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Lu H, Zhang H, Li L. Chemical tagging mass spectrometry: an approach for single-cell omics. Anal Bioanal Chem 2023; 415:6901-6913. [PMID: 37466681 PMCID: PMC10729908 DOI: 10.1007/s00216-023-04850-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023]
Abstract
Single-cell (SC) analysis offers new insights into the study of fundamental biological phenomena and cellular heterogeneity. The superior sensitivity, high throughput, and rich chemical information provided by mass spectrometry (MS) allow MS to emerge as a leading technology for molecular profiling of SC omics, including the SC metabolome, lipidome, and proteome. However, issues such as ionization suppression, low concentration, and huge span of dynamic concentrations of SC components lead to poor MS response for certain types of molecules. It is noted that chemical tagging/derivatization has been adopted in SCMS analysis, and this strategy has been proven an effective solution to circumvent these issues in SCMS analysis. Herein, we review the basic principle and general strategies of chemical tagging/derivatization in SCMS analysis, along with recent applications of chemical derivatization to single-cell metabolomics and multiplexed proteomics, as well as SCMS imaging. Furthermore, the challenges and opportunities for the improvement of chemical derivatization strategies in SCMS analysis are discussed.
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Affiliation(s)
- Haiyan Lu
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Hua Zhang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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2
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Wang Y, Zhang Y, Li PC, Guo J, Huo F, Yang J, Jia R, Wang J, Huang Q, Theodorescu D, Yu H, Yan C. Development of novel aptamer-based targeted chemotherapy for bladder cancer. Cancer Res 2022; 82:1128-1139. [DOI: 10.1158/0008-5472.can-21-2691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/08/2021] [Accepted: 01/18/2022] [Indexed: 12/24/2022]
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3
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Wang Y, Liu X, Wu L, Ding L, Effah CY, Wu Y, Xiong Y, He L. Construction and bioapplications of aptamer-based dual recognition strategy. Biosens Bioelectron 2022; 195:113661. [PMID: 34592501 DOI: 10.1016/j.bios.2021.113661] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 02/08/2023]
Abstract
Aptamer-based dual recognition strategy, using dual aptamers or the cooperation of aptamers with other recognition elements, can better utilize the advantages of each recognition molecule and increase the design flexibility to effectively overcome the limitations of a single molecule recognition strategy, thereby improving the sensitivity and selectivity and facilitating the regulation of biological process. Hence, this review systematically tracks the construction and application of dual aptamers recognition strategy in the versatile detection of protein biomarkers, pathogenic microorganisms, cancer cells, and the treatment of some diseases and, more importantly, in functional regulation and imaging of cell-surface protein receptors. Then, the cooperation of aptamers with other recognition elements are briefly introduced. Potential challenges facing this field have been highlighted, aiming to expand bioanalytical applications of aptamer-based dual or multiple recognition strategies and meet the growing demand for precision medicine.
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Affiliation(s)
- Ya Wang
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Xinlian Liu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Longjie Wu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Lihua Ding
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Clement Yaw Effah
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Yongjun Wu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Yamin Xiong
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| | - Leiliang He
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China.
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4
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5
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Czechowska K, Lannigan J, Wang L, Arcidiacono J, Ashhurst TM, Barnard RM, Bauer S, Bispo C, Bonilla DL, Brinkman RR, Cabanski M, Chang HD, Chakrabarti L, Chojnowski G, Cotleur B, Degheidy H, Dela Cruz GV, Eck S, Elliott J, Errington R, Filby A, Gagnon D, Gardner R, Green C, Gregory M, Groves CJ, Hall C, Hammes F, Hedrick M, Hoffman R, Icha J, Ivaska J, Jenner DC, Jones D, Kerckhof FM, Kukat C, Lanham D, Leavesley S, Lee M, Lin-Gibson S, Litwin V, Liu Y, Molloy J, Moore JS, Müller S, Nedbal J, Niesner R, Nitta N, Ohlsson-Wilhelm B, Paul NE, Perfetto S, Portat Z, Props R, Radtke S, Rayanki R, Rieger A, Rogers S, Rubbens P, Salomon R, Schiemann M, Sharpe J, Sonder SU, Stewart JJ, Sun Y, Ulrich H, Van Isterdael G, Vitaliti A, van Vreden C, Weber M, Zimmermann J, Vacca G, Wallace P, Tárnok A. Cyt-Geist: Current and Future Challenges in Cytometry: Reports of the CYTO 2018 Conference Workshops. Cytometry A 2020; 95:598-644. [PMID: 31207046 DOI: 10.1002/cyto.a.23777] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | - Joanne Lannigan
