1
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Möller C, Sharma R, Öz R, Reginato G, Cannavo E, Ceppi I, Sriram KK, Cejka P, Westerlund F. Xrs2/NBS1 promote end-bridging activity of the MRE11-RAD50 complex. Biochem Biophys Res Commun 2024; 695:149464. [PMID: 38217957 DOI: 10.1016/j.bbrc.2023.149464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/04/2023] [Accepted: 12/29/2023] [Indexed: 01/15/2024]
Abstract
DNA double strand breaks (DSBs) can be detrimental to the cell and need to be efficiently repaired. A first step in DSB repair is to bring the free ends in close proximity to enable ligation by non-homologous end-joining (NHEJ), while the more precise, but less available, repair by homologous recombination (HR) requires close proximity of a sister chromatid. The human MRE11-RAD50-NBS1 (MRN) complex, Mre11-Rad50-Xrs2 (MRX) in yeast, is involved in both repair pathways. Here we use nanofluidic channels to study, on the single DNA molecule level, how MRN, MRX and their constituents interact with long DNA and promote DNA bridging. Nanofluidics is a suitable method to study reactions on DNA ends since no anchoring of the DNA end(s) is required. We demonstrate that NBS1 and Xrs2 play important, but differing, roles in the DNA tethering by MRN and MRX. NBS1 promotes DNA bridging by MRN consistent with tethering of a repair template. MRX shows a "synapsis-like" DNA end-bridging, stimulated by the Xrs2 subunit. Our results highlight the different ways MRN and MRX bridge DNA, and the results are in agreement with their key roles in HR and NHEJ, respectively, and contribute to the understanding of the roles of NBS1 and Xrs2 in DSB repair.
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Affiliation(s)
- Carl Möller
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, SE, 41296, Sweden
| | - Rajhans Sharma
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, SE, 41296, Sweden
| | - Robin Öz
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, SE, 41296, Sweden
| | - Giordano Reginato
- Institute for Research in Biomedicine, Universitá della Svizzera Italiana, Bellinzona, CH 6500, Switzerland
| | - Elda Cannavo
- Institute for Research in Biomedicine, Universitá della Svizzera Italiana, Bellinzona, CH 6500, Switzerland
| | - Ilaria Ceppi
- Institute for Research in Biomedicine, Universitá della Svizzera Italiana, Bellinzona, CH 6500, Switzerland
| | - K K Sriram
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, SE, 41296, Sweden
| | - Petr Cejka
- Institute for Research in Biomedicine, Universitá della Svizzera Italiana, Bellinzona, CH 6500, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Switzerland
| | - Fredrik Westerlund
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, SE, 41296, Sweden.
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2
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Charlton BK, Downie DH, Noman I, Alves PU, Eling CJ, Laurand N. Surface Functionalisation of Self-Assembled Quantum Dot Microlasers with a DNA Aptamer. Int J Mol Sci 2023; 24:14416. [PMID: 37833863 PMCID: PMC10572750 DOI: 10.3390/ijms241914416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
The surface functionalisation of self-assembled colloidal quantum dot supraparticle lasers with a thrombin binding aptamer (TBA-15) has been demonstrated. The self-assembly of CdSSe/ZnS alloyed core/shell microsphere-shape CQD supraparticles emitting at 630 nm was carried out using an oil-in-water emulsion technique, yielding microspheres with an oleic acid surface and an average diameter of 7.3 ± 5.3 µm. Surface modification of the microspheres was achieved through a ligand exchange with mercaptopropionic acid and the subsequent attachment of TBA-15 using EDC/NHS coupling, confirmed by zeta potential and Fourier transform IR spectroscopy. Lasing functionality between 627 nm and 635 nm was retained post-functionalisation, with oleic acid- and TBA-coated microspheres exhibiting laser oscillation with thresholds as low as 4.10 ± 0.37 mJ·cm-2 and 7.23 ± 0.78 mJ·cm-2, respectively.
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Affiliation(s)
| | | | | | | | | | - Nicolas Laurand
- Technology & Innovation Centre, Institute of Photonics, University of Strathclyde, 99 George Street, Glasgow G1 1RD, UK; (B.K.C.); (D.H.D.); (I.N.); (P.U.A.); (C.J.E.)
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3
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Calabria D, Zangheri M, Pour SRS, Trozzi I, Pace A, Lazzarini E, Calabretta MM, Mirasoli M, Guardigli M. Luminescent Aptamer-Based Bioassays for Sensitive Detection of Food Allergens. BIOSENSORS 2022; 12:644. [PMID: 36005040 PMCID: PMC9405952 DOI: 10.3390/bios12080644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 02/06/2023]
Abstract
The presence of hidden allergens in food products, often due to unintended contamination along the food supply chain (production, transformation, processing, and transport), has raised the urgent need for rapid and reliable analytical methods for detecting trace levels of such species in food products. Indeed, food allergens represent a high-risk factor for allergic subjects due to potentially life-threatening adverse reactions. Portable biosensors based on immunoassays have already been developed as rapid, sensitive, selective, and low-cost analytical platforms that can replace analyses with traditional bench-top instrumentation. Recently, aptamers have attracted great interest as alternative biorecognition molecules for bioassays, since they can bind a variety of targets with high specificity and selectivity, and they enable the development of assays exploiting a variety of transduction and detection technologies. In particular, aptasensors based on luminescence detection have been proposed, taking advantage of the development of ultrasensitive tracers and enhancers. This review aims to summarize and discuss recent efforts in the field of food allergen analysis using aptamer-based bioassays with luminescence detection.
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Affiliation(s)
- Donato Calabria
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
- Interdepartmental Centre for Industrial Aerospace Research (CIRI AEROSPACE), Alma Mater Studiorum, University of Bologna, Via Baldassarre Canaccini 12, I-47121 Forlì, Italy
| | - Martina Zangheri
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
- Interdepartmental Centre for Industrial Agrofood Research (CIRI AGRO), Alma Mater Studiorum, University of Bologna, Via Quinto Bucci 336, I-47521 Cesena, Italy
- Interdepartmental Centre for Industrial Research in Advanced Mechanical Engineering Applications and Materials Technology (CIRI MAM), Alma Mater Studiorum, University of Bologna, Viale Risorgimento 2, I-40136 Bologna, Italy
| | - Seyedeh Rojin Shariati Pour
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
| | - Ilaria Trozzi
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
| | - Andrea Pace
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
| | - Elisa Lazzarini
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
| | - Maria Maddalena Calabretta
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
| | - Mara Mirasoli
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
- Interdepartmental Centre for Industrial Aerospace Research (CIRI AEROSPACE), Alma Mater Studiorum, University of Bologna, Via Baldassarre Canaccini 12, I-47121 Forlì, Italy
- Interdepartmental Centre for Industrial Research in Renewable Resources, Environment, Sea, and Energy (CIRI FRAME), Alma Mater Studiorum, University of Bologna, Via Sant’Alberto 163, I-48123 Ravenna, Italy
| | - Massimo Guardigli
- Department of Chemistry “Giacomo Ciamician”, Alma Mater Studiorum, University of Bologna, Via Francesco Selmi 2, I-40126 Bologna, Italy
- Interdepartmental Centre for Industrial Aerospace Research (CIRI AEROSPACE), Alma Mater Studiorum, University of Bologna, Via Baldassarre Canaccini 12, I-47121 Forlì, Italy
- Interdepartmental Centre for Industrial Research in Renewable Resources, Environment, Sea, and Energy (CIRI FRAME), Alma Mater Studiorum, University of Bologna, Via Sant’Alberto 163, I-48123 Ravenna, Italy
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4
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Pundir M, Papagerakis S, De Rosa MC, Chronis N, Kurabayashi K, Abdulmawjood S, Prince MEP, Lobanova L, Chen X, Papagerakis P. Emerging biotechnologies for evaluating disruption of stress, sleep, and circadian rhythm mechanism using aptamer-based detection of salivary biomarkers. Biotechnol Adv 2022; 59:107961. [DOI: 10.1016/j.biotechadv.2022.107961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/30/2022] [Accepted: 04/09/2022] [Indexed: 12/26/2022]
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Abramova AM, Goryacheva OA, Drozd DD, Novikova AS, Ponomareva TS, Strokin PD, Goryacheva IY. Luminescence Semiconductor Quantum Dots in Chemical Analysis. JOURNAL OF ANALYTICAL CHEMISTRY 2021. [DOI: 10.1134/s1061934821030023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Sharma S, Saini S, Khangembam M, Singh V. Nanomaterials-Based Biosensors for COVID-19 Detection-A Review. IEEE SENSORS JOURNAL 2021; 21:5598-5611. [PMID: 37974905 PMCID: PMC8768986 DOI: 10.1109/jsen.2020.3036748] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 10/31/2020] [Accepted: 11/03/2020] [Indexed: 11/19/2023]
Abstract
This review paper discusses the properties of nanomaterials, namely graphene, molybdenum disulfide, carbon nanotubes, and quantum dots for unique sensing applications. Based on the specific analyte to be detected and the functionalization techniques that are employed, some noteworthy sensors that have been developed are discussed. Further, biocompatible sensors fabricated from these materials capable of detecting specific chemical compounds are also highlighted for COVID-19 detection purposes, which can aid in efficient and reliable sensing as well as timely diagnosis.
