1
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Huang PJJ, Liu J. Simultaneous Detection of L-Lactate and D-Glucose Using DNA Aptamers in Human Blood Serum. Angew Chem Int Ed Engl 2023; 62:e202212879. [PMID: 36693796 DOI: 10.1002/anie.202212879] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023]
Abstract
L-lactate is a key metabolite indicative of physiological states, glycolysis pathways, and various diseases such as sepsis, heart attack, lactate acidosis, and cancer. Detection of lactate has been relying on a few enzymes that need additional oxidants. In this work, DNA aptamers for L-lactate were obtained using a library-immobilization selection method and the highest affinity aptamer reached a Kd of 0.43 mM as determined using isothermal titration calorimetry. The aptamers showed up to 50-fold selectivity for L-lactate over D-lactate and had little responses to other closely related analogs such as pyruvate or 3-hydroxybutyrate. A fluorescent biosensor based on the strand displacement method showed a limit of detection of 0.55 mM L-lactate, and the sensor worked in 90 % serum. Simultaneous detection of L-lactate and D-glucose in the same solution was achieved. This work has broadened the scope of aptamers to simple metabolites and provided a useful probe for continuous and multiplexed monitoring.
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Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
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2
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Liu Y, Liu J. Salt-Toggled Capture Selection of Uric Acid Binding Aptamers. Chembiochem 2023; 24:e202200564. [PMID: 36394510 DOI: 10.1002/cbic.202200564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/16/2022] [Indexed: 11/18/2022]
Abstract
Uric acid is the end-product of purine metabolism in humans and an important biomarker for many diseases. To achieve the detection of uric acid without using enzymes, we previously selected a DNA aptamer for uric acid with a Kd of 1 μM but the aptamer required multiple Na+ ions for binding. Saturated binding was achieved with around 700 mM Na+ and the binding at the physiological condition was much weaker. In this work, a new selection was performed by alternating Mg2+ -containing buffers with Na+ and Li+ . After 13 rounds of selection, a new aptamer sequence named UA-Mg-1 was obtained. Isothermal titration calorimetry confirmed aptamer binding in both selection buffers, and the Kd was around 8 μM. The binding of UA-Mg-1 to UA required only Mg2+ . This is an indicator of successful switching of metal dependency via the salt-toggled selection method. The UA-Mg-1 aptamer was engineered into a fluorescent biosensor based on the strand-displacement assay with a limit of detection of 0.5 μM uric acid in the selection buffer. Finally, comparison with the previously reported Na+ -dependent aptamer and a xanthine/uric acid riboswitch was also made.
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Affiliation(s)
- Yibo Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, N2L3G1, Waterloo, ON, Canada.,Centre for Eye and Vision Research (CEVR), 17 W Hong Kong Science Park, Hong Kong, 999077, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, N2L3G1, Waterloo, ON, Canada.,Centre for Eye and Vision Research (CEVR), 17 W Hong Kong Science Park, Hong Kong, 999077, China
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3
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Tang Y, Qi L, Liu Y, Guo L, Zhao R, Yang M, Du Y, Li B. CLIPON: A CRISPR-Enabled Strategy that Turns Commercial Pregnancy Test Strips into General Point-of-Need Test Devices. Angew Chem Int Ed Engl 2022; 61:e202115907. [PMID: 35064613 DOI: 10.1002/anie.202115907] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Indexed: 12/24/2022]
Abstract
Desirable biosensing assays need to be sensitive, specific, cost-effective, instrument-free, and versatile. Herein we report a new strategy termed CLIPON (CRISPR and Large DNA assembly Induced Pregnancy strips for signal-ON detection) that can deliver these traits. CLIPON integrates a commercial pregnancy test strip (PTS) with four biological elements: the human chorionic gonadotropin (hCG), CRISPR-Cas12a, crRNA and cauliflower-like large-sized DNA assemblies (CLD). CLIPON uses the Cas12a/crRNA complex both to recognize a target of interest and to release CLD-bound hCG so that target presence can translate into a colorimetric signal on the PTS. We demonstrate the versatility of CLIPON through sensitive and specific detection of HPV genomic DNA, SARS-CoV-2 genomic RNA and adenosine. We also engineer a cell phone app and a hand-held microchip to achieve signal quantification. CLIPON represents an attractive option for biosensing and point-of-care diagnostics.
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Affiliation(s)
- Yidan Tang
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
| | - Lijuan Qi
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China.,University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Yichen Liu
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China.,University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Lulu Guo
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China.,University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Rujian Zhao
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China.,University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Meiting Yang
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
| | - Yan Du
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China.,University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Bingling Li
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China.,University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
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4
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Tang Y, Qi L, Liu Y, Guo L, Zhao R, Yang M, Du Y, Li B. CLIPON: A CRISPR‐Enabled Strategy that Turns Commercial Pregnancy Test Strips into General Point‐of‐Need Test Devices. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202115907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yidan Tang
- State Key Lab of Electroanalytical Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
| | - Lijuan Qi
- State Key Lab of Electroanalytical Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Yichen Liu
- State Key Lab of Electroanalytical Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Lulu Guo
- State Key Lab of Electroanalytical Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Rujian Zhao
- State Key Lab of Electroanalytical Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Meiting Yang
- State Key Lab of Electroanalytical Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
| | - Yan Du
- State Key Lab of Electroanalytical Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Bingling Li
- State Key Lab of Electroanalytical Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230026 P. R. China
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5
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Qi X, Zhao Y, Su H, Wang L, Li L, Ma R, Yan X, Sun J, Wang S, Mao X. A label-free colorimetric aptasensor based on split aptamers-chitosan oligosaccharide-AuNPs nanocomposites for sensitive and selective detection of kanamycin. Talanta 2022; 238:123032. [PMID: 34857350 DOI: 10.1016/j.talanta.2021.123032] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 09/09/2021] [Accepted: 11/01/2021] [Indexed: 12/25/2022]
Abstract
Herein, the split aptamers, chitosan oligosaccharide, and AuNPs were combined as nanocomposites that present different formations to develop a label-free colorimetric aptasensor for rapid detection of small molecules. Kanamycin was chosen as a model target. Computational studies were performed to assist in the design of orientated immobilization of the split aptamers onto the AuNPs surface. Chitosan oligosaccharide was initially applied as an aggregation inducer of AuNPs, and chitopentaose was screened as the optimal. Under optimized conditions, the proposed aptasensor showed high sensitivity and selectivity, with a limit of detection of 20.58 nM, a linear range of 25-800 nM, and good recoveries of 98.49-104.9% and 85.69-107.0% when employed to detect kanamycin in tap water and milk samples, respectively. Only 55 min was needed for the whole assay. More importantly, this study can serve as a novel and robust reference for the aptasensing detection of other small molecules.
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Affiliation(s)
- Xiaoyan Qi
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, PR China
| | - Yinglin Zhao
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, PR China
| | - Haipeng Su
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, PR China
| | - Lele Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, PR China
| | - Ling Li
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, PR China
| | - Rui Ma
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, PR China
| | - Xiaochen Yan
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, PR China
| | - Jianan Sun
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, PR China
| | - Sai Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, PR China.
