suite 2, San Juan, Puerto Rico 00931-3346, United States
| | - Eduardo Nicolau
- Department
of Chemistry, University of Puerto Rico, Rio Piedras Campus, 17 Ave. Universidad
Ste. 1701, San Juan, Puerto
Rico 00925-2537, United
States
- Molecular
Sciences Research Center, University of
Puerto Rico, 1390 Ponce
De Leon Avenue, Suite 2, San Juan, Puerto Rico 00931-3346, United States
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93
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Oueslati R, Cheng C, Wu J, Chen J. Highly sensitive and specific on-site detection of serum cocaine by a low cost aptasensor. Biosens Bioelectron 2018. [PMID: 29524683 DOI: 10.1016/j.bios.2018.02.055] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cocaine is one of the most used illegal recreational drugs. Developing an on-site test for cocaine use detection has been a focus of research effort, since it is essential to the control and legal action against drug abuse. Currently most of cocaine detection methods are time-consuming and require special or expensive equipment, and the detection often suffers from high cross-reactivity with cocaine metabolites and relative low sensitivity with the best limit of detection reported at sub nanomolar (nM) level. In this work, an aptasensor has been developed using capacitive monitoring of sensor surface incorporating alternating current electrokinetics effects to speed up molecular transport and minimize matrix effects. The aptasensor is rapid, low cost, highly sensitive and specific as well as simple-to-use for the detection of cocaine from serum. The assay has a sample-to-result time of 30 s, a limit of detection of 7.8 fM, and a linear response for cocaine ranging from 14.5fM to 14.5pM in standard buffer, which are great improvements from other reported cocaine sensors. Special buffer is used for serum cocaine detection, and a limit of detection of 13.4 fM is experimentally demonstrated for cocaine spiked in human serum (equivalent to 1.34pM cocaine in neat serum). The specificity of the biosensor is also demonstrated with structurally similar chemicals, ecgonine ethyl ester and methylecgonidine. This biosensor shows high promise in detection of low levels of cocaine from complex matrices.
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Affiliation(s)
- Rania Oueslati
- Department of Electrical Engineering and Computer Science,The University of Tennessee, Knoxville, USA
| | - Cheng Cheng
- Department of Electrical Engineering and Computer Science,The University of Tennessee, Knoxville, USA
| | - Jayne Wu
- Department of Electrical Engineering and Computer Science,The University of Tennessee, Knoxville, USA.
| | - Jiangang Chen
- Department of Public Health, The University of Tennessee, Knoxville, USA
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94
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Thiha A, Ibrahim F, Muniandy S, Dinshaw IJ, Teh SJ, Thong KL, Leo BF, Madou M. All-carbon suspended nanowire sensors as a rapid highly-sensitive label-free chemiresistive biosensing platform. Biosens Bioelectron 2018; 107:145-152. [PMID: 29455024 DOI: 10.1016/j.bios.2018.02.024] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 02/04/2018] [Accepted: 02/08/2018] [Indexed: 01/16/2023]
Abstract
Nanowire sensors offer great potential as highly sensitive electrochemical and electronic biosensors because of their small size, high aspect ratios, and electronic properties. Nevertheless, the available methods to fabricate carbon nanowires in a controlled manner remain limited to expensive techniques. This paper presents a simple fabrication technique for sub-100 nm suspended carbon nanowire sensors by integrating electrospinning and photolithography techniques. Carbon Microelectromechanical Systems (C-MEMS) fabrication techniques allow fabrication of high aspect ratio carbon structures by patterning photoresist polymers into desired shapes and subsequent carbonization of resultant structures by pyrolysis. In our sensor platform, suspended nanowires were deposited by electrospinning while photolithography was used to fabricate support structures. We have achieved suspended carbon nanowires with sub-100 nm diameters in this study. The sensor platform was then integrated with a microfluidic chip to form a lab-on-chip device for label-free chemiresistive biosensing. We have investigated this nanoelectronics label-free biosensor's performance towards bacterial sensing by functionalization with Salmonella-specific aptamer probes. The device was tested with varying concentrations of Salmonella Typhimurium to evaluate sensitivity and various other bacteria to investigate specificity. The results showed that the sensor is highly specific and sensitive in detection of Salmonella with a detection limit of 10 CFU mL-1. Moreover, this proposed chemiresistive assay has a reduced turnaround time of 5 min and sample volume requirement of 5 µL which are much less than reported in the literature.