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Affiliation(s)
- Sakshi Sharma
- Department of Applied PhysicsDelhi Technological UniversityNew Delhi110042India
| | - Sonakshi Saini
- Department of Applied PhysicsDelhi Technological UniversityNew Delhi110042India
| | - Maya Khangembam
- Department of Applied PhysicsDelhi Technological UniversityNew Delhi110042India
| | - Vinod Singh
- Department of Applied PhysicsDelhi Technological UniversityNew Delhi110042India
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7
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Cho SW, Lim HJ, Chua B, Son A. Single-stranded DNA probe paired aptasensor with extra dye binding sites to enhance its fluorescence response in the presence of a target compound. RSC Adv 2021; 11:21796-21804. [PMID: 35478796 PMCID: PMC9034146 DOI: 10.1039/d1ra00971k] [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: 02/05/2021] [Accepted: 06/06/2021] [Indexed: 11/29/2022] Open
Abstract
The purpose of this study is to investigate the possibility of improving the performance of a DNA binding dye water quenching based aptasensor without changing or truncating the aptamer. To demonstrate the possibility of increasing the change in fluorescence of the aptasensor by pairing it with a suitable ssDNA probe, three ssDNA probes (probe 1, 2, and 3) were employed and the fluorescence from the bound dyes was measured. This showed that ssDNA probe 2 created the most additional binding sites. By varying the target compound concentration (0, 0.05, 0.5, 5, 50, and 500 mg L−1 4-n-nonylphenol), the corresponding change in the fluorescence signal of the unpaired and ssDNA probe paired aptasensors were measured and compared over a range of emission wavelengths. The response of all three ssDNA probe paired aptasensors showed good fit (R2 = 0.88–0.92) to a logarithmic response. The sensitivity of the aptasensor paired with ssDNA probe 2 was improved by ∼60%, whereas that of the aptasensor paired with ssDNA probe 3 was only improved by a marginal ∼3%. This study is a demonstration of using an appropriate ssDNA probe to increase the number of binding sites and hence the performance of a DNA binding dye and water quenched aptasensor. It is a possibility that can be extended to similar aptasensors without having to change or truncate the aptamer. Principle of an ssDNA paired aptasensor where extra dye binding sites are created to enhance its fluorescence response.![]()
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Affiliation(s)
- Seo Won Cho
- Department of Environmental Science and Engineering
- Ewha Womans University
- Seoul 03760
- Republic of Korea
- Department of Civil and Environmental Engineering
| | - Hyun Jeong Lim
- Department of Environmental Science and Engineering
- Ewha Womans University
- Seoul 03760
- Republic of Korea
| | - Beelee Chua
- School of Electrical Engineering
- Korea University
- Seoul 02841
- Republic of Korea
| | - Ahjeong Son
- Department of Environmental Science and Engineering
- Ewha Womans University
- Seoul 03760
- Republic of Korea
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8
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Application of Nanoscale Materials and Nanotechnology Against Viral Infection: A Special Focus on Coronaviruses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1352:173-193. [DOI: 10.1007/978-3-030-85109-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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9
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Alyamani BJ, Alsager OA, Zourob M. Label-Free Fluorescent Aptasensor for Small Targets via Displacement of Groove Bound Curcumin Molecules. SENSORS 2019; 19:s19194181. [PMID: 31561589 PMCID: PMC6806071 DOI: 10.3390/s19194181] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 09/24/2019] [Accepted: 09/24/2019] [Indexed: 12/12/2022]
Abstract
Signal transduction based on fluorescence is one of the most common optical aptasensors for small molecules. Sensors with a number of unique features including high sensitivity, low cost, and simple operation can be constructed easily. However, the label-free fluorescent approach is limited to synthetic dyes that bind strongly to the aptamer sequence and result in a diminished sensor operation with high detection limits. In this study, we report the use of curcumin as a fluorescent probe to signal aptamer/small target binding events. A substantial enhancement in curcumin's fluorescent emission was observed when bound into the grooves of vitamin D3 (VTD3) binding aptamer, as an example. However, the introduction of the target molecule causes the aptamer to undergo a conformational change that favors complexing the target molecule over binding the curcumin dye. The sensor was able to detect VTD3 down to 1 fM concentration in buffer solutions and extracted blood samples, operate at a wide dynamic range, and discriminate against potential biological interfering molecules including VTD2. The operation of the curcumin based fluorescent sensor is at least six orders of magnitude more sensitive than a VTD3 sensor constructed with the synthetic dye SYBR Green I. The generality of the reported label-free approach was applied with a previously isolated 75-mer bisphenol-A (BPA) aptamer, confirming that the reported sensing strategy is not confined on a particular aptamer sequence. Our work not only reports a novel sensor format for the detection of small molecules, but also serves fluorescent sensor's most pressing need being novel fluorophores for multiplex targets detection.
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Affiliation(s)
- Baraa J Alyamani
- National Center for Irradiation Technology, King Abdulaziz City for Science and Technology, P.O. Box 6086, Riyadh 11442, Saudi Arabia.
| | - Omar A Alsager
- National Center for Irradiation Technology, King Abdulaziz City for Science and Technology, P.O. Box 6086, Riyadh 11442, Saudi Arabia.
| | - Mohammed Zourob
- Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, Al Takhassusi Rd, Riyadh 11533, Saudi Arabia.
- King Faisal Specialist Hospital and Research Center, Zahrawi Street, Al Maather, Riyadh 12713, Saudi Arabia.
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10
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Abstract
Antibodies are large proteins generated in vivo to bind specifically to a wide spectrum of targets ranging from biological to environmental molecules. They play a vital role in research, diagnostics, sensing, and therapeutic applications. Over the past few decades, advancements have been made to improve the performance of antibodies, specifically in the area of immunosensors. However, there has been an urgent need for alternative high-quality recognition probes that can be produced synthetically in bulk quantity to ensure better reproducibility and lower cost, as well as avoiding the need of using animals in the production process. Aptamers are synthetic nucleic acid single-stranded (ss) DNAs or RNAs that can bind with high affinity and specificity to their targets. They can be generated via in vitro section protocol, known as systematic evolution of ligands by exponential enrichment (SELEX). The advantages of aptamers promoted their successful incorporation in several signal transduction schemes, some of which reached the commercial market for point-of-care and in-field applications. This chapter describes the two types of affinity reagents: antibodies and aptamers, and their methods of production, advantages, and limitations. The focus will be directed at their incorporation in analytical transduction methods and how aptamer molecular size as well as unique conformational change upon target binding has triggered the evolution of new sensing methods.
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Affiliation(s)
- Omar A. Alsager
- National Center for Irradiation Technology, Nuclear Science Research Institute, King Abdulaziz City for Science and Technology P.O. Box 6086 Riyadh 11442 Saudi Arabia
| | - Shimaa Eissa
- Department of Chemistry, Alfaisal University Al Zahrawi Street, Al Maather, Al Takhassusi Rd Riyadh 11533 Saudi Arabia
| | - Mohammed Zourob
- Department of Chemistry, Alfaisal University Al Zahrawi Street, Al Maather, Al Takhassusi Rd Riyadh 11533 Saudi Arabia
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11
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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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12
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Rodríguez-Rodríguez H, Acebrón M, Iborra FJ, Arias-Gonzalez JR, Juárez BH. Photoluminescence Activation of Organic Dyes via Optically Trapped Quantum Dots. ACS NANO 2019; 13:7223-7230. [PMID: 31194513 DOI: 10.1021/acsnano.9b02835] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Laser tweezers afford quantum dot (QD) manipulation for use as localized emitters. Here, we demonstrate fluorescence by radiative energy transfer from optically trapped colloidal QDs (donors) to fluorescent dyes (acceptors). To this end, we synthesized silica-coated QDs of different compositions and triggered their luminescence by simultaneous trapping and two-photon excitation in a microfluidic chamber filled with dyes. This strategy produces a near-field light source with great spatial maneuverability, which can be exploited to scan nanostructures. In this regard, we demonstrate induced photoluminescence of dye-labeled cells via optically trapped silica-coated colloidal QDs placed at their vicinity. Allocating nanoscale donors at controlled distances from a cell is an attractive concept in fluorescence microscopy because it dramatically reduces the number of excited dyes, which improves resolution by preventing interferences from the whole sample, while prolonging dye luminescence lifetime due to the lower power absorbed from the QDs.