- Flow Cytometry Core, University of Virginia, School of Medicine, 1300 Jefferson Park Ave., Charlottesville, Virginia
| | - Lili Wang
- Biosystems and Biomaterials Division, National Institute of Standards and Technology (NIST), 100 Bureau Drive, Stop 8312, Gaithersburg, Maryland
| | - Judith Arcidiacono
- Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland
| | - Thomas M Ashhurst
- Sydney Cytometry Facility, Discipline of Pathology, and Ramaciotti Facility for Human Systems Biology; Charles Perkins Centre, The University of Sydney and Centenary Institute, New South Wales, Australia
| | - Ruth M Barnard
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts SG1 2NY, UK
| | - Steven Bauer
- Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland
| | - Cláudia Bispo
- UCSF Parnassus Flow Cytometry Core Facility, 513 Parnassus Ave, San Francisco, California
| | - Diana L Bonilla
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ryan R Brinkman
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Terry Fox Laboratory, BC Cancer, Vancouver, Canada
| | - Maciej Cabanski
- Novartis Pharma AG, Fabrikstrasse 10-4.27.02, CH-4056, Basel, Switzerland
| | - Hyun-Dong Chang
- Schwiete-Laboratory Microbiota and Inflammation, German Rheumatism Research Centre Berlin (DRFZ), a Leibniz Institute, Berlin, Germany
| | - Lina Chakrabarti
- Research and Development, MedImmune, an AstraZeneca Company, One Medimmune Way, Gaithersburg, Maryland
| | - Grace Chojnowski
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Queensland 4006, Australia
| | | | - Heba Degheidy
- Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland
| | - Gelo V Dela Cruz
- Flow Cytometry Platform, Novo Nordisk Center for Stem Cell Biology - Danstem, University of Copenhagen, 3B Blegdamsvej, DK-2200, Copenhagen, Denmark
| | - Steven Eck
- Research and Development, MedImmune, an AstraZeneca Company, One Medimmune Way, Gaithersburg, Maryland
| | - John Elliott
- Biosystems and Biomaterials Division, National Institute of Standards and Technology (NIST), 100 Bureau Drive, Stop 8312, Gaithersburg, Maryland
| | | | - Andy Filby
- Newcastle University, Flow Cytometry Core Facility, Newcastle upon Tyne, Tyne and Wear NE1 7RU, UK
| | | | - Rui Gardner
- Memorial Sloan Kettering Cancer Center, Flow Cytometry Core, New York, New York
| | | | - Michael Gregory
- Division of Advanced Research Technologies, New York University Langone Health, New York, New York
| | - Christopher J Groves
- Research and Development, MedImmune, an AstraZeneca Company, One Medimmune Way, Gaithersburg, Maryland
| | | | - Frederik Hammes
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | | | | | - Jaroslav Icha
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Johanna Ivaska
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.,Department of Biochemistry, University of Turku, Turku, Finland
| | - Dominic C Jenner
- Defence Science and Technology Laboratory, Chemical Biological and Radiological Division, Porton Down, Salisbury, Wiltshire SP4 0JQ, UK
| | | | - Frederiek-Maarten Kerckhof
- Center for Microbial Ecology and Technology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Christian Kukat
- FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931, Köln, Germany
| | | | | | - Michael Lee
- The University California San Francisco, 505 Parnassus Ave, San Francisco, California
| | - Sheng Lin-Gibson
- Biosystems and Biomaterials Division, National Institute of Standards and Technology (NIST), 100 Bureau Drive, Stop 8312, Gaithersburg, Maryland
| | - Virginia Litwin
- Memorial Sloan Kettering Cancer Center, Flow Cytometry Core, New York, New York
| | | | - Jenny Molloy
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | | | - Susann Müller
- Working Group Flow Cytometry, Department of Environmental Microbiology, Helmholtz Center for Environmental Research (UFZ), Leipzig, Germany
| | - Jakub Nedbal
- Marylou Ingram ISAC Scholar, King's College London, UK
| | - Raluca Niesner
- Marylou Ingram ISAC Scholar, German Rheumatism Research Centre, Berlin, Germany
| | - Nao Nitta
- Department of Chemistry, The University of Tokyo
| | - Betsy Ohlsson-Wilhelm
- SciGro, North Central Office, Foster Plaza 5, Suite 300/PMB 20, 651 Holiday Drive, Pittsburgh, Pennsylvania
| | - Nicole E Paul
- LMA CyTOF Core, Dana-Faber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts
| | - Stephen Perfetto
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institute of Health (NIH), 40 Convent Drive, Bethesda, Maryland
| | - Ziv Portat
- Weizmann Institute of Science, Life Sciences Core Facilities, Flow Cytometry Unit, Rehovot, 7610001, Israel
| | - Ruben Props
- Center for Microbial Ecology and Technology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Stefan Radtke
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, Washington
| | - Radhika Rayanki
- Research and Development, MedImmune, an AstraZeneca Company, One Medimmune Way, Gaithersburg, Maryland
| | - Aja Rieger
- Faculty of Medicine and Dentistry Flow Cytometry Facility, Department of Medical Microbiology & Immunology, University of Alberta, 6-020C Katz Group Centre for Pharmacy and Health Research, Canada
| | - Samson Rogers
- TTP plc, Melbourn Science Park, Melbourn, Hertfordshire SG8 6EE, UK
| | - Peter Rubbens