| | - Xiangzhao Mao
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, PR China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, PR China
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6
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Alkhamis O, Canoura J, Bukhryakov KV, Tarifa A, DeCaprio AP, Xiao Y. DNA Aptamer–Cyanine Complexes as Generic Colorimetric Small‐Molecule Sensors. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Obtin Alkhamis
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
- Department of Chemistry North Carolina State University 2620 Yarbrough Dr. Raleigh NC 27695 USA
| | - Juan Canoura
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
- Department of Chemistry North Carolina State University 2620 Yarbrough Dr. Raleigh NC 27695 USA
| | - Konstantin V. Bukhryakov
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Anamary Tarifa
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Anthony P. DeCaprio
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Yi Xiao
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
- Department of Chemistry North Carolina State University 2620 Yarbrough Dr. Raleigh NC 27695 USA
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7
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Li H, Gao J, Cao L, Xie X, Fan J, Wang H, Wang H, Nie Z. A DNA Molecular Robot that Autonomously Walks on the Cell Membrane to Drive Cell Motility. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108210] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Hao Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology Hunan University Changsha 410082 P. R. China
- School of Pharmaceutical Sciences (Shenzhen) Sun Yat-sen University Shenzhen 518107 P. R. China
| | - Jing Gao
- State Key Laboratory of Electroanalytical Chemistry Research Center of Biomembranomics Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun 130022 Jilin P. R. China
| | - Lei Cao
- State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology Hunan University Changsha 410082 P. R. China
| | - Xuan Xie
- State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology Hunan University Changsha 410082 P. R. China
| | - Jiahui Fan
- State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology Hunan University Changsha 410082 P. R. China
| | - Hongda Wang
- State Key Laboratory of Electroanalytical Chemistry Research Center of Biomembranomics Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun 130022 Jilin P. R. China
| | - Hong‐Hui Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology Hunan University Changsha 410082 P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology Hunan University Changsha 410082 P. R. China
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8
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Alkhamis O, Canoura J, Bukhryakov KV, Tarifa A, DeCaprio AP, Xiao Y. DNA Aptamer-Cyanine Complexes as Generic Colorimetric Small-Molecule Sensors. Angew Chem Int Ed Engl 2021; 61:e202112305. [PMID: 34706127 DOI: 10.1002/anie.202112305] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Indexed: 12/31/2022]
Abstract
Aptamers are promising biorecognition elements for sensors. However, aptamer-based assays often lack the requisite levels of sensitivity and/or selectivity because they typically employ structure-switching aptamers with attenuated affinity and/or utilize reporters that require aptamer labeling or which are susceptible to false positives. Dye-displacement assays offer a label-free, sensitive means for overcoming these issues, wherein target binding liberates a dye that is complexed with the aptamer, producing an optical readout. However, broad utilization of these assays has been limited. Here, we demonstrate a rational approach to develop colorimetric cyanine dye-displacement assays that can be broadly applied to DNA aptamers regardless of their structure, sequence, affinity, or the physicochemical properties of their targets. Our approach should accelerate the development of mix-and-measure assays that could be applied for diverse analytical applications.
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Affiliation(s)
- Obtin Alkhamis
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA.,Department of Chemistry, North Carolina State University, 2620 Yarbrough Dr., Raleigh, NC, 27695, USA
| | - Juan Canoura
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA.,Department of Chemistry, North Carolina State University, 2620 Yarbrough Dr., Raleigh, NC, 27695, USA
| | - Konstantin V Bukhryakov
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Anamary Tarifa
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Anthony P DeCaprio
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Yi Xiao
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA.,Department of Chemistry, North Carolina State University, 2620 Yarbrough Dr., Raleigh, NC, 27695, USA
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9
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Li H, Gao J, Cao L, Xie X, Fan J, Wang H, Wang HH, Nie Z. A DNA Molecular Robot that Autonomously Walks on the Cell Membrane to Drive Cell Motility. Angew Chem Int Ed Engl 2021; 60:26087-26095. [PMID: 34490693 DOI: 10.1002/anie.202108210] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/17/2021] [Indexed: 11/09/2022]
Abstract
Synthetic molecular robots can execute sophisticated molecular tasks at nanometer resolution. However, a molecular robot capable of controlling cellular behavior remains unexplored. Herein, we report a self-propelled DNA robot operating on the cell membrane to control the migration of a cell. Driven by DNAzyme catalytic activity, the DNA robot could autonomously and stepwise move on the membrane-floating cell-surface receptors in a stochastic manner and simultaneously trigger the receptor-dimerization to activate downstream signaling for cell motility. The cell membrane-associated continuous motion and operation of a DNA robot allowed for the ultrasensitive regulation of MET/AKT signaling and cytoskeleton remodeling to enhance cell migration. Finally, we designed distinct conditional DNA robots to orthogonally manipulate the cell migration in a coculture of mixed cell populations. We have developed a novel strategy to engineer a cell-driving molecular robot, representing a promising avenue for precise cell manipulation with nanoscale resolution.
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Affiliation(s)
- Hao Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China.,School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, P. R. China
| | - Jing Gao
- State Key Laboratory of Electroanalytical Chemistry, Research Center of Biomembranomics, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, Jilin, P. R. China
| | - Lei Cao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Xuan Xie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Jiahui Fan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Hongda Wang
- State Key Laboratory of Electroanalytical Chemistry, Research Center of Biomembranomics, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, Jilin, P. R. China
| | - Hong-Hui Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
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10
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Yu H, Alkhamis O, Canoura J, Liu Y, Xiao Y. Advances and Challenges in Small‐Molecule DNA Aptamer Isolation, Characterization, and Sensor Development. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202008663] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Haixiang Yu
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Obtin Alkhamis
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Juan Canoura
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Yingzhu Liu
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
| | - Yi Xiao
- Department of Chemistry and Biochemistry Florida International University 11200 SW 8th Street Miami FL 33199 USA
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11
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Yu H, Alkhamis O, Canoura J, Liu Y, Xiao Y. Advances and Challenges in Small-Molecule DNA Aptamer Isolation, Characterization, and Sensor Development. Angew Chem Int Ed Engl 2021; 60:16800-16823. [PMID: 33559947 PMCID: PMC8292151 DOI: 10.1002/anie.202008663] [Citation(s) in RCA: 156] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 11/16/2021] [Indexed: 12/12/2022]
Abstract
Aptamers are short oligonucleotides isolated in vitro from randomized libraries that can bind to specific molecules with high affinity, and offer a number of advantages relative to antibodies as biorecognition elements in biosensors. However, it remains difficult and labor-intensive to develop aptamer-based sensors for small-molecule detection. Here, we review the challenges and advances in the isolation and characterization of small-molecule-binding DNA aptamers and their use in sensors. First, we discuss in vitro methodologies for the isolation of aptamers, and provide guidance on selecting the appropriate strategy for generating aptamers with optimal binding properties for a given application. We next examine techniques for characterizing aptamer-target binding and structure. Afterwards, we discuss various small-molecule sensing platforms based on original or engineered aptamers, and their detection applications. Finally, we conclude with a general workflow to develop aptamer-based small-molecule sensors for real-world applications.
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Affiliation(s)
- Haixiang Yu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Obtin Alkhamis
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Juan Canoura
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Yingzhu Liu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
| | - Yi Xiao
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA
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12
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Li G, Wei Y, Ma L, Mao Y, Xun R, Deng Y. A novel highly sensitive soy aptasensor for antigen β-conglycinin determination. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:3059-3067. [PMID: 34137405 DOI: 10.1039/d1ay00701g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
β-Conglycinin, composed of three subunits (α', α and β), is the main allergen of soy protein which can cause severe allergic reactions, such as diarrhea, decreased growth performance and even death. Among them, the β subunit is more stable and difficult to remove, being one of the main nutritional inhibitors, which can be used to evaluate the concentration of β-conglycinin. However, there is no effective, accurate method for its β subunit rapid detection. Herein, we have successfully selected a high affinity β subunit aptamer (Kd = 6.9 nM) and developed a highly sensitive aptasensor. The aptasensor displayed high specificity and the β subunit at a concentration of 70-350 nM could be detected with a detection limit of 4.48 nM (3S/N). In addition, the recoveries of β subunit were more than 90%, demonstrating its practical properties for complicated conditions such as food quality control and disease diagnosis, without requiring expensive and sophisticated equipment.