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Affiliation(s)
- Héctor Rodríguez-Rodríguez
- IMDEA Nanoscience , Faraday 9, Campus de Cantoblanco, 28049 Madrid , Spain
- Department of Applied Physical Chemistry , Universidad Autónoma de Madrid , Cantoblanco, 28049 Madrid , Spain
| | - María Acebrón
- IMDEA Nanoscience , Faraday 9, Campus de Cantoblanco, 28049 Madrid , Spain
| | - Francisco J Iborra
- National Center for Biotechnology (CNB-CSIC) , Campus de Cantoblanco, 28049 Madrid , Spain
| | | | - Beatriz H Juárez
- IMDEA Nanoscience , Faraday 9, Campus de Cantoblanco, 28049 Madrid , Spain
- Department of Applied Physical Chemistry , Universidad Autónoma de Madrid , Cantoblanco, 28049 Madrid , Spain
- Condensed Matter Physics Center (IFIMAC) , Universidad Autónoma de Madrid , 28049 Madrid , Spain
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13
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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: 127] [Impact Index Per Article: 25.4] [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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14
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Hanif A, Farooq R, Rehman MU, Khan R, Majid S, Ganaie MA. Aptamer based nanobiosensors: Promising healthcare devices. Saudi Pharm J 2019; 27:312-319. [PMID: 30976173 PMCID: PMC6438676 DOI: 10.1016/j.jsps.2018.11.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/22/2018] [Indexed: 12/20/2022] Open
Abstract
Nanobiosensors based on aptamer are extensively being studied as potent analytical tools in clinical analysis. These biosensors provide high sensitivity, fast response, specificity and desired portability in addition to simplicity and decreased cost compared to conventional methods. The purpose of this manuscript is to provide readers with an overview of current advances about electrochemical, electrochemiluminescent and photoelectrochemical aptasensors from the sea of available literature. These are mainly used for determination of protein-based biomarkers, especially for cancer diagnosis. Here in we have given special emphasis on nanosize-based aptasensors which have been reported to show considerable improvement in the analytical performance.
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Affiliation(s)
- Aamir Hanif
- City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong Special Administrative Region
| | - Rabia Farooq
- Department of Biochemistry, Govt Medical College (GMC) Srinagar, J&K 190010, India
| | - Muneeb U. Rehman
- Department of Biochemistry, Govt Medical College (GMC) Srinagar, J&K 190010, India
| | - Rehan Khan
- Nanotherapeutics, Institute of Nanoscience & Technology (DST-INST), Habitat Centre Phase 10, Mohali, Punjab, India
| | - Sabhiya Majid
- Department of Biochemistry, Govt Medical College (GMC) Srinagar, J&K 190010, India
| | - Majid Ahmad Ganaie
- Department of Pharmacology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
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15
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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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16
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Aptamer-Modified Semiconductor Quantum Dots for Biosensing Applications. SENSORS 2017; 17:s17081736. [PMID: 28788080 PMCID: PMC5579848 DOI: 10.3390/s17081736] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 06/21/2017] [Accepted: 07/07/2017] [Indexed: 02/04/2023]
Abstract
Semiconductor quantum dots have attracted extensive interest in the biosensing area because of their properties, such as narrow and symmetric emission with tunable colors, high quantum yield, high stability and controllable morphology. The introduction of various reactive functional groups on the surface of semiconductor quantum dots allows one to conjugate a spectrum of ligands, antibodies, peptides, or nucleic acids for broader and smarter applications. Among these ligands, aptamers exhibit many advantages including small size, high chemical stability, simple synthesis with high batch-to-batch consistency and convenient modification. More importantly, it is easy to introduce nucleic acid amplification strategies and/or nanomaterials to improve the sensitivity of aptamer-based sensing systems. Therefore, the combination of semiconductor quantum dots and aptamers brings more opportunities in bioanalysis. Here we summarize recent advances on aptamer-functionalized semiconductor quantum dots in biosensing applications. Firstly, we discuss the properties and structure of semiconductor quantum dots and aptamers. Then, the applications of biosensors based on aptamer-modified semiconductor quantum dots by different signal transducing mechanisms, including optical, electrochemical and electrogenerated chemiluminescence approaches, is discussed. Finally, our perspectives on the challenges and opportunities in this promising field are provided.
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17
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Wang J, Gu Y, Liu L, Wang C, Wang J, Ding S, Li J, Qiu L, Jiang P. Novel application of fluorescence coupled capillary electrophoresis to resolve the interaction between the G-quadruplex aptamer and thrombin. J Sep Sci 2017; 40:3161-3167. [PMID: 28594110 DOI: 10.1002/jssc.201700456] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 05/27/2017] [Accepted: 05/31/2017] [Indexed: 12/17/2022]
Abstract
The dynamic binding status between the thrombin and its G-quadruplex aptamers and the stability of its interaction partners were probed using our previously established fluorescence-coupled capillary electrophoresis method. A 29-nucleic acid thrombin binding aptamer was chosen as a model to study its binding affinity with the thrombin ligand. First, the effects of the cations on the formation of G-quadruplex from unstructured 29-nucleic acid thrombin binding aptamer were examined. Second, the rapid binding kinetics between the thrombin and 6-carboxyfluorescein labeled G-quadruplex aptamer was measured. Third, the stability of G-quadruplex aptamer-thrombin complex was also examined in the presence of the interfering species. Remarkably, it was found that the complementary strand of 29-nucleic acid thrombin binding aptamer could compete with G-quadruplex aptamer and thus disassociated the G-quadruplex structure into an unstructured aptamer. These data suggest that our in-house established fluorescence-coupled capillary electrophoresis assay could be applied to binding studies of the G-quadruplex aptamers, thrombin, and their ligands, while overcoming the complicated and costly approaches currently available.
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Affiliation(s)
- Jianhao Wang
- School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, Jiangsu, P.R. China
| | - Yaqin Gu
- School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, Jiangsu, P.R. China
| | - Li Liu
- School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, Jiangsu, P.R. China
| | - Cheli Wang
- School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, Jiangsu, P.R. China
| | - Jianpeng Wang
- School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, Jiangsu, P.R. China
| | - Shumin Ding
- School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, Jiangsu, P.R. China
| | - Jinping Li
- School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, Jiangsu, P.R. China.,Department of Biomedical Science, Mercer University School of Medicine, Savannah, GA, USA
| | - Lin Qiu
- School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, Jiangsu, P.R. China
| | - Pengju Jiang
- School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou, Jiangsu, P.R. China
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18
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Huang X, Liu Y, Yung B, Xiong Y, Chen X. Nanotechnology-Enhanced No-Wash Biosensors for in Vitro Diagnostics of Cancer. ACS NANO 2017; 11:5238-5292. [PMID: 28590117 DOI: 10.1021/acsnano.7b02618] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
In vitro biosensors have been an integral component for early diagnosis of cancer in the clinic. Among them, no-wash biosensors, which only depend on the simple mixing of the signal generating probes and the sample solution without additional washing and separation steps, have been found to be particularly attractive. The outstanding advantages of facile, convenient, and rapid response of no-wash biosensors are especially suitable for point-of-care testing (POCT). One fast-growing field of no-wash biosensor design involves the usage of nanomaterials as signal amplification carriers or direct signal generating elements. The analytical capacity of no-wash biosensors with respect to sensitivity or limit of detection, specificity, stability, and multiplexing detection capacity is largely improved because of their large surface area, excellent optical, electrical, catalytic, and magnetic properties. This review provides a comprehensive overview of various nanomaterial-enhanced no-wash biosensing technologies and focuses on the analysis of the underlying mechanism of these technologies applied for the early detection of cancer biomarkers ranging from small molecules to proteins, and even whole cancerous cells. Representative examples are selected to demonstrate the proof-of-concept with promising applications for in vitro diagnostics of cancer. Finally, a brief discussion of common unresolved issues and a perspective outlook on the field are provided.