- KERMIT, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Robert Salomon
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, New South Wales, Australia
| | - Matthias Schiemann
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Munich, Germany
| | - John Sharpe
- Cytonome/ST LLC, 9 Oak Park Drive, Bedford, Massachusetts
| | | | - Jennifer J Stewart
- Flow Contract Site Laboratory, LLC 18323, Bothell, Everett Highway, Suite 110, Bothell, Washington
| | | | - Henning Ulrich
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Gert Van Isterdael
- VIB Flow Core, VIB Center for Inflammation Research, Technologiepark-Zwijnaarde 71, B-9052, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | | | - Caryn van Vreden
- Sydney Cytometry Facility and Ramaciotti Facility for Human Systems Biology, The University of Sydney and Centenary Institute, Camperdown, New South Wales 2050, Australia
| | - Michael Weber
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts
| | - Jacob Zimmermann
- Mucosal Immunology and Host-Microbial Mutualism laboratories, Department for BioMedical Research, University of Bern, Bern, Switzerland
| | | | - Paul Wallace
- Roswell Park Comprehensive Cancer Center, New York
| | - Attila Tárnok
- Institute for Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig, Leipzig, Germany.,Department Therapy Validation, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
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6
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Hwang K, Mou Q, Lake RJ, Xiong M, Holland B, Lu Y. Metal-Dependent DNAzymes for the Quantitative Detection of Metal Ions in Living Cells: Recent Progress, Current Challenges, and Latest Results on FRET Ratiometric Sensors. Inorg Chem 2019; 58:13696-13708. [PMID: 31364355 PMCID: PMC7176321 DOI: 10.1021/acs.inorgchem.9b01280] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Many different metal ions are involved in various biological functions including metallomics and trafficking, and yet there are currently effective sensors for only a few metal ions, despite the first report of metal sensors for calcium more than 40 years ago. To expand upon the number of metal ions that can be probed in biological systems, we and other laboratories employ the in vitro selection method to obtain metal-specific DNAzymes with high specificity for a metal ion and then convert these DNAzymes into fluorescent sensors for these metal ions using a catalytic beacon approach. In this Forum Article, we summarize recent progress made in developing these DNAzyme sensors to probe metal ions in living cells and in vivo, including several challenges that we were able to overcome for this application, such as DNAzyme delivery, spatiotemporal control, and signal amplification. Furthermore, we have identified a key remaining challenge for the quantitative detection of metal ions in living cells and present a new design and the results of a Förster resonance energy transfer (FRET)-based DNAzyme sensor for the ratiometric quantification of Zn2+ in HeLa cells. By converting existing DNAzyme sensors into a ratiometric readout without compromising the fundamental catalytic function of the DNAzymes, this FRET-based ratiometric DNAzyme design can readily be applied to other DNAzyme sensors as a major advance in the field to develop much more quantitative metal-ion probes for biological systems.
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Affiliation(s)
- Kevin Hwang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Quanbing Mou
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Ryan J. Lake
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Mengyi Xiong
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Institute of Chemical Biology and Nanomedicine, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Brandalynn Holland
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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7
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Wu J, Lin JM. Microfluidic Technology for Single-Cell Capture and Isolation. MICROFLUIDICS FOR SINGLE-CELL ANALYSIS 2019. [DOI: 10.1007/978-981-32-9729-6_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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8
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Lyu Y, Teng IT, Zhang L, Guo Y, Cai R, Zhang X, Qiu L, Tan W. Comprehensive Regression Model for Dissociation Equilibria of Cell-Specific Aptamers. Anal Chem 2018; 90:10487-10493. [PMID: 30039967 PMCID: PMC6522138 DOI: 10.1021/acs.analchem.8b02484] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A comprehensive nonlinear regression model for dissociation equilibria of cell-specific aptamers is proposed by considering the effect of receptor expression level. Benefiting from the global regression of simultaneous equations, the fitted parameters reach a very significant level, indicating the statistical validity of this updated model. According to the fitting results, we found that dissociation constants fitted using the previous model are obviously larger than the updated values, which can be explained by the effect of receptor number on curve fitting. In addition, equivalent receptor density can be estimated using the updated model, which may lead to some new judgments about reported results of cell-SELEX.