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Affiliation(s)
- Guohui Li
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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13
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Chang T, He S, Amini R, Li Y. Functional Nucleic Acids Under Unusual Conditions. Chembiochem 2021; 22:2368-2383. [PMID: 33930229 DOI: 10.1002/cbic.202100087] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/24/2021] [Indexed: 02/06/2023]
Abstract
Functional nucleic acids (FNAs), including naturally occurring ribozymes and riboswitches as well as artificially created DNAzymes and aptamers, have been popular molecular toolboxes for diverse applications. Given the high chemical stability of nucleic acids and their ability to fold into diverse sequence-dependent structures, FNAs are suggested to be highly functional under unusual reaction conditions. This review will examine the progress of research on FNAs under conditions of low pH, high temperature, freezing conditions, and the inclusion of organic solvents and denaturants that are known to disrupt nucleic acid structures. The FNA species to be discussed include ribozymes, riboswitches, G-quadruplex-based peroxidase mimicking DNAzymes, RNA-cleaving DNAzymes, and aptamers. Research within this space has not only revealed the hidden talents of FNAs but has also laid important groundwork for pursuing these intriguing functional macromolecules for unique applications.
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Affiliation(s)
- Tianjun Chang
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
- Department of Biology, Institute of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, Henan, P. R. China
| | - Sisi He
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
- School of Science, Harbin Institute of Technology (Shenzhen), University Town, Shenzhen, 518055, Guangdong, P. R. China
| | - Ryan Amini
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
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14
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Luo Y, Jin Z, Wang J, Ding P, Pei R. The isolation of a DNA aptamer to develop a fluorescent aptasensor for the thiamethoxam pesticide. Analyst 2021; 146:1986-1995. [PMID: 33502393 DOI: 10.1039/d0an01967d] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Aptamers, which are called chemical antibodies for their high affinity and specificity to targets, have great potential as analytical tools to detect pesticides. In this work, a DNA aptamer for thiamethoxam was isolated by an improved SELEX (systematic evolution of ligands by exponential enrichment) strategy, in which the ssDNA library was fixed on streptavidin-agarose beads through a short biotin labeled complementary strand. After 13 rounds of selection, the random ssDNA pool was successfully enriched. Three sequences were chosen as aptamer candidates through sequencing and analysis and were transformed into fluorescent probes to evaluate their interactions with thiamethoxam. A fluorescent turn-on aptasensor for thiamethoxam based on the best aptamer (FAM-Thi13) and a short quenching strand were further designed and showed a quantitative linear range from 10 to 1000 nM with a detection limit of 1.23 nM for thiamethoxam. Molecular docking and molecular dynamics were used to investigate the binding site of the main probe of the aptasensor (FAM-Thi13) and thiamethoxam. Satisfactory results were also obtained in quantifying thiamethoxam in environmental water samples by the developed fluorescent aptasensor.
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Affiliation(s)
- Yu Luo
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China.
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15
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Li Y, Liu J. Highly Specific Recognition of Guanosine Using Engineered Base-Excised Aptamers. Chemistry 2020; 26:13644-13651. [PMID: 32700427 DOI: 10.1002/chem.202001835] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/20/2020] [Indexed: 12/18/2022]
Abstract
Purines and their derivatives are highly important molecules in biology for nucleic acid synthesis, energy storage, and signaling. Although many DNA aptamers have been obtained for binding adenine derivatives such as adenosine, adenosine monophosphate, and adenosine triphosphate, success for the specific binding of guanosine has been limited. Instead of performing new aptamer selections, we report herein a base-excision strategy to engineer existing aptamers to bind guanosine. Both a Na+ -binding aptamer and the classical adenosine aptamer have been manipulated as base-excising scaffolds. A total of seven guanosine aptamers were designed, of which the G16-deleted Na+ aptamer showed the highest bindng specificity and affinity for guanosine with an apparent dissociation constant of 0.78 mm. Single monophosphate difference in the target molecule was also recognizable. The generality of both the aptamer scaffold and excised site were systematically studied. Overall, this work provides a few guanosine binding aptamers by using a non-SELEX method. It also provides deeper insights into the engineering of aptamers for molecular recognition.
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Affiliation(s)
- Yuqing Li
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
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16
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Haghighi FH, Binaymotlagh R, Mirahmadi-Zare SZ, Hadadzadeh H. Aptamer/magnetic nanoparticles decorated with fluorescent gold nanoclusters for selective detection and collection of human promyelocytic leukemia (HL-60) cells from a mixture. NANOTECHNOLOGY 2020; 31:025605. [PMID: 31557732 DOI: 10.1088/1361-6528/ab484a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In the present work, a fluorescent gold nanoclusters (GNCs)/superparamagnetic (Fe3O4/GNCs) nanoprobe was prepared via a facile approach for the selective detection and imaging of human leukemica cancer cells (HL-60). (γ-Mercaptopropyl)trimethoxysilane (MPS) was used as a stabilizer to prepare functionalized GNCs. The prepared GNCs@MPS was then self-assembly decorated on the surface of Fe3O4@SiO2 nanoparticles followed by poly(ethylene glycol) dimethacrylate (PGD) addition at room temperature to form Fe3O4/GNCs nanoprobe. Surface functionalization of the Fe3O4/GNCs with the thiol-modified KH1C12 aptamer was done through thiol-en click reaction between PGD and the thiol group of the aptamer. An extensive characterization of the Fe3O4/GNCs revealed strong red fluorescence (λ em = 627 nm), T 2-based contrast agent for MRI and excellent colloidal and photo stability in buffer medium. So, the aptamer-functionalized Fe3O4/GNCs nanoprobe (Fe3O4/GNCs/Aptamer) is capable to uptake and dual-image HL-60 cancer cells from a mixture. Furthermore, the MRI signal intensity of the pictures decreased linearly with an increase in the concentrations of the nanoprobe. It is also enable to detect cancer cells from a range of concentrations 10 up to 200 cells μL-1. The fluorescent/magnetic characteristics of the nanoprobe are of great significance for MRI-based and fluorescence imaging and collection of HL-60 cancer cells which implies potential help for the development of early diagnosis of highly malignant human leukemia.
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Affiliation(s)
- Farid Hajareh Haghighi
- Department of Molecular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan 81651-31378, Iran. Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111, Iran
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17
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Development of a chemiluminescent aptasensor for ultrasensitive and selective detection of aflatoxin B1 in peanut and milk. Talanta 2019; 201:52-57. [PMID: 31122460 DOI: 10.1016/j.talanta.2019.03.109] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 03/29/2019] [Accepted: 03/30/2019] [Indexed: 12/14/2022]
Abstract
More and more attention about food safety leads to a research hotspot to develop new detection methods for food contaminant. To address the problems of serious interference and low sensitivity, a chemiluminescent aptasensor for the detection of aflatoxin B1(AFB1) in food was developed in this paper. It is based on horseradish peroxidase (HRP) catalyze the luminol chemiluminescence reaction. The hybridization chain reaction (HCR) signal amplification strategy has been used to improve the detection sensitivity. Magnetic separation could further reduce background signal obviously at the same time. AFB1 as a model of analyte to test the capability of our developed assay system. Under the optimal experimental conditions, CL intensity showed a good linear correlation with the concentrations of AFB1 ranging from 0.5 to 40 ng mL-1. The limit of detection was estimated 0.2 ng mL-1 based on 3 times of the signal-to-noise ratio which is lower than those of the previously reported sensors. It could be used to detect AFB1 content in real samples, such as peanuts and milk which were purchased in local supermarket. The results proved that the sensing system has good anti-interference and selectivity. In all, it has potential for practical application in food safety field.