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Affiliation(s)
- Aung Thiha
- Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia; Centre for Innovation in Medical Engineering (CIME), Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Fatimah Ibrahim
- Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia; Centre for Innovation in Medical Engineering (CIME), Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Shalini Muniandy
- Centre for Innovation in Medical Engineering (CIME), Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia; Nanotechnology and Catalysis Research Centre, Institute of Graduate Studies, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Ignatius Julian Dinshaw
- Nanotechnology and Catalysis Research Centre, Institute of Graduate Studies, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Swe Jyan Teh
- Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia; Centre for Innovation in Medical Engineering (CIME), Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kwai Lin Thong
- Centre for Innovation in Medical Engineering (CIME), Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia; Microbiology Unit, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Bey Fen Leo
- Centre for Innovation in Medical Engineering (CIME), Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Biomedical Imaging, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Marc Madou
- Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia; Centre for Innovation in Medical Engineering (CIME), Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA; Department of Mechanical and Aerospace Engineering, University of California, Irvine, CA 92697, USA
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95
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Fluorescence Sensing Using DNA Aptamers in Cancer Research and Clinical Diagnostics. Cancers (Basel) 2017; 9:cancers9120174. [PMID: 29261171 PMCID: PMC5742822 DOI: 10.3390/cancers9120174] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 12/14/2017] [Accepted: 12/16/2017] [Indexed: 12/12/2022] Open
Abstract
Among the various advantages of aptamers over antibodies, remarkable is their ability to tolerate a large number of chemical modifications within their backbone or at the termini without losing significant activity. Indeed, aptamers can be easily equipped with a wide variety of reporter groups or coupled to different carriers, nanoparticles, or other biomolecules, thus producing valuable molecular recognition tools effective for diagnostic and therapeutic purposes. This review reports an updated overview on fluorescent DNA aptamers, designed to recognize significant cancer biomarkers both in soluble or membrane-bound form. In many examples, the aptamer secondary structure switches induced by target recognition are suitably translated in a detectable fluorescent signal using either fluorescently-labelled or label-free aptamers. The fluorescence emission changes, producing an enhancement (“signal-on”) or a quenching (“signal-off”) effect, directly reflect the extent of the binding, thereby allowing for quantitative determination of the target in bioanalytical assays. Furthermore, several aptamers conjugated to fluorescent probes proved to be effective for applications in tumour diagnosis and intraoperative surgery, producing tumour-type specific, non-invasive in vivo imaging tools for cancer pre- and post-treatment assessment.
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96
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Ghosh R, Chatterjee DP, Das S, Mukhopadhyay TK, Datta A, Nandi AK. Influence of Hofmeister I - on Tuning Optoelectronic Properties of Ampholytic Polythiophene by Varying pH and Conjugating with RNA. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:12739-12749. [PMID: 29028346 DOI: 10.1021/acs.langmuir.7b03147] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A significant tuning of optoelectronic properties of polythiophene (PT) chains due to Hofmeister iodide (I-) ion is demonstrated in ampholytic polythiophene [polythiophene-g-poly{(N,N,N-trimethylamino iodide)ethyl methacrylate-co-methacrylic acid}, APT] at different pHs. In acidic medium, the absorption and emission signals of PT chromophore exhibit appreciable blue shift in the presence of I- as counteranion only. The cooperative effect of undissociated -COOH and quaternary ammonium groups immobilize I- near the apolar PT chain causing threading of grafted chains and hence twisting of the backbone attributing to the blue shift. As medium pH is increased, dethreading of the PT backbone occurs due to ionization of -COOH group, releasing quencher iodide ions from the vicinity of the PT chains resulting in a red shift in absorption and a sharp hike in fluorescence intensity (390 times) for an increase of excitons lifetime. With an increase of pH, morphology changes from a multivesicular aggregate with vacuoles to smaller size vesicles and finally to nanofibrillar network structure. Dethreading is also found when APT interacts with RNA showing a significant hike of fluorescence (22 times) for displacing iodide ions forming a nanofibrillar network morphology. Threading and dethreading also affect the resistance, capacitance, and Warburg impedance values of APT. Molecular dynamics simulation of a model APT chain in a water box supports the threading at lower pH where the iodide ions pose nearer to the PT chain than that at higher pH causing dethreading. So the influence of Hofmeister I- ion is established for tuning the optoelectronic properties of a novel PT based polyampholyte by changing pH or by conjugating with RNA.