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Affiliation(s)
- Yifan Lyu
- Institute of Molecular Medicine, Renji Hospital, School of Medicine and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People’s Republic of China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Inter-face, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - I-Ting Teng
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Inter-face, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Liqin Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People’s Republic of China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Inter-face, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Yian Guo
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Inter-face, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Ren Cai
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People’s Republic of China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Inter-face, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Xiaobing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People’s Republic of China
| | - Liping Qiu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People’s Republic of China
| | - Weihong Tan
- Institute of Molecular Medicine, Renji Hospital, School of Medicine and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People’s Republic of China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Inter-face, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
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Tsuchiya A, Hashim SN, Ise S, Furuhata T, Kawai K, Wakabayashi R, Goto M, Kamiya N, Sando S. BODIPY-labeled Fluorescent Aptamer Sensors for Turn-on Sensing of Interferon-gamma and Adenine Compounds on Cells. ANAL SCI 2018; 32:543-7. [PMID: 27169654 DOI: 10.2116/analsci.32.543] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
An on-cell aptamer sensor has the potential to reveal cell-cell communications by signalling molecules. We attempted to design new fluorescent aptamer sensors for the sensing of IFN-γ and adenine compounds on cells. BODIPY-labeled external quencher-free aptamer sensors have allowed a turn-on detection of the target molecule with improved off/on efficiency.
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Affiliation(s)
- Akira Tsuchiya
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo
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10
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Lyu D, Chen S, Guo W. Liposome Crosslinked Polyacrylamide/DNA Hydrogel: a Smart Controlled-Release System for Small Molecular Payloads. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1704039. [PMID: 29479856 DOI: 10.1002/smll.201704039] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 01/19/2018] [Indexed: 06/08/2023]
Abstract
A novel stimuli-responsive hydrogel system with liposomes serving as both noncovalent crosslinkers and functional small molecules carriers for controlled-release is developed. Liposomes can crosslink polyacrylamide copolymers functionalized with cholesterol-modified DNA motifs to yield a DNA hydrogel system, due to the hydrophobic interaction between cholesteryl groups and the lipid bilayer of liposomes. Functional information encoded DNA motifs on the polymer backbones endow the hydrogel with programmable smart responsive properties. In a model system, the hydrogel exhibits stimuli-responsive gel-to-sol transformation triggered by the opening of DNA motifs upon the presence of a restriction endonuclease enzyme, EcoR I, or temperature change, realizing the controlled-release of liposomes which are highly efficient carriers of active small molecules payloads. Two active molecules, 1,1-dioctadecyl-3,3,3,3-tetramethylindodicarbocyanine perchlorate (DiIC18(5)) and calcein, are chosen as the hydrophobic and hydrophilic model payloads, respectively, to address the feasibility of the releasing strategy. Moreover, the hydrogel exhibits injectable property as well as self-recovery behaviors.
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Affiliation(s)
- Danya Lyu
- College of Chemistry, Research Center for Analytical Sciences, Tianjin Key Laboratory of Molecular Recognition and Biosensing, and State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Shanshan Chen
- College of Chemistry, Research Center for Analytical Sciences, Tianjin Key Laboratory of Molecular Recognition and Biosensing, and State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Weiwei Guo
- College of Chemistry, Research Center for Analytical Sciences, Tianjin Key Laboratory of Molecular Recognition and Biosensing, and State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300071, China
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11
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Harroun SG, Prévost-Tremblay C, Lauzon D, Desrosiers A, Wang X, Pedro L, Vallée-Bélisle A. Programmable DNA switches and their applications. NANOSCALE 2018; 10:4607-4641. [PMID: 29465723 DOI: 10.1039/c7nr07348h] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
DNA switches are ideally suited for numerous nanotechnological applications, and increasing efforts are being directed toward their engineering. In this review, we discuss how to engineer these switches starting from the selection of a specific DNA-based recognition element, to its adaptation and optimisation into a switch, with applications ranging from sensing to drug delivery, smart materials, molecular transporters, logic gates and others. We provide many examples showcasing their high programmability and recent advances towards their real life applications. We conclude with a short perspective on this exciting emerging field.