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18
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Munzar JD, Ng A, Juncker D. Duplexed aptamers: history, design, theory, and application to biosensing. Chem Soc Rev 2019; 48:1390-1419. [PMID: 30707214 DOI: 10.1039/c8cs00880a] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nucleic acid aptamers are single stranded DNA or RNA sequences that specifically bind a cognate ligand. In addition to their widespread use as stand-alone affinity binding reagents in analytical chemistry, aptamers have been engineered into a variety of ligand-specific biosensors, termed aptasensors. One of the most common aptasensor formats is the duplexed aptamer (DA). As defined herein, DAs are aptasensors containing two nucleic acid elements coupled via Watson-Crick base pairing: (i) an aptamer sequence, which serves as a ligand-specific receptor, and (ii) an aptamer-complementary element (ACE), such as a short DNA oligonucleotide, which is designed to hybridize to the aptamer. The ACE competes with ligand binding, such that DAs generate a signal upon ligand-dependent ACE-aptamer dehybridization. DAs possess intrinsic advantages over other aptasensor designs. For example, DA biosensing designs generalize across DNA and RNA aptamers, DAs are compatible with many readout methods, and DAs are inherently tunable on the basis of nucleic acid hybridization. However, despite their utility and popularity, DAs have not been well defined in the literature, leading to confusion over the differences between DAs and other aptasensor formats. In this review, we introduce a framework for DAs based on ACEs, and use this framework to distinguish DAs from other aptasensor formats and to categorize cis- and trans-DA designs. We then explore the ligand binding dynamics and chemical properties that underpin DA systems, which fall under conformational selection and induced fit models, and which mirror classical SN1 and SN2 models of nucleophilic substitution reactions. We further review a variety of in vitro and in vivo applications of DAs in the chemical and biological sciences, including riboswitches and riboregulators. Finally, we present future directions of DAs as ligand-responsive nucleic acids. Owing to their tractability, versatility and ease of engineering, DA biosensors bear a great potential for the development of new applications and technologies in fields ranging from analytical chemistry and mechanistic modeling to medicine and synthetic biology.
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Affiliation(s)
- Jeffrey D Munzar
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
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19
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Qu H, Wang L, Liu J, Zheng L. Direct Screening for Cytometric Bead Assays for Adenosine Triphosphate. ACS Sens 2018; 3:2071-2078. [PMID: 30084633 DOI: 10.1021/acssensors.8b00224] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Cytometric bead assays have caught much attention because of their many exceptional advantages. Unfortunately, the immobilization of existing molecular recognition elements including monoclonal antibodies and aptamers onto solid particles may lead to the functional failure of the molecular recognition elements since they are generally obtained in free state. Herein we develop a powerful screening approach for direct and rapid discovery of aptamer based cytometric bead assays (AB-CBAs) by individually measuring the functional activity of every aptamer particles in a library and sorting them at rates of up to 108 particles per hour. The strategy is based on the transformation of molecular libraries into pools of monoclonal aptamer particles so that one individual particle displays ∼105 copies of an identical aptamer sequence. Our library design incorporates a two-color fluorescent reporter system in which changes in aptamer structure generate an optical readout, such that we can use fluorescence-activated cell sorting to rapidly and selectively separate the individual aptamer particles that exhibit large fluorescent signal change upon target binding. For demonstration, we isolated AB-CBA aptamer particles with high signaling performance for ATP after just 3 rounds of screening. We believe that the rapid and direct screening features of this strategy make it an excellent platform for generating AB-CBAs for for a wide range of important analytes.
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Affiliation(s)
- Hao Qu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Lu Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Jian Liu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Lei Zheng
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
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20
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Bayat P, Nosrati R, Alibolandi M, Rafatpanah H, Abnous K, Khedri M, Ramezani M. SELEX methods on the road to protein targeting with nucleic acid aptamers. Biochimie 2018; 154:132-155. [PMID: 30193856 DOI: 10.1016/j.biochi.2018.09.001] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 09/02/2018] [Indexed: 12/14/2022]
Abstract
Systematic evolution of ligand by exponential enrichment (SELEX) is an efficient method used to isolate high-affinity single stranded oligonucleotides from a large random sequence pool. These SELEX-derived oligonucleotides named aptamer, can be selected against a broad spectrum of target molecules including proteins, cells, microorganisms and chemical compounds. Like antibodies, aptamers have a great potential in interacting with and binding to their targets through structural recognition and are therefore called "chemical antibodies". However, aptamers offer advantages over antibodies including smaller size, better tissue penetration, higher thermal stability, lower immunogenicity, easier production, lower cost of synthesis and facilitated conjugation or modification with different functional moieties. Thus, aptamers represent an attractive substitution for protein antibodies in the fields of biomarker discovery, diagnosis, imaging and targeted therapy. Enormous interest in aptamer technology triggered the development of SELEX that has underwent numerous modifications since its introduction in 1990. This review will discuss the recent advances in SELEX methods and their advantages and limitations. Aptamer applications are also briefly outlined in this review.
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Affiliation(s)
- Payam Bayat
- Department of Immunology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Rahim Nosrati
- Cellular and Molecular Research Center, Faculty of Medicine, Guilan University of Medical Sciences, Rasht, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Houshang Rafatpanah
- Inflammation and Inflammatory Diseases Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mostafa Khedri
- Department of Immunology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
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21
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Li H, Wang M, Shi T, Yang S, Zhang J, Wang HH, Nie Z. A DNA-Mediated Chemically Induced Dimerization (D-CID) Nanodevice for Nongenetic Receptor Engineering To Control Cell Behavior. Angew Chem Int Ed Engl 2018; 57:10226-10230. [PMID: 29944203 DOI: 10.1002/anie.201806155] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Indexed: 12/31/2022]
Abstract
Small-molecule regulation is a powerful switching tool to manipulate cell signal transduction for a desired function; however, most available methods usually require genetic engineering to endow cells with responsiveness to user-defined small molecules. Herein, we demonstrate a nongenetic approach for small-molecule-controlled receptor activation and consequent cell behavior manipulation that is based on DNA-mediated chemically induced dimerization (D-CID). D-CID uses a programmable chemical-responsive DNA nanodevice to trigger DNA strand displacement and induce the activation of c-Met, a tyrosine kinase receptor cognate for hepatocyte growth factor, through dimerization. Through the use of various functional nucleic acids, including aptamers and DNAzymes, as recognition modules, the versatility of D-CID in inducing c-Met signaling upon addition of various small-molecular or ionic cues, including ATP, histidine, and Zn2+ , is demonstrated. Moreover, owing its multi-input properties, D-CID can be used to manipulate the behaviors of multiple cell populations simultaneously in a selective and programmable fashion.
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Affiliation(s)
- Hao Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Changsha, 410082, P. R. China
| | - Miao Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Changsha, 410082, P. R. China
| | - Tianhui Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Changsha, 410082, P. R. China
| | - Sihui Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Changsha, 410082, P. R. China
| | - Jinghui Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Changsha, 410082, P. R. China
| | - Hong-Hui Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Changsha, 410082, P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Changsha, 410082, P. R. China
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22
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Li H, Wang M, Shi T, Yang S, Zhang J, Wang HH, Nie Z. A DNA-Mediated Chemically Induced Dimerization (D-CID) Nanodevice for Nongenetic Receptor Engineering To Control Cell Behavior. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806155] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Hao Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 P. R. China
| | - Miao Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 P. R. China
| | - Tianhui Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 P. R. China
| | - Sihui Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 P. R. China
| | - Jinghui Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 P. R. China
| | - Hong-Hui Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; College of Biology; Hunan University; Changsha 410082 P. R. China
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23
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Wei B, Zhang J, Ou X, Lou X, Xia F, Vallée-Bélisle A. Engineering Biosensors with Dual Programmable Dynamic Ranges. Anal Chem 2018; 90:1506-1510. [PMID: 29300471 DOI: 10.1021/acs.analchem.7b04852] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Although extensively used in all fields of chemistry, molecular recognition still suffers from a significant limitation: host-guest binding displays a fixed, hyperbolic dose-response curve, which limits its usefulness in many applications. Here we take advantage of the high programmability of DNA chemistry and propose a universal strategy to engineer biorecognition-based sensors with dual programmable dynamic ranges. Using DNA aptamers as our model recognition element and electrochemistry as our readout signal, we first designed a dual signaling "signal-on" and "signal-off" adenosine triphosphate (ATP) sensor composed of a ferrocene-labeled ATP aptamer in complex to a complementary, electrode-bound, methylene-blue labeled DNA. Using this simple "dimeric" sensor, we show that we can easily (1) tune the dynamic range of this dual-signaling sensor through base mutations on the electrode-bound DNA, (2) extend the dynamic range of this sensor by 2 orders of magnitude by using a combination of electrode-bound strands with varying affinity for the aptamers, (3) create an ultrasensitive dual signaling sensor by employing a sequestration strategy in which a nonsignaling, high affinity "depletant" DNA aptamer is added to the sensor surface, and (4) engineer a sensor that simultaneously provides extended and ultrasensitive readouts. These strategies, applicable to a wide range of biosensors and chemical systems, should broaden the application of molecular recognition in various fields of chemistry.