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Affiliation(s)
- Xiaolin Huang
- State Key Laboratory of Food Science and Technology, Nanchang University , Nanchang 330047, P. R. China
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH) , Bethesda, Maryland 20892, United States
| | - Yijing Liu
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH) , Bethesda, Maryland 20892, United States
| | - Bryant Yung
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH) , Bethesda, Maryland 20892, United States
| | - Yonghua Xiong
- State Key Laboratory of Food Science and Technology, Nanchang University , Nanchang 330047, P. R. China
| | - Xiaoyuan Chen
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH) , Bethesda, Maryland 20892, United States
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19
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Shamsipur M, Nasirian V, Barati A, Mansouri K, Vaisi-Raygani A, Kashanian S. Determination of cDNA encoding BCR/ABL fusion gene in patients with chronic myelogenous leukemia using a novel FRET-based quantum dots-DNA nanosensor. Anal Chim Acta 2017; 966:62-70. [PMID: 28372728 DOI: 10.1016/j.aca.2017.02.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/31/2017] [Accepted: 02/13/2017] [Indexed: 01/05/2023]
Abstract
In the present study, we developed a sensitive method based on fluorescence resonance energy transfer (FRET) for the determination of the BCR/ABL fusion gene, which is used as a biomarker to confirm the clinical diagnosis of both chronic myelogenous leukemia (CML) and acute lymphocytic leukemia (ALL). For this purpose, CdTe quantum dots (QDs) were conjugated to amino-modified 18-mer oligonucleotide ((N)DNA) to form the QDs-(N)DNA nanosensor. In the presence of methylene blue (MB) as an intercalator, the hybridization of QDs-(N)DNA with the target BCR/ABL fusion gene (complementary DNA), brings the MB (acceptor) at close proximity of the QDs (donor), leading to FRET upon photoexcitation of the QDs. The enhancement in the emission intensity of MB was used to follow up the hybridization, which was linearly proportional to concentration of the target complementary DNA in a range from 1.0 × 10-9 to 1.25 × 10-7 M. The detection limit of the proposed method was obtained to be 1.5 × 10-10 M. Finally, the feasibility and selectivity of the proposed nanosensor was evaluated by the analysis of derived nucleotides from both mismatched sequences and clinical samples of patients with leukemia as real samples.
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Affiliation(s)
- Mojtaba Shamsipur
- Department of Chemistry, Razi University, Kermanshah 6714967346, Iran.
| | - Vahid Nasirian
- Department of Chemistry, Razi University, Kermanshah 6714967346, Iran
| | - Ali Barati
- Department of Chemistry, Razi University, Kermanshah 6714967346, Iran
| | - Kamran Mansouri
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Asad Vaisi-Raygani
- Department of Biochemistry School of Medicine Kermanshah University of Medical Sciences, Kermanshah 6714869914, Iran
| | - Soheila Kashanian
- Department of Chemistry, Razi University, Kermanshah 6714967346, Iran
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20
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Fischer C, Wessels H, Paschke-Kratzin A, Fischer M. Aptamers: Universal capture units for lateral flow applications. Anal Biochem 2017; 522:53-60. [PMID: 28111303 DOI: 10.1016/j.ab.2017.01.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 01/11/2017] [Accepted: 01/18/2017] [Indexed: 01/07/2023]
Abstract
The present work demonstrates the implementation of aptamers as capture molecules for a wide range of target classes in lateral flow assay applications. The targets were chosen in order to cover a wide range of target classes (small sized - metabolite, medium sized - protein, and large sized - whole cell/spore). For each target class one target molecule was selected as representative and appropriate aptamers were used for lateral flow assay development. The work points out that the implementation of aptamers as capture molecules in a universal lateral flow test platform was successful independent form target size. Furthermore, the limit of detection for p-aminohippuric acid in urine (200 ppm), lysozyme in white wine (20 ppm), and Alicyclobacillus spores in buffered orange juice (>8 CFU/mL) were determined using aptamers as capture molecules. The whole approach is considered as a proof of concept, regarding the ability of aptamers as an alternative to antibodies (in conjunction with directive 2010/63/EU on the protection of animals used for scientific purposes) in lateral flow applications.
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Affiliation(s)
- Christin Fischer
- Hamburg School of Food Science; Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Hauke Wessels
- Hamburg School of Food Science; Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Angelika Paschke-Kratzin
- Hamburg School of Food Science; Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Markus Fischer
- Hamburg School of Food Science; Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany.
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21
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Lv X, Zhang Y, Liu G, Du L, Wang S. Aptamer-based fluorescent detection of ochratoxin A by quenching of gold nanoparticles. RSC Adv 2017. [DOI: 10.1039/c7ra01474k] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A simple, rapid, low cost and highly sensitive method for the detection of ochratoxin A (OTA) was developed based on the principle that dispersed AuNPs show a better fluorescence quenching effect than aggregated AuNPs.
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Affiliation(s)
- Xin Lv
- Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology
- School of Chemistry and Chemical Engineering
- Liaocheng University
- Liaocheng 252059
- China
| | - Yuanfu Zhang
- Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology
- School of Chemistry and Chemical Engineering
- Liaocheng University
- Liaocheng 252059
- China
| | - Guofu Liu
- College of Life Science
- Liaocheng University
- Liaocheng 252059
- China
| | - Lingyun Du
- Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology
- School of Chemistry and Chemical Engineering
- Liaocheng University
- Liaocheng 252059
- China
| | - Shuhao Wang
- Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology
- School of Chemistry and Chemical Engineering
- Liaocheng University
- Liaocheng 252059
- China
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22
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Dai Z, Gao Q, Cheung MC, Leung HM, Lau TCK, Sleiman HF, Lai KWC, Lo PK. A highly versatile platform based on geometrically well-defined 3D DNA nanostructures for selective recognition and positioning of multiplex targets. NANOSCALE 2016; 8:18291-18295. [PMID: 27775745 DOI: 10.1039/c6nr05411k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We develop a versatile recognition system based on 3D triangular-shaped DNA nanotubes by integrating three different aptamer sequences along the three edges. This would allow multiple binding activities to be combined into a single system. The versatility of this nanotube platform can also provide a framework for spatial orientation and positioning of different aptamer-binding ligands in a 'pea-pod' architecture.
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Affiliation(s)
- Ziwen Dai
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, Chinaand Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China.
| | - Qi Gao
- Department of Mechanical and Biomedical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China
| | - Man Ching Cheung
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, Chinaand Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China.
| | - Hoi Man Leung
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, Chinaand Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China.
| | - Terrence Chi Kong Lau
- Department of Biomedical Sciences, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 2K6, Canada
| | - King Wai Chiu Lai
- Department of Mechanical and Biomedical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China
| | - Pik Kwan Lo
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, Chinaand Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China.
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23
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Page LE, Zhang X, Tyrakowski CM, Ho CT, Snee PT. Synthesis and characterization of DNA-quantum dot conjugates for the fluorescence ratiometric detection of unlabelled DNA. Analyst 2016; 141:6251-6258. [PMID: 27704090 DOI: 10.1039/c6an01760f] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A quantum dot-based ratiometrically responsive fluorescent sensor for unlabeled single-stranded DNA (ssDNA) is reported. Several technical issues concerning the development of high yield ssDNA-QD conjugation chemistry were addressed. The DNA sensor was synthesized by conjugating methacrylic phosphoramidite-functional oligonucleotides to water-soluble cadmium zinc sulfide core/zinc sulfide shell quantum dots (CdZnS/ZnS QDs). Duplex DNA was formed when the QD-bound ssDNA was incubated with its complement. Next, titration with PicoGreen resulted in FRET energy transfer from the dot to the dsDNA intercalating dye. The resulting ratio of the dye to QD integrated emissions is a calibratable metric for label-free DNA detection with a LOD of 3.8 nmol.
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Affiliation(s)
- Leah Elizabeth Page
- Department of Chemistry, the University of Illinois at Chicago, 845 W. Taylor St., Chicago, Il 60607-2405, USA.