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Affiliation(s)
- Scott G Harroun
- Laboratory of Biosensors & Nanomachines, Département de Chimie, Université de Montréal, Montréal, Québec H3C 3J7, Canada.
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12
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Tseng YT, Harroun SG, Wu CW, Mao JY, Chang HT, Huang CC. Satellite-like Gold Nanocomposites for Targeted Mass Spectrometry Imaging of Tumor Tissues. Nanotheranostics 2017; 1:141-153. [PMID: 29071183 PMCID: PMC5646720 DOI: 10.7150/ntno.18897] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 02/25/2017] [Indexed: 11/30/2022] Open
Abstract
We have developed a simple, rapid, high-throughput cancer diagnosis system using functional nanoparticles (NPs) consisting of poly(catechin) capped-gold NPs (Au@PC NPs) and smaller nucleolin-binding aptamer (AS1411) conjugated gold NPs (AS1411-Au NPs). The AS1411-Au NPs/Au@PC NP is used as a targeting agent in laser desorption/ionization mass spectrometry (LDI-MS)-based tumor tissue imaging. Self-assembled core-shell Au@PC NPs are synthesized by a simple reaction of tetrachloroaurate(III) with catechin. Au@PC NPs with a well-defined and dense poly(catechin) shell (~40-60 nm) on the surface of each Au core (~60-80 nm) are obtained through careful control of the ratio of catechin to gold ions, as well as the pH of the reaction solution. Furthermore, we have shown that AS1411-conjugated Au NPs (13-nm) self-assembled on Au@PC NP can from a satellite-like gold nanocomposite. The high density of AS1411-Au NPs on the surface of Au@PC NP enhances multivalent binding with nucleolin molecules on tumor cell membranes. We have employed LDI-MS to detect AS1411-Au NPs/Au@PC NPs labeled nucleolin-overexpressing MCF-7 breast cancer cells through the monitoring of Au cluster ions ([Aun]+; 1 ≤ n ≤ 3). The ultrahigh signal amplification from Au NPs through the formation of a huge number of [Aun]+ ions results in a sensing platform with a limit of detection of 100 MCF-7 cells mL-1. Further, we have applied the satellite-like AS1411-Au NPs/Au@PC NP nanocomposite as a labeling agent for tumor tissue imaging by LDI-MS. Our nanocomposite-assisted LDI-MS imaging platform can be extended for simultaneous analysis of different tumor markers on cell membranes when using different ligand-modified metal nanoparticles.
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Affiliation(s)
- Yu-Ting Tseng
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Scott G Harroun
- Department of Chemistry, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Chien-Wei Wu
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Ju-Yi Mao
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 20224, Taiwan
| | - Huan-Tsung Chang
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan.,Department of Chemistry, Chung Yuan Christian University, Taoyuan City 32023, Taiwan
| | - Chih-Ching Huang
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 20224, Taiwan.,Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 20224, Taiwan.,School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
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13
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Fan D, Zhu X, Zhai Q, Wang E, Dong S. Polydopamine Nanotubes as an Effective Fluorescent Quencher for Highly Sensitive and Selective Detection of Biomolecules Assisted with Exonuclease III Amplification. Anal Chem 2016; 88:9158-65. [PMID: 27575055 DOI: 10.1021/acs.analchem.6b02282] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
In this work, the effective fluorescence quenching ability of polydopamine nanotubes (PDANTs) toward various fluorescent dyes was studied and further applied to fluorescent biosensing for the first time. The PDANTs could quench the fluorophores with different emission frequencies, aminomethylcoumarin acetate (AMCA), 6-carboxyfluorescein (FAM), 6-carboxytetramethylrhodamine (TAMRA), and Cy5. All the quenching efficiencies reached to more than 97%. Taking advantage of PDANTs' different affinities toward ssDNA and dsDNA and utilizing the complex of FAM-labeled ssDNA and PDANTs as a sensing platform, we achieved highly sensitive and selective detection of human immunodeficiency virus (HIV) DNA and adenosine triphosphate (ATP) assisted with Exonuclease III amplification. The limits of detection (LODs) of HIV DNA and ATP reached to 3.5 pM and 150 nM, respectively, which were all lower than that of previous nanoquenchers with Exo III amplification, and the platform also presented good applicability in biological samples. Fluorescent sensing applications of this nanotube enlightened other targets detection based upon it and enriched the building blocks of fluorescent sensing platforms. This polydopamine nanotube also possesses excellent biocompatibility and biodegradability, which is suitable for future drug delivery, cell imaging, and other biological applications.