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Affiliation(s)
- Benmei Wei
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan 430074, P. R. China
| | - Juntao Zhang
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan 430074, P. R. China
| | - Xiaowen Ou
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan 430074, P. R. China
| | - Xiaoding Lou
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan 430074, P. R. China
| | - Fan Xia
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan 430074, P. R. China
| | - Alexis Vallée-Bélisle
- Laboratory Biosensors & Nanomachines, Département de Chimie, Université de Montréal , Montréal, Québec H3T 1J4, Canada
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Rogers E, Heitsch C. New insights from cluster analysis methods for RNA secondary structure prediction. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:278-94. [PMID: 26971529 DOI: 10.1002/wrna.1334] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 12/03/2015] [Accepted: 12/17/2015] [Indexed: 01/12/2023]
Abstract
A widening gap exists between the best practices for RNA secondary structure prediction developed by computational researchers and the methods used in practice by experimentalists. Minimum free energy predictions, although broadly used, are outperformed by methods which sample from the Boltzmann distribution and data mine the results. In particular, moving beyond the single structure prediction paradigm yields substantial gains in accuracy. Furthermore, the largest improvements in accuracy and precision come from viewing secondary structures not at the base pair level but at lower granularity/higher abstraction. This suggests that random errors affecting precision and systematic ones affecting accuracy are both reduced by this 'fuzzier' view of secondary structures. Thus experimentalists who are willing to adopt a more rigorous, multilayered approach to secondary structure prediction by iterating through these levels of granularity will be much better able to capture fundamental aspects of RNA base pairing. WIREs RNA 2016, 7:278-294. doi: 10.1002/wrna.1334 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Emily Rogers
- School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0765, USA
| | - Christine Heitsch
- School of Mathematics, Georgia Institute of Technology, Atlanta, GA 30332-0160, USA
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25
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26
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Liu M, Zhang W, Zhang Q, Brennan JD, Li Y. Biosensing by Tandem Reactions of Structure Switching, Nucleolytic Digestion, and DNA Amplification of a DNA Assembly. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503182] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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27
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Liu M, Zhang W, Zhang Q, Brennan JD, Li Y. Biosensing by Tandem Reactions of Structure Switching, Nucleolytic Digestion, and DNA Amplification of a DNA Assembly. Angew Chem Int Ed Engl 2015; 54:9637-41. [PMID: 26119600 DOI: 10.1002/anie.201503182] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 05/28/2015] [Indexed: 12/20/2022]
Abstract
ϕ29 DNA polymerase (ϕ29DP) is able to carry out repetitive rounds of DNA synthesis using a circular DNA template by rolling circle amplification (RCA). It also has the ability to execute 3'-5' digestion of single-stranded but not double-stranded DNA. A biosensor engineering strategy is presented that takes advantage of these two properties of ϕ29DP coupled with structure-switching DNA aptamers. The design employs a DNA assembly made of a circular DNA template, a DNA aptamer, and a pre-primer. The DNA assembly is unable to undergo RCA in the absence of cognate target owing to the formation of duplex structures. The presence of the target, however, triggers a structure-switching event that causes nucleolytic conversion of the pre-primer by ϕ29DP into a mature primer to facilitate RCA. This method relays target detection by the aptamer to the production of massive DNA amplicons, giving rise to dramatically enhanced detection sensitivity.
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Affiliation(s)
- Meng Liu
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada)
| | - Wenqing Zhang
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada)
| | - Qiang Zhang
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada)
| | - John D Brennan
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada).
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada). .,Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada).
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28
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Wang F, Liu S, Lin M, Chen X, Lin S, Du X, Li H, Ye H, Qiu B, Lin Z, Guo L, Chen G. Colorimetric detection of microcystin-LR based on disassembly of orient-aggregated gold nanoparticle dimers. Biosens Bioelectron 2015; 68:475-480. [PMID: 25621999 DOI: 10.1016/j.bios.2015.01.037] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 01/10/2015] [Accepted: 01/16/2015] [Indexed: 12/22/2022]
Abstract
Recently we demonstrated oriented formation of gold nanoparticle (AuNP) dimers for ultrasensitive sensing oligonucleotides (J. Am. Chem. Soc. 2013, 135, 12338). Herein, we investigate the reverse process of this sensing mechanism using target analytes to disassemble the orient-aggregated AuNP dimers. This enables us to expand the analytes from oligonucleotides to other molecules, e.g. highly sensitive and selective determination of microcystin-LR (MC-LR) is selected for a demonstration in this work. Aptamers specific to the target molecules are used as linkers to prepare the AuNP dimers. In the presence of the target molecule, the aptamer changes its structure to bind the target molecule. Thus the pre-formed AuNP dimers are disassembled. As a result, the solution color is changed from blue to red. This sensing design retains the advantages of the previously developed sensors based on target molecules guided formation of AuNP dimers, e.g. the overwhelming sensitivity and stability comparing with those non-oriented sensors based on the formation of large aggregates, with the additional advantages as follows: 1) the target molecules are expanded from oligonucleotides to arbitrary molecules that can specifically bind to aptamers; 2) the color change is completed within 5 min, while the previous sensor based on the formation of AuNP dimers cost ~1 hour to obtain stable responses.
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Affiliation(s)
- Fangfang Wang
- Institute of Nanomedicine and Nanobiosensing, Ministry of Education Key Laboratory of Analysis and Detection Technology for Food Safety; College of Chemistry, Fuzhou University, Fuzhou 350116, China
| | - Shuzhen Liu
- Institute of Nanomedicine and Nanobiosensing, Ministry of Education Key Laboratory of Analysis and Detection Technology for Food Safety; College of Chemistry, Fuzhou University, Fuzhou 350116, China
| | - Mingxia Lin
- Institute of Nanomedicine and Nanobiosensing, Ministry of Education Key Laboratory of Analysis and Detection Technology for Food Safety; College of Chemistry, Fuzhou University, Fuzhou 350116, China
| | - Xing Chen
- Institute of Nanomedicine and Nanobiosensing, Ministry of Education Key Laboratory of Analysis and Detection Technology for Food Safety; College of Chemistry, Fuzhou University, Fuzhou 350116, China
| | - Shiru Lin
- Institute of Nanomedicine and Nanobiosensing, Ministry of Education Key Laboratory of Analysis and Detection Technology for Food Safety; College of Chemistry, Fuzhou University, Fuzhou 350116, China
| | - Xiazhen Du
- Institute of Nanomedicine and Nanobiosensing, Ministry of Education Key Laboratory of Analysis and Detection Technology for Food Safety; College of Chemistry, Fuzhou University, Fuzhou 350116, China
| | - He Li
- Institute of Nanomedicine and Nanobiosensing, Ministry of Education Key Laboratory of Analysis and Detection Technology for Food Safety; College of Chemistry, Fuzhou University, Fuzhou 350116, China
| | - Hongbin Ye
- Institute of Nanomedicine and Nanobiosensing, Ministry of Education Key Laboratory of Analysis and Detection Technology for Food Safety; College of Chemistry, Fuzhou University, Fuzhou 350116, China
| | - Bin Qiu
- Institute of Nanomedicine and Nanobiosensing, Ministry of Education Key Laboratory of Analysis and Detection Technology for Food Safety; College of Chemistry, Fuzhou University, Fuzhou 350116, China
| | - Zhenyu Lin
- Institute of Nanomedicine and Nanobiosensing, Ministry of Education Key Laboratory of Analysis and Detection Technology for Food Safety; College of Chemistry, Fuzhou University, Fuzhou 350116, China
| | - Longhua Guo
- Institute of Nanomedicine and Nanobiosensing, Ministry of Education Key Laboratory of Analysis and Detection Technology for Food Safety; College of Chemistry, Fuzhou University, Fuzhou 350116, China.
| | - Guonan Chen
- Institute of Nanomedicine and Nanobiosensing, Ministry of Education Key Laboratory of Analysis and Detection Technology for Food Safety; College of Chemistry, Fuzhou University, Fuzhou 350116, China
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29
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Xie L, Cheng H, Qi H, Wang T, Zhao H, Huang G, Du Y. Nanostructural morphology master-regulated the cell capture efficiency of multivalent aptamers. RSC Adv 2015. [DOI: 10.1039/c5ra01919b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The nanostructural features of stretched multivalent aptamers significantly improve the cell enrichment efficiency to about 16 fold higher than normal multivalent aptamers.