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Affiliation(s)
- Radhakanta Ghosh
- Polymer Science Unit, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032, India
| | - Dhruba P Chatterjee
- Polymer Science Unit, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032, India
| | - Sujoy Das
- Polymer Science Unit, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032, India
| | - Titas K Mukhopadhyay
- Polymer Science Unit, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032, India
| | - Ayan Datta
- Polymer Science Unit, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032, India
| | - Arun K Nandi
- Polymer Science Unit, Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032, India
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97
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Manickam A, Singh R, McDermott M, Wood N, Bolouki S, Naraghi-Arani P, Johnson K, Kuimelis RG, Schoolnik G, Hassibi A. A Fully Integrated CMOS Fluorescence Biochip for DNA and RNA Testing. IEEE JOURNAL OF SOLID-STATE CIRCUITS 2017; 52:2857-2870. [PMID: 30853715 PMCID: PMC6407865 DOI: 10.1109/jssc.2017.2754363] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Design and successful implementation of a fully-integrated CMOS fluorescence biochip for DNA/RNA testing in molecular diagnostics (MDx) is presented. The biochip includes a 32×32 array of continuous wave fluorescence detection biosensing elements. Each biosensing element is capable of having unique DNA probe sequences, wavelength-selective multi-dielectric emission filter (OD of 3.6), resistive heater for thermal cycling, and a high performance and programmable photodetector. The dimension of each biosensor is 100µm×100µm with a 50µm×50µm Nwell-Psub photodiode acting as the optical transducer, and a ΣΔ modulator based photocurrent sensor. The measured photodetector performance shows ~116 dB detection dynamic range (10fA - 10nA) over the 25°C - 100°C temperature range, while being ~1 dB away from the fundamental shot-noise limit. To empirically demonstrate the compatibility of this biochip with MDx applications, we have successfully utilized the array and its thermal cycling capability to adopt a 7-plex panel for detection of 6 human upper respiratory viruses.
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98
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99
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100
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Abatemarco J, Sarhan MF, Wagner JM, Lin JL, Liu L, Hassouneh W, Yuan SF, Alper HS, Abate AR. RNA-aptamers-in-droplets (RAPID) high-throughput screening for secretory phenotypes. Nat Commun 2017; 8:332. [PMID: 28835641 PMCID: PMC5569033 DOI: 10.1038/s41467-017-00425-7] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/23/2017] [Indexed: 11/21/2022] Open
Abstract
Synthetic biology and metabolic engineering seek to re-engineer microbes into "living foundries" for the production of high value chemicals. Through a "design-build-test" cycle paradigm, massive libraries of genetically engineered microbes can be constructed and tested for metabolite overproduction and secretion. However, library generation capacity outpaces the rate of high-throughput testing and screening. Well plate assays are flexible but with limited throughput, whereas droplet microfluidic techniques are ultrahigh-throughput but require a custom assay for each target. Here we present RNA-aptamers-in-droplets (RAPID), a method that greatly expands the generality of ultrahigh-throughput microfluidic screening. Using aptamers, we transduce extracellular product titer into fluorescence, allowing ultrahigh-throughput screening of millions of variants. We demonstrate the RAPID approach by enhancing production of tyrosine and secretion of a recombinant protein in Saccharomyces cerevisiae by up to 28- and 3-fold, respectively. Aptamers-in-droplets affords a general approach for evolving microbes to synthesize and secrete value-added chemicals.Screening libraries of genetically engineered microbes for secreted products is limited by the available assay throughput. Here the authors combine aptamer-based fluorescent detection with droplet microfluidics to achieve high throughput screening of yeast strains engineered for enhanced tyrosine or streptavidin production.
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Affiliation(s)
- Joseph Abatemarco
- Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St Stop C0400, Austin, Texas, 78712, USA
| | - Maen F Sarhan
- Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, 94158, California, USA
- California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, 94158, California, USA
| | - James M Wagner
- Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St Stop C0400, Austin, Texas, 78712, USA
| | - Jyun-Liang Lin
- Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St Stop C0400, Austin, Texas, 78712, USA
| | - Leqian Liu
- Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, 94158, California, USA
- California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, 94158, California, USA
| | - Wafa Hassouneh
- Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, 94158, California, USA
- California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, 94158, California, USA
- Chan Zuckerberg Biohub, San Francisco, 94158, California, USA
| | - Shuo-Fu Yuan
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, Texas, 78712, USA
| | - Hal S Alper
- Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St Stop C0400, Austin, Texas, 78712, USA.
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, Texas, 78712, USA.
| | - Adam R Abate
- Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, 94158, California, USA.
- California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, 94158, California, USA.
- Chan Zuckerberg Biohub, San Francisco, 94158, California, USA.
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