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Affiliation(s)
- Daoqing Fan
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, China.,University of Chinese Academy of Sciences , Beijing, 100039, China
| | - Xiaoqing Zhu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, China.,University of Chinese Academy of Sciences , Beijing, 100039, China
| | - Qingfeng Zhai
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, China.,University of Chinese Academy of Sciences , Beijing, 100039, China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, China.,University of Chinese Academy of Sciences , Beijing, 100039, China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, China.,University of Chinese Academy of Sciences , Beijing, 100039, China
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14
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Kakoti A, Goswami P. Multifaceted analyses of the interactions between human heart type fatty acid binding protein and its specific aptamers. Biochim Biophys Acta Gen Subj 2016; 1861:3289-3299. [PMID: 27545084 DOI: 10.1016/j.bbagen.2016.08.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 07/20/2016] [Accepted: 08/17/2016] [Indexed: 12/26/2022]
Abstract
BACKGROUND Aptamer-protein interaction studies have been mainly confined to dissociation constant (Kd) determination. A combinatorial approach involving limited proteolysis mass spectroscopy, molecular docking and CD studies is reported here to elucidate the specific interactions involved. METHODS To generate aptamers specific for human FABP3, SELEX was performed incorporating counter SELEX cycles against control FABPs and GST tag, followed by their characterization by EMSA, CD and SVD analysis. Based on computationally obtained aptamer-protein complex models, the interacting aptamer, and protein residues were predicted and supported by limited proteolysis experiments. RESULTS Two aptamers N13 and N53 specific for human fatty acid binding protein (FABP3) were isolated with corresponding Kd of 0.0743±0.0142μM and 0.3337±0.1485μM for FABP3 interactions. Both aptamers possess stable B-DNA structures at salt concentration of 100mM and pH range (6-9). The N13 aptamer led interaction involved 3 salt bridges and 2 hydrogen bonds, whereas N53 had 2 salt bridges with 8 hydrogen and 7 hydrophobic interactions. CONCLUSIONS The aptamers generated are the first to be reported against human FABP3. The higher interaction footprint of N53 incited synergistic conformational changes in both N53 and FABP3 during interaction, leading to a decline in binding affinity in comparison to N13 which corroborated to the calculated Kd values. GENERAL SIGNIFICANCE This combinatorial method may be used to retrieve the possible specific binding modes and interaction patterns involved in large aptamer-protein complexes. Thus the method can be exploited to identify the optimum aptamer length for in-depth structure-function studies and its tailored applications.
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Affiliation(s)
- Ankana Kakoti
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Pranab Goswami
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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15
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Xu M, Gao Z, Zhou Q, Lin Y, Lu M, Tang D. Terbium ion-coordinated carbon dots for fluorescent aptasensing of adenosine 5'-triphosphate with unmodified gold nanoparticles. Biosens Bioelectron 2016; 86:978-984. [PMID: 27498324 DOI: 10.1016/j.bios.2016.07.105] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 07/28/2016] [Accepted: 07/29/2016] [Indexed: 01/11/2023]
Abstract
This work reports on a novel time-resolved fluorescent aptasensing platform for the quantitative monitoring of adenosine 5'-triphosphate (ATP) by interaction of dispersive/agglomerate gold nanoparticles (AuNPs) with terbium ion-coordinated carbon dots (Tb-CDs). To construct such a fluorescent nanoprobe, Tb-CDs with high-efficient fluorescent intensity are first synthesized by the microwave method with terbium ions (Tb(3+)). The aptasensing system consists of ATP aptamer, AuNP and Tb-CD. The dispersive/agglomerate gold nanoparticles are acquired through the reaction of the aptamer with target ATP. Upon target ATP introduction, the aptamers bind with the analytes to form new aptamer-ATP complexes and coat on the surface of AuNPs to inhibit their aggregation in the high salt solution. In this case, the fluorescent signal of Tb-CDs is quenched by the dispersive AuNPs on the basis of the fluorescence resonance energy transfer (FRET). At the absence of target analyte, gold nanoparticles tend to aggregate in the high salt state even if the aptamers are present. Thus, the added Tb-CDs maintain their intrinsic fluorescent intensity. Experimental results indicated that the aptasensing system exhibited good fluorescent responses toward ATP in the dynamic range from 40nM to 4.0μM with a detection limit of 8.5nM at 3sblank criterion. The repeatability and intermediate precision is less than 9.5% at three concentrations including 0.04, 0.4 and 2.0μM ATP. The selectivity was acceptable toward guanosine 5'-triphosphate, uridine 5'-triphosphate and cytidine 5'-triphosphate. The methodology was applied to evaluate the blank human serum spiked with target ATP, and the recoveries (at 3 concentration levels) ranged between 97.0% and 103.7%. Importantly, this detection scheme is rapid, simple, cost-effective, and does not require extensive sample preparation or separation.