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Affiliation(s)
- Liping Xie
- College of Life and Health Science
- Northeastern University
- Shenyang 110819
- China
| | - Hao Cheng
- Department of Biomedical Engineering
- School of Medicine
- Tsinghua University
- Beijing 100084
- China
| | - Hao Qi
- Key Laboratory of Systems Bioengineering
- Ministry of Education (Tianjin University)
- Tianjin
- China
- School of Chemical Engineering and Technology
| | - Tongzhou Wang
- Department of Biomedical Engineering
- School of Medicine
- Tsinghua University
- Beijing 100084
- China
| | - Hui Zhao
- Department of Biomedical Engineering
- School of Medicine
- Tsinghua University
- Beijing 100084
- China
| | - Guoliang Huang
- Department of Biomedical Engineering
- School of Medicine
- Tsinghua University
- Beijing 100084
- China
| | - Yanan Du
- Department of Biomedical Engineering
- School of Medicine
- Tsinghua University
- Beijing 100084
- China
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30
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Wang Y, Tang L, Li Z, Lin Y, Li J. In situ simultaneous monitoring of ATP and GTP using a graphene oxide nanosheet-based sensing platform in living cells. Nat Protoc 2014; 9:1944-55. [PMID: 25058642 DOI: 10.1038/nprot.2014.126] [Citation(s) in RCA: 168] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Here we present a detailed protocol for in situ multiple fluorescence monitoring of adenosine-5'-triphosphate (ATP) and guanosine-5'-triphosphate (GTP) in MCF-7 breast cancer cells by using graphene oxide nanosheet (GO-nS) and DNA/RNA aptamers. FAM-labeled ATP aptamer and Cy5-modified GTP aptamer are used to construct the multiple aptamer/GO-nS sensing platform through 'π-π stacking' between aptamers and GO-nS. Binding of aptamers to GO-nS guarantees the fluorescence resonance energy transfer between fluorophores and GO-nS, resulting in 'fluorescence off'. When the aptamer/GO-nS are transported inside the cells via endocytosis, the conformation of the aptamers will change on interaction with cellular ATP and GTP. On the basis of the fluorescence 'off/on' switching, simultaneous sensing and imaging of ATP and GTP in vitro and in situ have been realized through fluorescence and confocal microscopy techniques. In this protocol, we describe the synthesis of GO and GO-nS, preparation of aptamer/GO-nS platform, in vitro detection of ATP and GTP, and how to use this platform to realize intracellular ATP and GTP imaging in cultured MCF-7 cells. The preparation of GO-nS is anticipated to take 7-14 d, and assays involving microscopy imaging and MCF-7 cells culturing can be performed in 2-3 d.
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Affiliation(s)
- Ying Wang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing, China
| | - Longhua Tang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing, China
| | - Zhaohui Li
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Yuehe Lin
- 1] Pacific Northwest National Laboratory, Richland, Washington, USA. [2] School of Mechanical and Materials Engineering, Washington State University, Pullman, Washington, USA
| | - Jinghong Li
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing, China
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31
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Yang X, Wang Y, Wang K, Wang Q, Wang P, Lin M, Chen N, Tan Y. DNA aptamer-based surface plasmon resonance sensing of human C-reactive protein. RSC Adv 2014. [DOI: 10.1039/c4ra05011h] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
DNA aptamers for CRP were selected and investigated using SPR technology, which will be of benefit for constructing CRP sensors.
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Affiliation(s)
- Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
- Changsha 410082, China
| | - Yaning Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
- Changsha 410082, China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
- Changsha 410082, China
| | - Qing Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
- Changsha 410082, China
| | - Pei Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
- Changsha 410082, China
| | - Min Lin
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
- Changsha 410082, China
| | - Nandi Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
- Changsha 410082, China
| | - Yuyu Tan
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
- Changsha 410082, China
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32
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Zhang C, Wang L, Tu Z, Sun X, He Q, Lei Z, Xu C, Liu Y, Zhang X, Yang J, Liu X, Xu Y. Organophosphorus pesticides detection using broad-specific single-stranded DNA based fluorescence polarization aptamer assay. Biosens Bioelectron 2013; 55:216-9. [PMID: 24384262 DOI: 10.1016/j.bios.2013.12.020] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 11/13/2013] [Accepted: 12/06/2013] [Indexed: 10/25/2022]
Abstract
An approach is developed to detect the organophosphorus pesticides via competitive binding to a recombinant broad-specificity DNA aptamer with a molecular beacon (MB), the binding of the MB to the aptamer results in the activation of a fluorescent signal, which can be measured for pesticide quantification. Aptamers selected via the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) were structurally modified and truncated to narrow down the binding region of the target, which indicated that loops of the aptamer contributed different functions for different chemical recognition. Thereafter, a variant fused by two different minimum functional structures, was clarified with broad specificity and increased affinity. Further molecular docking and molecular dynamics simulations was conducted to understand the molecular interaction between DNA structure and chemicals. 3D modeling revealed a hot spot area formed by 3 binding sites, forces including hydrogen bonds and van der Waals interactions appear to play a significant role in enabling and stabilizing the binding of chemicals. Finally, an engineered aptamer based approach for the detection of organophosphorus pesticides was successfully applied in a test using a real sample, the limit of quantification (LOQ) for phorate, profenofos, isocarbophos, and omethoate reached 19.2, 13.4, 17.2, and 23.4 nM (0.005 mg L(-1)), respectively.
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Affiliation(s)
- Cunzheng Zhang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanjing East Road 235, Nanchang 330047, China; Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture, Institute of Food Safety, Jiangsu Academy of Agricultural Sciences, Zhongling Street 50, Nanjing 210014, China
| | - Li Wang
- Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture, Institute of Food Safety, Jiangsu Academy of Agricultural Sciences, Zhongling Street 50, Nanjing 210014, China
| | - Zhui Tu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanjing East Road 235, Nanchang 330047, China
| | - Xing Sun
- Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture, Institute of Food Safety, Jiangsu Academy of Agricultural Sciences, Zhongling Street 50, Nanjing 210014, China
| | - Qinghua He
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanjing East Road 235, Nanchang 330047, China
| | - Zhaojing Lei
- Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture, Institute of Food Safety, Jiangsu Academy of Agricultural Sciences, Zhongling Street 50, Nanjing 210014, China
| | - Chongxin Xu
- Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture, Institute of Food Safety, Jiangsu Academy of Agricultural Sciences, Zhongling Street 50, Nanjing 210014, China
| | - Yuan Liu
- Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture, Institute of Food Safety, Jiangsu Academy of Agricultural Sciences, Zhongling Street 50, Nanjing 210014, China
| | - Xiao Zhang
- Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture, Institute of Food Safety, Jiangsu Academy of Agricultural Sciences, Zhongling Street 50, Nanjing 210014, China
| | - Jingyi Yang
- Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture, Institute of Food Safety, Jiangsu Academy of Agricultural Sciences, Zhongling Street 50, Nanjing 210014, China
| | - Xianjin Liu
- Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture, Institute of Food Safety, Jiangsu Academy of Agricultural Sciences, Zhongling Street 50, Nanjing 210014, China.
| | - Yang Xu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanjing East Road 235, Nanchang 330047, China.