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24
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Fischer C, Klockmann S, Wessels H, Hünniger T, Schrader J, Paschke-Kratzin A, Fischer M. Aptamer-based trapping of phytosphingosine in urine samples. J Biotechnol 2016; 238:30-34. [PMID: 27637314 DOI: 10.1016/j.jbiotec.2016.09.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/01/2016] [Accepted: 09/12/2016] [Indexed: 01/11/2023]
Abstract
Usually, small molecules like single metabolites used in clinical diagnostic can be quantified by instrumental approaches like LC-MS or bioanalytical techniques using antibodies or aptamers as selective receptors. The present work comprises the generation of aptamers with an affinity towards the medically relevant metabolite phytosphingosine via the previously reported just in time-Selection approach (Hünniger et al., 2014). The whole approach could be seen as a proof of concept to extend the existing just in time-Selection protocol for selection towards small molecules with dissociation constants in the low nanomolar range. Moreover it is conceivable that the shown methods could be quickly adapted to further scopes. Aptamers could be applied for clean-up or concentration processes prior to further analysis. As an example, we used the selected aptamers towards phytosphingosine bound to magnetic particles for affinity enrichment in both selection buffer and urine samples. As an outcome, enrichment factors of up to 9-fold (selection buffer)/4-fold (urine samples) were achieved by this approach.
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Affiliation(s)
- Christin Fischer
- HAMBURG SCHOOL OF FOOD SCIENCE; Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Sven Klockmann
- HAMBURG SCHOOL OF FOOD SCIENCE; Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Hauke Wessels
- HAMBURG SCHOOL OF FOOD SCIENCE; Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Tim Hünniger
- HAMBURG SCHOOL OF FOOD SCIENCE; Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Jil Schrader
- HAMBURG SCHOOL OF FOOD SCIENCE; Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Angelika Paschke-Kratzin
- HAMBURG SCHOOL OF FOOD SCIENCE; Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Markus Fischer
- HAMBURG SCHOOL OF FOOD SCIENCE; Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany.
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25
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Gladkovskaya O, Gun'ko YK, O'Connor GM, Gogvadze V, Rochev Y. In one harness: the interplay of cellular responses and subsequent cell fate after quantum dot uptake. Nanomedicine (Lond) 2016; 11:2603-15. [PMID: 27618947 DOI: 10.2217/nnm-2016-0068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Rapid growth and expansion of engineered nanomaterials will occur when the technology can be used safely. Quantum dots have excellent prospects in clinical applications, but the issue of toxicity has not yet been resolved. To enable their medical implementation, the effect on, and mechanisms in, live cells should be clearly known and predicted. A massive amount of experimental data dedicated to nanotoxicity has been accumulated to-date, but it lacks a logical structure. The current challenge is to organize existing knowledge into lucid biological and mathematical models. In our review we aim to describe the interplay of various cell death mechanisms triggered by quantum dots as a consequence of particle parameters and experimental conditions.
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Affiliation(s)
- Olga Gladkovskaya
- KAUST Catalysis Centre, King Abdullah University of Science & Technology, Thuwal Jeddah 23955-6900, Kingdom of Saudi Arabia.,School of Physics, National University of Ireland, Galway, Ireland.,CÚRAM - Centre for Research in Medical Devices, Galway, Ireland
| | - Yuri K Gun'ko
- CRANN & School of Chemistry, Trinity College Dublin, Ireland.,ITMO University, 197101 Saint Petersburg, Russia
| | | | - Vladimir Gogvadze
- Division of Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Box 210, 171 77 Stockholm, Sweden.,MV Lomonosov Moscow State University, 119991 Moscow, Russia.,Institute of Theoretical & Experimental Biophysics, Pushchino, 142290 Russia
| | - Yury Rochev
- CÚRAM - Centre for Research in Medical Devices, Galway, Ireland.,School of Chemistry, National University of Ireland, Galway, Ireland.,Sechenov First Moscow State Medical University, Institute for Regenerative Medicine
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26
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Hildebrandt N, Spillmann CM, Algar WR, Pons T, Stewart MH, Oh E, Susumu K, Díaz SA, Delehanty JB, Medintz IL. Energy Transfer with Semiconductor Quantum Dot Bioconjugates: A Versatile Platform for Biosensing, Energy Harvesting, and Other Developing Applications. Chem Rev 2016; 117:536-711. [DOI: 10.1021/acs.chemrev.6b00030] [Citation(s) in RCA: 457] [Impact Index Per Article: 57.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Niko Hildebrandt
- NanoBioPhotonics
Institut d’Electronique Fondamentale (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, 91400 Orsay, France
| | | | - W. Russ Algar
- Department
of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Thomas Pons
- LPEM;
ESPCI Paris, PSL Research University; CNRS; Sorbonne Universités, UPMC, F-75005 Paris, France
| | | | - Eunkeu Oh
- Sotera Defense Solutions, Inc., Columbia, Maryland 21046, United States
| | - Kimihiro Susumu
- Sotera Defense Solutions, Inc., Columbia, Maryland 21046, United States
| | - Sebastian A. Díaz
- American Society for Engineering Education, Washington, DC 20036, United States
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27
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Lin X, Sun X, Luo S, Liu B, Yang C. Development of DNA-based signal amplification and microfluidic technology for protein assay: A review. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.02.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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28
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Overview of nano-enabled screening of drug-facilitated crime: A promising tool in forensic investigation. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2015.07.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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29
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Weng X, Neethirajan S. A microfluidic biosensor using graphene oxide and aptamer-functionalized quantum dots for peanut allergen detection. Biosens Bioelectron 2016; 85:649-656. [PMID: 27240012 DOI: 10.1016/j.bios.2016.05.072] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 05/20/2016] [Accepted: 05/22/2016] [Indexed: 11/25/2022]
Abstract
The increasing prevalence of food allergies and the intake of packing foods in the past two decades urge the need for more rapid, accurate, and sensitive assays to detect potential allergens in food in order to control the allergen content. Most of the commercial analytical tools for allergen detection rely on immunoassays such as ELISA. As far as disadvantages, ELISA can be time-consuming and expensive. Biosensors appear as a suitable alternative for the detection of allergens because they are rapid, highly sensitive, selective, less expensive, environmentally friendly, and easy to handle. In this study, we developed a microfluidic system integrated with a quantum dots (Qdots) aptamer functionalized graphene oxide (GO) nano-biosensor for simple, rapid, and sensitive food allergen detection. The biosensor utilized Qdots-aptamer-GO complexes as probes to undergo conformational change upon interaction with the food allergens, resulting in fluorescence changes due to the fluorescence quenching and recovering properties of GO by adsorption and desorption of aptamer-conjugated Qdots. This one-step 'turn on' homogenous assay in a ready-to-use microfluidic chip took ~10min to achieve a quantitative detection of Ara h 1, one of the major allergens appearing in peanuts. The results suggested this system had remarkable sensitivity and selectivity. The integration of a microfluidics platform in a homemade miniaturized optical analyzer provides a promising way for the rapid, cost-effective, and accurate on-site determination of food allergens. This biosensor can also be extended to the detection of other food allergens with a selection of corresponding aptamers.
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Affiliation(s)
- Xuan Weng
- BioNano Laboratory, School of Engineering, University of Guelph, Guelph, Canada N1G 2W1
| | - Suresh Neethirajan
- BioNano Laboratory, School of Engineering, University of Guelph, Guelph, Canada N1G 2W1.
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30
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Lao YH, Chi CW, Friedrich SM, Peck K, Wang TH, Leong KW, Chen LC. Signal-on Protein Detection via Dye Translocation between Aptamer and Quantum Dot. ACS APPLIED MATERIALS & INTERFACES 2016; 8:12048-12055. [PMID: 27101438 DOI: 10.1021/acsami.6b02871] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A unique interaction between the cyanine dye and negatively charged quantum dot is used to construct a signal-on biaptameric quantum dot (QD) Förster resonance energy transfer (FRET) beacon for protein detection and distinct aptamer characterization. The beacon comprises a pair of aptamers, one intercalated with the cyanine dye (YOYO-3) and the other conjugated to a negatively charged, carboxyl-QD. When the target protein is present, structural folding and sandwich association of the two aptamers take place. As a consequence, YOYO-3 is displaced from the folded aptamer and transferred to the unblocked QD surface to yield a target concentration-dependent FRET signal. As a proof-of-principle, we demonstrate the detection of thrombin ranging from nanomolar to submicromolar concentrations and confirm the dye translocation using cylindrical illumination confocal spectroscopy (CICS). The proposed beacon provides a simple, rapid, signal-on FRET detection for protein as well as a potential platform for distinct aptamer screening.