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Affiliation(s)
- Mingdi Xu
- Key Laboratory of Analysis and Detection for Food Safety (MOE&Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou, 350108 PR China
| | - Zhuangqiang Gao
- Key Laboratory of Analysis and Detection for Food Safety (MOE&Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou, 350108 PR China
| | - Qian Zhou
- Key Laboratory of Analysis and Detection for Food Safety (MOE&Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou, 350108 PR China
| | - Youxiu Lin
- Key Laboratory of Analysis and Detection for Food Safety (MOE&Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou, 350108 PR China
| | - Minghua Lu
- Institute of Environmental and Analytical Science, School of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan, 475004 PR China.
| | - Dianping Tang
- Key Laboratory of Analysis and Detection for Food Safety (MOE&Fujian Province), Institute of Nanomedicine and Nanobiosensing, Department of Chemistry, Fuzhou University, Fuzhou, 350108 PR China.
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16
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Lv Y, Peng R, Zhou Y, Zhang X, Tan W. Catalytic self-assembly of a DNA dendritic complex for efficient gene silencing. Chem Commun (Camb) 2016; 52:1413-5. [PMID: 26626818 PMCID: PMC4713312 DOI: 10.1039/c5cc06937h] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A catalytic self-assembled DNA dendritic complex was herein reported and used for siRNA-based gene silencing. This kind of one-pot DNA dendrimer can be conveniently prepared as needed, and it was demonstrated to have better silencing efficiency and lower cytotoxicity than commercial cationic lipid transfection agents.
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Affiliation(s)
- Yifan Lv
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha 410082, China.
| | - Ruizi Peng
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha 410082, China.
| | - Yu Zhou
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha 410082, China.
| | - Xiaobing Zhang
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha 410082, China.
| | - Weihong Tan
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha 410082, China. and Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Shands Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, USA.
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17
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Abstract
In the past two decades, aptamers have emerged as a novel class of molecular recognition probes comprising uniquely-folded short RNA or single-stranded DNA oligonucleotides that bind to their cognate targets with high specificity and affinity. Aptamers, often referred to as "chemical antibodies", possess several highly desirable features for clinical use. They can be chemically synthesized and are easily conjugated to a wide range of reporters for different applications, and are able to rapidly penetrate tissues. These advantages significantly enhance their clinical applicability, and render them excellent alternatives to antibody-based probes in cancer diagnostics and therapeutics. Aptamer probes based on fluorescence, colorimetry, magnetism, electrochemistry, and in conjunction with nanomaterials (e.g., nanoparticles, quantum dots, single-walled carbon nanotubes, and magnetic nanoparticles) have provided novel ultrasensitive cancer diagnostic strategies and assays. Furthermore, promising aptamer targeted-multimodal tumor imaging probes have been recently developed in conjunction with fluorescence, positron emission tomography (PET), single-photon emission computed tomography (SPECT), and magnetic resonance imaging (MRI). The capabilities of the aptamer-based platforms described herein underscore the great potential they hold for the future of cancer detection. In this review, we highlight the most prominent recent developments in this rapidly advancing field.
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Affiliation(s)
- Hongguang Sun
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA.
| | - Weihong Tan
- Department of Chemistry and Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Shands Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611-7200, USA
| | - Youli Zu
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA.
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18
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Qiang W, Hu H, Sun L, Li H, Xu D. Aptamer/Polydopamine Nanospheres Nanocomplex for in Situ Molecular Sensing in Living Cells. Anal Chem 2015; 87:12190-6. [PMID: 26556471 DOI: 10.1021/acs.analchem.5b03075] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A nanocomplex was developed for molecular sensing in living cells, based on the fluorophore-labeled aptamer and the polydopamine nanospheres (PDANS). Due to the interaction between ssDNA and PDANS, the aptamer was adsorbed onto the surface of PDANS forming the aptamer/PDANS nanocomplex, and the fluorescence was quenched by PDANS through Förster resonance energy transfer (FRET). In vitro assay, the introduction of adenosine triphosphate (ATP) led to the dissociation of the aptamer from the PDANS and the recovery of the fluorescence. The retained fluorescence of the nanocomplex was found to be linear with the concentration of ATP in the range of 0.01-2 mM, and the nanocomplex was highly selective toward ATP. For the strong protecting capability to nucleic acids from enzymatic cleavage and the excellent biocompatibility of PDANS, the nanocomplex was transported into cells and successfully realized "signal on" sensing of ATP in living cells; moreover, the nanocomplex could be employed for ATP semiquantification. This design provides a strategy to develop biosensors based on the polydopamine nanomaterials for intracellular molecules analysis. For the advantages of polydopamine, it would be an excellent candidate for many biological applications, such as gene and drug delivery, intracellular imaging, and in vivo monitoring.