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33
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Xie L, Yan X, Du Y. An aptamer based wall-less LSPR array chip for label-free and high throughput detection of biomolecules. Biosens Bioelectron 2013; 53:58-64. [PMID: 24121209 DOI: 10.1016/j.bios.2013.09.031] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 09/12/2013] [Accepted: 09/12/2013] [Indexed: 12/14/2022]
Abstract
Despite recent progress in localized surface plasmon resonance (LSPR) based bio-sensing, it remains challenging to achieve sensitive and high throughput LSPR detection with facilities available in common laboratories. Here we developed a wall-less LSPR array chip for facile, label-free and high throughput detection of biomolecules using a normal microplate reader. The wall-less LSPR array chip was fabricated by immobilizing plasmonic nanoparticles (NPs) on a hydrophilic-hydrophobic patterned glass slide, enabling high throughput detection. The wall-less configuration simplifies chip fabrication and sample processing, and enables miniaturization to significantly reduce sample and reagent consumption. A double-gold NPs enhanced system comprising of 13-nm-gold NPs conjugated to aptamer modified 39-nm-gold NPs on glass substrate was adopted to constitute competitive replacement assay for signal amplification in small molecule (i.e. ATP) detection. Upon enhancement, the detection sensitivity of ATP was augmented by 5 orders of magnitude from 0.01 µM to 100 µM measured by the laboratory microplate reader. The wall-less LSPR sensor chip can be widely applied for miniaturized and high throughput detection of a variety of targets in biomedical applications and environmental monitoring using facilities available in common laboratories.
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Affiliation(s)
- Liping Xie
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
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34
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Lau PS, Lai CK, Li Y. Quality control certification of RNA aptamer-based detection. Chembiochem 2013; 14:987-92. [PMID: 23592300 DOI: 10.1002/cbic.201300134] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Indexed: 12/19/2022]
Abstract
Aptamers are single-stranded DNA or RNA molecules with a defined tertiary structure for molecular recognition. Numerous RNA aptamers with excellent binding affinity and specificity have been reported; they constitute an attractive reservoir of molecular recognition elements for biosensor development. However, RNA is relatively unstable owing to spontaneous hydrolysis and nuclease degradation. Thus, RNA aptamer-based biosensors are prone to producing false-positive signals. Here, we present an RNA aptamer biosensor design strategy that utilises an internal control to distinguish target binding from false-positive signals. The sequence of a chosen RNA aptamer is expanded so that it can form three consecutive short RNA-DNA duplexes with 1) a quencher-labelled DNA strand (Q(1)DNA), 2) a dual-fluorophore-labelled DNA strand (F(1)DNAF(2)) and 3) another quencher-labelled DNA strand (Q(2)DNA). The addition of a target releases Q(2)DNA from the duplex assembly, and produces the expected positive signal from F(2). However, the authenticity of target recognition is validated only if no signal is generated from F(1). We have successfully engineered two fluorescent reporters by using an RNA aptamer that binds thrombin and one that binds theophylline. Both reporters show the expected binding affinity and specificity, and are capable of reporting system malfunction when treated with nucleases and chemical denaturants. This strategy provides a simple and reliable way to ensure high-quality detection when RNA aptamers are employed as molecular-recognition elements.
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Affiliation(s)
- Pui Sai Lau
- Department of Biochemistry and Biomedical Sciences, Department of Chemistry and Chemical Biology, and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4K1, Canada
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35
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Lv S, Guan Y, Wang D, Du Y. Aptamer based strategy for cytosensing and evaluation of HER-3 on the surface of MCF-7 cells by using the signal amplification of nucleic acid-functionalized nanocrystals. Anal Chim Acta 2013; 772:26-32. [PMID: 23540244 DOI: 10.1016/j.aca.2013.02.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Revised: 02/05/2013] [Accepted: 02/11/2013] [Indexed: 10/27/2022]
Abstract
The electrochemical detection of cell lines of MCF-7 (human breast cancer) has been reported, using magnetic beads for the separation tool and high-affinity DNA aptamers for signal recognition. The high specificity was obtained by using the magnetic beads and aptamers, and the good sensitivity was realized with the signal amplification of DNA capped CdS or PbS nanocrystals. The ASV (anodic stripping voltammetry) technology was employed for the detection of cadmic cation and lead ions, for electrochemical assay of the amount of the target cells and biomarkers on the membrane of target cells, respectively. This electrochemical method could respond to as low as 100 cells mL(-1) of cancer cells with a linear calibration range from 1.0×10(2) to 1.0×10(6) cells mL(-1), showing very high sensitivity. Moreover, the amounts of HER-3 which were overexpressed on MCF-7 cells were calculated correspond to be 3.56×10(4) anti-HER-3 antibody molecules. In addition, the assay was able to differentiate between different types of target and control cells based on the aptamers and magnetic beads used in the assay, indicating the wide applicability of the assay for early and accurate diagnose of cancers.
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Affiliation(s)
- Shaoping Lv
- Departmen of Neurology, Provinvial Hospital affiliated Shandong University, Jinan, Shandong, PR China
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36
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Wu J, Coradin T, Aimé C. Reversible bioresponsive aptamer-based nanocomposites: ATP binding and removal from DNA-grafted silica nanoparticles. J Mater Chem B 2013; 1:5353-5359. [DOI: 10.1039/c3tb20499e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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37
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Wang L, Liu X, Zhang Q, Zhang C, Liu Y, Tu K, Tu J. Selection of DNA aptamers that bind to four organophosphorus pesticides. Biotechnol Lett 2012; 34:869-74. [PMID: 22261866 DOI: 10.1007/s10529-012-0850-6] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Accepted: 01/05/2012] [Indexed: 11/25/2022]
Abstract
Single-stranded DNA (ssDNA) aptamers against four organophosphorus pesticides (phorate, profenofos, isocarbophos and omethoate) were simultaneously isolated from an immobilized random ssDNA library by systematic evolution of ligands by exponential enrichment (SELEX) technique. After 12 rounds of in vitro selection, five ssDNA aptamer candidates were selected and their binding affinities were identified by a novel method using a molecular beacon. Two of the five ssDNA sequences, SS2-55 and SS4-54, demonstrated higher affinities and specificities to the four organophosphorus pesticides. They were defined as broad-spectrum aptamers binding to four different targets and their simulated secondary structures showed highly distinct features with typical stem and loop structures. The dissociation constant of SS2-55 and SS4-54 binding to the four organophosphorus pesticides ranged from 0.8 to 2.5 μM. These aptamers offered application potential in the analysis and/or neutralization of the residues of the four organophosphorus pesticides.
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Affiliation(s)
- Li Wang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
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38
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Zhang K, Sefah K, Tang L, Zhao Z, Zhu G, Ye M, Sun W, Goodison S, Tan W. A novel aptamer developed for breast cancer cell internalization. ChemMedChem 2011; 7:79-84. [PMID: 22170627 DOI: 10.1002/cmdc.201100457] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 10/31/2011] [Indexed: 11/11/2022]
Abstract
Breast cancer affects one in eight women in the United States, with a mortality rate that is second only to lung cancer. Although chemotherapy is widely used in breast cancer treatment, its side effects remain a challenge. One way to address this problem is through drug delivery by the internalization of cell-type-specific probes. Although nucleic acid aptamers are excellent probes for molecular recognition, only a few studies have demonstrated that aptamers can be internalized into living cells. Therefore, herein we report the development of a cancer-cell-specific DNA aptamer probe, KMF2-1a. By using the cell-SELEX method, this aptamer was selected against breast cancer cell line MCF-10AT1. Our results show that KMF2-1a is internalized efficiently and specifically to the endosome of target breast cancer cells. These results indicate that KMF2-1a is a promising agent for cell-type-specific intracellular delivery with both diagnostic and therapeutic implications.