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Affiliation(s)
- Yeh-Hsing Lao
- Department of Biomedical Engineering, Columbia University , New York, New York 10027, United States
| | - Chun-Wei Chi
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University , Taipei 10617, Taiwan
| | | | - Konan Peck
- Institute of Biomedical Sciences, Academia Sinica , Taipei 11529, Taiwan
| | | | - Kam W Leong
- Department of Biomedical Engineering, Columbia University , New York, New York 10027, United States
| | - Lin-Chi Chen
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University , Taipei 10617, Taiwan
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Samanta A, Medintz IL. Nanoparticles and DNA - a powerful and growing functional combination in bionanotechnology. NANOSCALE 2016; 8:9037-95. [PMID: 27080924 DOI: 10.1039/c5nr08465b] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Functionally integrating DNA and other nucleic acids with nanoparticles in all their different physicochemical forms has produced a rich variety of composite nanomaterials which, in many cases, display unique or augmented properties due to the synergistic activity of both components. These capabilities, in turn, are attracting greater attention from various research communities in search of new nanoscale tools for diverse applications that include (bio)sensing, labeling, targeted imaging, cellular delivery, diagnostics, therapeutics, theranostics, bioelectronics, and biocomputing to name just a few amongst many others. Here, we review this vibrant and growing research area from the perspective of the materials themselves and their unique capabilities. Inorganic nanocrystals such as quantum dots or those made from gold or other (noble) metals along with metal oxides and carbon allotropes are desired as participants in these hybrid materials since they can provide distinctive optical, physical, magnetic, and electrochemical properties. Beyond this, synthetic polymer-based and proteinaceous or viral nanoparticulate materials are also useful in the same role since they can provide a predefined and biocompatible cargo-carrying and targeting capability. The DNA component typically provides sequence-based addressability for probes along with, more recently, unique architectural properties that directly originate from the burgeoning structural DNA field. Additionally, DNA aptamers can also provide specific recognition capabilities against many diverse non-nucleic acid targets across a range of size scales from ions to full protein and cells. In addition to appending DNA to inorganic or polymeric nanoparticles, purely DNA-based nanoparticles have recently surfaced as an excellent assembly platform and have started finding application in areas like sensing, imaging and immunotherapy. We focus on selected and representative nanoparticle-DNA materials and highlight their myriad applications using examples from the literature. Overall, it is clear that this unique functional combination of nanomaterials has far more to offer than what we have seen to date and as new capabilities for each of these materials are developed, so, too, will new applications emerge.
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Affiliation(s)
- Anirban Samanta
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA. and College of Science, George Mason University, Fairfax, Virginia 22030, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA.
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An ascorbic acid sensor based on cadmium sulphide quantum dots. Anal Bioanal Chem 2016; 408:3699-706. [PMID: 27023220 DOI: 10.1007/s00216-016-9454-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 02/25/2016] [Accepted: 02/28/2016] [Indexed: 12/29/2022]
Abstract
We present a Förster resonance energy transfer (FRET)-based fluorescence detection of vitamin C [ascorbic acid (AA)] using cadmium sulphide quantum dots (CdS QDs) and diphenylcarbazide (DPC). Initially, DPC was converted to diphenylcarbadiazone (DPCD) in the presence of CdS QDs to form QD-DPCD. This enabled excited-state energy transfer from the QDs to DPCD, which led to the fluorescence quenching of QDs. The QD-DPCD solution was used as the sensor solution. In the presence of AA, DPCD was converted back to DPC, resulting in the fluorescence recovery of CdS QDs. This fluorescence recovery can be used to detect and quantify AA. Dynamic range and detection limit of this sensing system were found to be 60-300 nM and 2 nM, respectively. We also performed fluorescence lifetime analyses to confirm existence of FRET. Finally, the sensor responded with equal accuracy to actual samples such as orange juice and vitamin C tablets. Graphical abstract Schematic showing the FRET based fluorescence detection of ascorbic acid.
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Kumar V, Palazzolo S, Bayda S, Corona G, Toffoli G, Rizzolio F. DNA Nanotechnology for Cancer Therapy. Am J Cancer Res 2016; 6:710-25. [PMID: 27022418 PMCID: PMC4805665 DOI: 10.7150/thno.14203] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 01/27/2016] [Indexed: 02/07/2023] Open
Abstract
DNA nanotechnology is an emerging and exciting field, and represents a forefront frontier for the biomedical field. The specificity of the interactions between complementary base pairs makes DNA an incredible building material for programmable and very versatile two- and three-dimensional nanostructures called DNA origami. Here, we analyze the DNA origami and DNA-based nanostructures as a drug delivery system. Besides their physical-chemical nature, we dissect the critical factors such as stability, loading capability, release and immunocompatibility, which mainly limit in vivo applications. Special attention was dedicated to highlighting the boundaries to be overcome to bring DNA nanostructures closer to the bedside of patients.
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Zhang C, Ding C, Xiang D, Li L, Ji X, He Z, Xian Y. DNA Functionalized Fluorescent Quantum Dots for Bioanalytical Applications. CHINESE J CHEM 2016. [DOI: 10.1002/cjoc.201500906] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Abstract
Nucleic acid aptamers are promising alternatives to antibodies in analytics. They are generally obtained through an iterative SELEX protocol that enriches a population of synthetic oligonucleotides to a subset that can recognize the chosen target molecule specifically and avidly. A wide range of targets is recognized by aptamers. Once identified and optimized for performance, aptamers can be reproducibly synthesized and offer other key features, like small size, low cost, sensitivity, specificity, rapid response, stability, and reusability. This makes them excellent options for sensory units in a variety of analytical platforms including those with electrochemical, optical, and mass sensitive transduction detection. Many novel sensing strategies have been developed by rational design to take advantage of the tendency of aptamers to undergo conformational changes upon target/analyte binding and employing the principles of base complementarity that can drive the nucleic acid structure. Despite their many advantages over antibodies, surprisingly few aptamers have yet been integrated into commercially available analytical devices. In this review, we discuss how to select and engineer aptamers for their identified application(s), some of the challenges faced in developing aptamers for analytics and many examples of their reported successful performance as sensors in a variety of analytical platforms.
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Affiliation(s)
- Muslum Ilgu
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames IA 50011, USA. and Aptalogic Inc., Ames IA 50014, USA
| | - Marit Nilsen-Hamilton
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames IA 50011, USA. and Aptalogic Inc., Ames IA 50014, USA and Ames Laboratory, US DOE, Ames IA 50011, USA
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Seok Kim Y, Ahmad Raston NH, Bock Gu M. Aptamer-based nanobiosensors. Biosens Bioelectron 2016; 76:2-19. [DOI: 10.1016/j.bios.2015.06.040] [Citation(s) in RCA: 263] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 06/10/2015] [Accepted: 06/17/2015] [Indexed: 01/24/2023]
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Wang JC, Ku HY, Shieh DB, Chuang HS. A bead-based fluorescence immunosensing technique enabled by the integration of Förster resonance energy transfer and optoelectrokinetic concentration. BIOMICROFLUIDICS 2016; 10:014113. [PMID: 26865906 PMCID: PMC4733077 DOI: 10.1063/1.4940938] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/17/2016] [Indexed: 05/04/2023]
Abstract
Bead-based immunosensing has been growing as a promising technology in the point-of-care diagnostics due to great flexibility. For dilute samples, functionalized particles can be used to collect dispersed analytes and act as carriers for particle manipulation. To realize rapid and visual immunosensing, Förster resonance energy transfer (FRET) was used herein to ensure only the diabetic biomarker, lipocalin 1, to be detected. The measurement was made in an aqueous droplet sandwiched between two parallel plate electrodes. With an electric field and a focused laser beam applying on the microchip simultaneously, the immunocomplexes in the droplet were further concentrated to enhance the FRET fluorescent signal. The optoelectrokinetic technique, termed rapid electrokinetic patterning (REP), has been proven to be excellent in dynamic and programmable particle manipulation. Therefore, the detection can be complete within several tens of seconds. The lower detection limit of the REP-enabled bead-based diagnosis reached nearly 5 nM. The combinative use of FRET and the optoelectrokinetic technique for the bead-based immunosensing enables a rapid measure to diagnose early stage diseases and dilute analytes.