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Affiliation(s)
- Kejing Zhang
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
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39
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Zhong H, Zhang Q, Zhang S. High-Intensity Fluorescence Imaging and Sensitive Electrochemical Detection of Cancer Cells by using an Extracellular Supramolecular Reticular DNA-Quantum Dot Sheath. Chemistry 2011; 17:8388-94. [DOI: 10.1002/chem.201003585] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 04/11/2011] [Indexed: 01/04/2023]
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40
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Xing C, Zheng Z, Zhang B, Tang J. Nanoscale Patterning of Multicomponent Proteins by Bias‐Assisted Atomic Force Microscopy Nanolithography. Chemphyschem 2011; 12:1262-5. [DOI: 10.1002/cphc.201100026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Indexed: 11/07/2022]
Affiliation(s)
- Chunyan Xing
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun 130022 (China), Fax: (+86) 4318‐5262‐430
- Graduate School of Chinese Academy of Sciences, Beijing 100049 (China)
| | - Zhikun Zheng
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun 130022 (China), Fax: (+86) 4318‐5262‐430
| | - Bailin Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun 130022 (China), Fax: (+86) 4318‐5262‐430
| | - Jilin Tang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun 130022 (China), Fax: (+86) 4318‐5262‐430
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41
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He J, Liu Y, Fan M, Liu X. Isolation and identification of the DNA aptamer target to acetamiprid. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2011; 59:1582-1586. [PMID: 21306108 DOI: 10.1021/jf104189g] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
As an alternative to antibodies, aptamers have a great potential as analytical tools for pesticide detection. In this work, aptamers targeting acetamiprid were selected by a specific systematic evolution of ligands by exponential enrichment (SELEX) strategy, where a single-stranded DNA (ssDNA) library was immobilized and target modification was eliminated. After 18 rounds of repeated selection, the ssDNA pool was enriched and then 14 sequences were selected and carefully identified. At last, an acetamiprid-specific aptamer with the apparent dissociation constant (K(d)) estimated to be 4.98 μM was successfully obtained. Further work is ongoing to develop an aptamer-based detection method for field determination of this pesticides in agricultural products and environmental samples.
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Affiliation(s)
- Jiang He
- College of Food Science and Engineering, Northwest A&F University , Yangling, Shaanxi 712100, People's Republic of China
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42
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Ma DL, Chan DSH, Man BYW, Leung CH. Oligonucleotide-based luminescent detection of metal ions. Chem Asian J 2011; 6:986-1003. [PMID: 21337527 DOI: 10.1002/asia.201000870] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Indexed: 01/20/2023]
Abstract
Metal ions are prevalent in biological systems and are critically involved in essential life processes. However, excess concentrations of metals can pose a serious danger to living organisms. Oligonucleotides represent a versatile sensing platform for the detection of various molecular entities including metal ions. This review summarizes the recent advances in the development of oligonucleotide-based luminescent detection methods for metal ions.
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Affiliation(s)
- Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, China.
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43
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Lau PS, Coombes BK, Li Y. A general approach to the construction of structure-switching reporters from RNA aptamers. Angew Chem Int Ed Engl 2011; 49:7938-42. [PMID: 20845339 DOI: 10.1002/anie.201002621] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Pui Sai Lau
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main St. W., Hamilton, ON L8N 3Z5, Canada
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44
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Hu J, Wu J, Li C, Zhu L, Zhang WY, Kong G, Lu Z, Yang CJ. A G-quadruplex aptamer inhibits the phosphatase activity of oncogenic protein Shp2 in vitro. Chembiochem 2011; 12:424-30. [PMID: 21290544 DOI: 10.1002/cbic.201000470] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Indexed: 11/07/2022]
Abstract
Shp2 is a member of the protein tyrosine phosphatase (PTP) family, which regulates a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. Using a recombinant Shp2-GST protein as the target and GST as a counter target, we have identified two classes of single-stranded DNA aptamers that selectively bind to Shp2 with a K(d) in the nanomolar range. Structural studies of the most abundant sequence in the enriched library, HJ24, revealed a parallel G-quadruplex as the core binding domain. Furthermore, this aptamer was found to be an effective inhibitor of Shp2 phosphatase, an effect which was readily reversed by using the cDNA of HJ24. In view of these characteristics, this aptamer has the potential to be used for further development of Shp2 assays and therapeutics for the treatment of Shp2-dependent cancers and other diseases.
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Affiliation(s)
- Jia Hu
- State Key Laboratory for Physical Chemistry of Solid Surfaces, The Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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45
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Lau PS, Coombes BK, Li Y. A General Approach to the Construction of Structure-Switching Reporters from RNA Aptamers. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201002621] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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46
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Chen Y, Munteanu AC, Huang YF, Phillips J, Zhu Z, Mavros M, Tan W. Mapping receptor density on live cells by using fluorescence correlation spectroscopy. Chemistry 2009; 15:5327-36. [PMID: 19360825 DOI: 10.1002/chem.200802305] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Study of the density, spatial distribution, and molecular interactions of receptors on the cell membrane provides the knowledge required to understand cellular behavior and biological functions, as well as to discover, design, and screen novel therapeutic agents. However, the mapping of receptor distribution and the monitoring of ligand-receptor interactions on live cells in a spatially and temporally ordered manner are challenging tasks. In this paper, we apply fluorescence correlation spectroscopy (FCS) to map receptor densities on live cell membranes by introducing fluorescently marked aptamer molecules, which specifically bind to certain cell-surface receptors. The femtoliter-sized (0.4 fL) observation volume created by FCS allows fluorescent-aptamer detection down to 2 molecules and appears to be an ideal and highly sensitive biophysical tool for studying molecular interactions on live cells. Fluorophore-labeled aptamers were chosen for receptor recognition because of their high binding affinity and specificity. Aptamer sgc8, generated for specific cell recognition by a process called cell systematic evolution of ligands by exponential enrichment, was determined by FCS to have a binding affinity in the picomolar range (dissociation constant K(d)=790+/-150 pM) with its target membrane receptor, human protein tyrosine kinase-7 (PTK7), a potential cancer biomarker. We then constructed a cellular model and applied this aptamer-receptor interaction to estimate receptor densities and distributions on the cell surface. Specifically, different expression levels of PTK7 were studied by using human leukemia CCRF-CEM cells (1300+/-190 receptors microm(-2)) and HeLa cervical cancer cells (550+/-90 receptors microm(-2)). Competition studies with excess nonlabeled aptamers and proteinase treatment studies proved the validity of the density-estimation approach. With its intrinsic advantages of direct measurement, high sensitivity, fast analysis, and single-cell measurement, this FCS density-estimation approach holds potential for future applications in molecular-interaction studies and density estimations for subcellular structures and membrane receptors.
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Affiliation(s)
- Yan Chen
- Department of Chemistry, Shands Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL 32611, USA
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Ali MM, Li Y. Colorimetric sensing by using allosteric-DNAzyme-coupled rolling circle amplification and a peptide nucleic acid-organic dye probe. Angew Chem Int Ed Engl 2009; 48:3512-5. [PMID: 19360817 DOI: 10.1002/anie.200805966] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Target detection by the naked eye: The action of an RNA-cleaving allosteric DNAzyme in response to ligand binding was coupled to a rolling circle amplification process to generate long single-stranded DNA molecules for colorimetric sensing (see scheme). Upon hybridization of the resulting DNA with a complementary PNA sequence in the presence of a duplex-binding dye, the color of the dye changed from blue to purple.
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Affiliation(s)
- M Monsur Ali
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, ON L8N 3Z5, Canada
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Ali M, Li Y. Colorimetric Sensing by Using Allosteric-DNAzyme-Coupled Rolling Circle Amplification and a Peptide Nucleic Acid-Organic Dye Probe. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200805966] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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49
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Raddatz MSL, Dolf A, Endl E, Knolle P, Famulok M, Mayer G. Enrichment of cell-targeting and population-specific aptamers by fluorescence-activated cell sorting. Angew Chem Int Ed Engl 2008; 47:5190-3. [PMID: 18512861 DOI: 10.1002/anie.200800216] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Marie-Sophie L Raddatz
- Life and Medical Science, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
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Raddatz M, Dolf A, Endl E, Knolle P, Famulok M, Mayer G. Enrichment of Cell‐Targeting and Population‐Specific Aptamers by Fluorescence‐Activated Cell Sorting. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200800216] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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