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Affiliation(s)
| | - Hu-Yao Ku
- Department of Biomedical Engineering, National Cheng Kung University , Tainan, Taiwan
| | - Dar-Bin Shieh
- Medical Device Innovation Center, National Cheng Kung University , Tainan, Taiwan
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38
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Colorimetric thrombin assay using aptamer-functionalized gold nanoparticles acting as a peroxidase mimetic. Mikrochim Acta 2015. [DOI: 10.1007/s00604-015-1674-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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39
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Sharon E, Enkin N, Albada HB, Willner I. Aptasensors based on supramolecular structures of nucleic acid-stabilized Ag nanoclusters. Chem Commun (Camb) 2015; 51:1100-3. [PMID: 25449885 DOI: 10.1039/c4cc08263j] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Two-sized luminescent nucleic acid-functionalized Ag nanoclusters (NCs) are implemented for the analysis and multiplexed detection of adenosine monophosphate, AMP, and of cocaine using aptamer-ligand complexes.
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Affiliation(s)
- Etery Sharon
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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40
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Hu J, Kim J, Easley CJ. Quantifying Aptamer-Protein Binding via Thermofluorimetric Analysis. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2015; 7:7358-7362. [PMID: 26366207 PMCID: PMC4562029 DOI: 10.1039/c5ay00837a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Effective aptamer-based protein assays require coupling to a quantitative reporter of aptamer-protein binding. Typically, this involves a direct optical or electrochemical readout of DNA hybridization or an amplification step coupled to the readout. However, method development is often hampered by the multiplicity of aptamer-target binding mechanisms, which can interfere with the hybridization step. As a simpler and more generalizable readout of aptamer-protein binding, we report that thermofluorimetric analysis (TFA) can be used to quantitatively assay protein levels. Sub-nanomolar detection (0.74 nM) of platelet-derived growth factor (PDGF) with its corresponding aptamer is shown as a test case. In the presence of various DNA intercalating dyes, protein-bound aptamers exhibit a change in fluorescence intensity compared to the intercalated, unbound aptamer. This allows thermal resolution of bound and unbound aptamers using fluorescence melting analysis (-dF/dT curves). Remarkably, the homogeneous optical method allows subtraction of autofluorescence in human serum, giving PDGF detection limits of 1.8 and 10.7 nM in serum diluted 1:7 and 1:3, respectively. We have thus demonstrated that bound and unbound aptamers can be thermally resolved in a homogeneous format using a simple qPCR instrument-even in human serum. The simplicity of this approach provides an important step toward a robust, generalizable readout of aptamer-protein binding.
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Affiliation(s)
- Juan Hu
- Department of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, AL 36849
| | - Joonyul Kim
- Department of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, AL 36849
| | - Christopher J. Easley
- Department of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, AL 36849
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Nucleic Acid Aptamers: An Emerging Tool for Biotechnology and Biomedical Sensing. SENSORS 2015; 15:16281-313. [PMID: 26153774 PMCID: PMC4541879 DOI: 10.3390/s150716281] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 06/26/2015] [Accepted: 06/30/2015] [Indexed: 02/06/2023]
Abstract
Detection of small molecules or proteins of living cells provides an exceptional opportunity to study genetic variations and functions, cellular behaviors, and various diseases including cancer and microbial infections. Our aim in this review is to give an overview of selected research activities related to nucleic acid-based aptamer techniques that have been reported in the past two decades. Limitations of aptamers and possible approaches to overcome these limitations are also discussed.
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42
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Zhou W, Huang PJJ, Ding J, Liu J. Aptamer-based biosensors for biomedical diagnostics. Analyst 2015; 139:2627-40. [PMID: 24733714 DOI: 10.1039/c4an00132j] [Citation(s) in RCA: 337] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Aptamers are single-stranded nucleic acids that selectively bind to target molecules. Most aptamers are obtained through a combinatorial biology technique called SELEX. Since aptamers can be isolated to bind to almost any molecule of choice, can be readily modified at arbitrary positions and they possess predictable secondary structures, this platform technology shows great promise in biosensor development. Over the past two decades, more than one thousand papers have been published on aptamer-based biosensors. Given this progress, the application of aptamer technology in biomedical diagnosis is still in a quite preliminary stage. Most previous work involves only a few model aptamers to demonstrate the sensing concept with limited biomedical impact. This Critical Review aims to summarize progress that might enable practical applications of aptamers for biological samples. First, general sensing strategies based on the unique properties of aptamers are summarized. Each strategy can be coupled to various signaling methods. Among these, a few detection methods including fluorescence lifetime, flow cytometry, upconverting nanoparticles, nanoflare technology, magnetic resonance imaging, electronic aptamer-based sensors, and lateral flow devices have been discussed in more detail since they are more likely to work in a complex sample matrix. The current limitations of this field include the lack of high quality aptamers for clinically important targets. In addition, the aptamer technology has to be extensively tested in a clinical sample matrix to establish reliability and accuracy. Future directions are also speculated to overcome these challenges.
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Affiliation(s)
- Wenhu Zhou
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Central South University, Tongzipo Road #172, Changsha 410013, Hunan, PR China.
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43
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QD-Based FRET Probes at a Glance. SENSORS 2015; 15:13028-51. [PMID: 26053750 PMCID: PMC4507597 DOI: 10.3390/s150613028] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 05/20/2015] [Accepted: 05/22/2015] [Indexed: 12/21/2022]
Abstract
The unique optoelectronic properties of quantum dots (QDs) give them significant advantages over traditional organic dyes, not only as fluorescent labels for bioimaging, but also as emissive sensing probes. QD sensors that function via manipulation of fluorescent resonance energy transfer (FRET) are of special interest due to the multiple response mechanisms that may be utilized, which in turn imparts enhanced flexibility in their design. They may also function as ratiometric, or "color-changing" probes. In this review, we describe the fundamentals of FRET and provide examples of QD-FRET sensors as grouped by their response mechanisms such as link cleavage and structural rearrangement. An overview of early works, recent advances, and various models of QD-FRET sensors for the measurement of pH and oxygen, as well as the presence of metal ions and proteins such as enzymes, are also provided.
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44
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Lee J, Moon SU, Lee YS, Ali BA, Al-Khedhairy AA, Ali D, Ahmed J, Al Salem AM, Kim S. Quantum dot-based molecular beacon to monitor intracellular microRNAs. SENSORS 2015; 15:12872-83. [PMID: 26043176 PMCID: PMC4507685 DOI: 10.3390/s150612872] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 05/26/2015] [Accepted: 05/29/2015] [Indexed: 11/23/2022]
Abstract
Fluorescence monitoring of endogenous microRNA (miRNA or miR) activity related to neuronal development using nano-sized materials provides crucial information on miRNA expression patterns in a noninvasive manner. In this study, we report a new method to monitor intracellular miRNA124a using quantum dot-based molecular beacon (R9-QD-miR124a beacon). The R9-QD-miR124a beacon was constructed using QDs and two probes, miR124a-targeting oligomer and arginine rich cell-penetrating peptide (R9 peptide). The miR124a-targeting oligomer contains a miR124a binging sequence and a black hole quencher 1 (BHQ1). In the absence of target miR124a, the R9-QD-miR124a beacon forms a partial duplex beacon and remained in quenched state because the BHQ1 quenches the fluorescence signal of the R9-QD-miR124a beacon. The binding of miR124a to the miR124a binding sequence of the miR124a-targeting oligomer triggered the separation of the BHQ1 quencher and subsequent signal-on of a red fluorescence signal. Moreover, enhanced cellular uptake was achieved by conjugation with the R9 peptide, which resulted in increased fluorescent signal of the R9-QD-miR124a beacons in P19 cells during neurogenesis due to the endogenous expression of miR124a.
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Affiliation(s)
- Jonghwan Lee
- Institute for Bio-Medical Convergence, College of Medicine, Kwandong Catholic University, Gangneung-si, Gangwon-do 270-701, Korea.
- Catholic Kwandong University International St. Mary's Hospital, Incheon Metropolitan City 404-834, Korea.
| | - Sung Ung Moon
- Institute for Bio-Medical Convergence, College of Medicine, Kwandong Catholic University, Gangneung-si, Gangwon-do 270-701, Korea.
- Catholic Kwandong University International St. Mary's Hospital, Incheon Metropolitan City 404-834, Korea.
| | - Yong Seung Lee
- Institute for Bio-Medical Convergence, College of Medicine, Kwandong Catholic University, Gangneung-si, Gangwon-do 270-701, Korea.
- Catholic Kwandong University International St. Mary's Hospital, Incheon Metropolitan City 404-834, Korea.
| | - Bahy A Ali
- Aljeraisy DNA Research Chair, Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
- Department of Nucleic Acids Research, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Technological Applications, Alexandria 21934, Egypt.
| | | | - Daoud Ali
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Javed Ahmed
- Aljeraisy DNA Research Chair, Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Abdullah M Al Salem
- Aljeraisy DNA Research Chair, Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Soonhag Kim
- Institute for Bio-Medical Convergence, College of Medicine, Kwandong Catholic University, Gangneung-si, Gangwon-do 270-701, Korea.
- Catholic Kwandong University International St. Mary's Hospital, Incheon Metropolitan City 404-834, Korea.
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Yin J, Zhang A, Dong C, Ren J. An aptamer-based single particle method for sensitive detection of thrombin using fluorescent quantum dots as labeling probes. Talanta 2015; 144:13-9. [PMID: 26452786 DOI: 10.1016/j.talanta.2015.05.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Revised: 05/10/2015] [Accepted: 05/12/2015] [Indexed: 01/28/2023]
Abstract
In this study, an aptamer-based single particle method was developed for the thrombin detection in human serum samples using fluorescence correlation spectroscopy (FCS). In this method, quantum dots (QDs) were used as the fluorescent probes and thrombin-binding aptamer (TBA) was used as molecular recognition unit. When two QDs probes labeled with TBA (QD-TBA1 and QD-TBA2) are mixed in a sample containing thrombin targets, the binding of targets will cause QDs to form dimers (or oligomers) with bigger sizes, which leads to the nearly double increase in the characteristic diffusion time of QDs in the detection volume of FCS. FCS method can detect the change in the characteristic diffusion time of QDs. Firstly, the diffusion and blinking behaviors of QD-TBA probes in the presence of thrombin were investigated by FCS and total internal reflection fluorescence microscopy (TIRFM) imaging system, and the experimental results documented that QD-TBAs were bound together with "one-by-one" structure when thrombin were added into the solution. And then, the assay conditions were optimized in order to improve the sensitivity and specificity of this method. Under the optimized conditions, the linear range of the method is from 5.0 nM to 500 nM of thrombin, and the limit of detection is about 2.6 nM. Finally, this method was applied to homogeneous determination of thrombin in human serum samples.
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Affiliation(s)
- Jinjin Yin
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China
| | - Aidi Zhang
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China
| | - Chaoqing Dong
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China
| | - Jicun Ren
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China.
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46
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Juul S, Obliosca JM, Liu C, Liu YL, Chen YA, Imphean DM, Knudsen BR, Ho YP, Leong KW, Yeh HC. NanoCluster Beacons as reporter probes in rolling circle enhanced enzyme activity detection. NANOSCALE 2015; 7:8332-7. [PMID: 25901841 PMCID: PMC4441223 DOI: 10.1039/c5nr01705j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
As a newly developed assay for the detection of endogenous enzyme activity at the single-catalytic-event level, Rolling Circle Enhanced Enzyme Activity Detection (REEAD) has been used to measure enzyme activity in both single human cells and malaria-causing parasites, Plasmodium sp. Current REEAD assays rely on organic dye-tagged linear DNA probes to report the rolling circle amplification products (RCPs), the cost of which may hinder the widespread use of REEAD. Here we show that a new class of activatable probes, NanoCluster Beacons (NCBs), can simplify the REEAD assays. Easily prepared without any need for purification and capable of large fluorescence enhancement upon hybridization, NCBs are cost-effective and sensitive. Compared to conventional fluorescent probes, NCBs are also more photostable. As demonstrated in reporting the human topoisomerases I (hTopI) cleavage-ligation reaction, the proposed NCBs suggest a read-out format attractive for future REEAD-based diagnostics.
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Affiliation(s)
- Sissel Juul
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Judy M. Obliosca
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Cong Liu
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Yen-Liang Liu
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Yu-An Chen
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Darren M. Imphean
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Birgitta R. Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus C, Denmark
| | - Yi-Ping Ho
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus C, Denmark
| | - Kam W. Leong
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Hsin-Chih Yeh
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX 78712, USA
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47
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Zhang Y, Zhu C, Zhang L, Tan C, Yang J, Chen B, Wang L, Zhang H. DNA-templated silver nanoclusters for multiplexed fluorescent DNA detection. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:1385-9. [PMID: 25491417 DOI: 10.1002/smll.201402044] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 09/28/2014] [Indexed: 05/28/2023]
Abstract
Novel label-free/conjugation-free molecular beacons are designed based on DNA templated-silver nanoclusters for multiplexed DNA detection. The assay is implemented in solution, which makes it easy for the in-situ and real-time analysis. This study demonstrates a new method for multiplexd detection of biological molecules by using fluorescent Ag nanocluster-based molecular beacon probes.
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Affiliation(s)
- Ying Zhang
- Key Laboratory for Organic Electronics and Information Displays and Institute of Advanced Materials, National Jiangsu Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, Nanjing, 210023, P. R. China; School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
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48
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Lu X, Zhao Y, Zhang J, Lu X, Wang Y, Liu C. Copper ion-induced fluorescence band shift of CdTe quantum dots: a highly specific strategy for visual detection of Cu2+ with a portable UV lamp. Analyst 2015; 140:7859-63. [DOI: 10.1039/c5an01963j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Visual detection of Cu2+ is realized based on a copper-induced fluorescence band shift rather than an intensity change of CdTe QDs.
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Affiliation(s)
- Xiaohui Lu
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education; College of Chemistry and Environmental Science
- Hebei University
- Baoding 071002
- P. R. China
| | - Yunjie Zhao
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education; College of Chemistry and Environmental Science
- Hebei University
- Baoding 071002
- P. R. China
| | - Jinjun Zhang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education; College of Chemistry and Environmental Science
- Hebei University
- Baoding 071002
- P. R. China
| | - Xiaozhen Lu
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education; College of Chemistry and Environmental Science
- Hebei University
- Baoding 071002
- P. R. China
| | - Yucong Wang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education; College of Chemistry and Environmental Science
- Hebei University
- Baoding 071002
- P. R. China
| | - Chenghui Liu
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
- Xi'an 710062
- P. R. China
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Saberian-Borujeni M, Johari-Ahar M, Hamzeiy H, Barar J, Omidi Y. Nanoscaled aptasensors for multi-analyte sensing. ACTA ACUST UNITED AC 2014; 4:205-15. [PMID: 25671177 PMCID: PMC4298712 DOI: 10.15171/bi.2014.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Revised: 09/03/2014] [Accepted: 11/08/2014] [Indexed: 12/21/2022]
Abstract
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Introduction: Nanoscaled aptamers (Aps), as short single-stranded DNA or RNA oligonucleotides, are able to bind to their specific targets with high affinity, upon which they are considered as powerful diagnostic and analytical sensing tools (the so-called "aptasensors"). Aptamers are selected from a random pool of oligonucleotides through a procedure known as "systematic evolution of ligands by exponential enrichment".
Methods: In this work, the most recent studies in the field of aptasensors are reviewed and discussed with a main focus on the potential of aptasensors for the multianalyte detection(s).
Results: Due to the specific folding capability of aptamers in the presence of analyte, aptasensors have substantially successfully been exploited for the detection of a wide range of small and large molecules (e.g., drugs and their metabolites, toxins, and associated biomarkers in various diseases) at very low concentrations in the biological fluids/samples even in presence of interfering species.
Conclusion: Biological samples are generally considered as complexes in the real biological media. Hence, the development of aptasensors with capability to determine various targets simultaneously within a biological matrix seems to be our main challenge. To this end, integration of various key scientific dominions such as bioengineering and systems biology with biomedical researches are inevitable.
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Affiliation(s)
- Mehdi Saberian-Borujeni
- Research Center for Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Johari-Ahar
- Research Center for Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Hamzeiy
- Research Center for Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jaleh Barar
- Research Center for Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yadollah Omidi
- Research Center for Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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Li S, Gao Z, Shao N. Non-covalent conjugation of CdTe QDs with lysozyme binding DNA for fluorescent sensing of lysozyme in complex biological sample. Talanta 2014; 129:86-92. [DOI: 10.1016/j.talanta.2014.04.062] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Revised: 04/15/2014] [Accepted: 04/21/2014] [Indexed: 12/13/2022]
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