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Affiliation(s)
- Weibing Qiang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University , 22 Hankou Road, Nanjing, Jiangsu 210093, China
| | - Hongting Hu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University , 22 Hankou Road, Nanjing, Jiangsu 210093, China
| | - Liang Sun
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University , 22 Hankou Road, Nanjing, Jiangsu 210093, China
| | - Hui Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University , 22 Hankou Road, Nanjing, Jiangsu 210093, China
| | - Danke Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University , 22 Hankou Road, Nanjing, Jiangsu 210093, China
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19
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Lv Y, Hu R, Zhu G, Zhang X, Mei L, Liu Q, Qiu L, Wu C, Tan W. Preparation and biomedical applications of programmable and multifunctional DNA nanoflowers. Nat Protoc 2015; 10:1508-24. [PMID: 26357007 DOI: 10.1038/nprot.2015.078] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We describe a comprehensive protocol for the preparation of multifunctional DNA nanostructures termed nanoflowers (NFs), which are self-assembled from long DNA building blocks generated via rolling-circle replication (RCR) of a designed template. NF assembly is driven by liquid crystallization and dense packaging of building blocks, which eliminates the need for conventional Watson-Crick base pairing. As a result of dense DNA packaging, NFs are resistant to nuclease degradation, denaturation or dissociation at extremely low concentrations. By manually changing the template sequence, many different functional moieties including aptamers, bioimaging agents and drug-loading sites could be easily integrated into NF particles, making NFs ideal candidates for a variety of applications in biomedicine. In this protocol, the preparation of multifunctional DNA NFs with highly tunable sizes is described for applications in cell targeting, intracellular imaging and drug delivery. Preparation and characterization of functional DNA NFs takes ∼5 d; the following biomedical applications take ∼10 d.
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Affiliation(s)
- Yifan Lv
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha, China
| | - Rong Hu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha, China.,Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Shands Cancer Center, University of Florida Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida, USA
| | - Guizhi Zhu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha, China.,Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Shands Cancer Center, University of Florida Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida, USA
| | - Xiaobing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha, China
| | - Lei Mei
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha, China
| | - Qiaoling Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha, China
| | - Liping Qiu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha, China.,Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Shands Cancer Center, University of Florida Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida, USA
| | - Cuichen Wu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha, China.,Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Shands Cancer Center, University of Florida Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida, USA
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha, China.,Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Shands Cancer Center, University of Florida Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida, USA
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20
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Nucleic Acid Aptamers: An Emerging Tool for Biotechnology and Biomedical Sensing. SENSORS 2015; 15:16281-313. [PMID: 26153774 PMCID: PMC4541879 DOI: 10.3390/s150716281] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 06/26/2015] [Accepted: 06/30/2015] [Indexed: 02/06/2023]
Abstract
Detection of small molecules or proteins of living cells provides an exceptional opportunity to study genetic variations and functions, cellular behaviors, and various diseases including cancer and microbial infections. Our aim in this review is to give an overview of selected research activities related to nucleic acid-based aptamer techniques that have been reported in the past two decades. Limitations of aptamers and possible approaches to overcome these limitations are also discussed.
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21
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A fluorescent biosensing platform based on the polydopamine nanospheres intergrating with Exonuclease III-assisted target recycling amplification. Biosens Bioelectron 2015; 71:143-149. [PMID: 25897884 DOI: 10.1016/j.bios.2015.04.029] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 03/30/2015] [Accepted: 04/12/2015] [Indexed: 11/20/2022]
Abstract
Rapid, cost-effective, sensitive and specific analysis of biomolecules is important in the modern healthcare system. Here, a fluorescent biosensing platform based on the polydopamine nanospheres (PDANS) intergrating with Exonuclease III (Exo III) was developed. Due to the interaction between the ssDNA and the PDANS, the fluorescence of 6-carboxyfluorescein (FAM) labelled in the probe would been quenched by PDANS through FRET. While, in the present of the target DNA, the probe DNA would hybridize with the target DNA to form the double-strand DNA complex. Thus, Exo III could catalyze the stepwise removal of mononucleotides from 3'-terminus in the probe DNA, releasing the target DNA. As the FAM was released from the probe DNA, the fluorescence would no longer been quenched, led to the signal on. As one target DNA molecule could undergo a number of cycles to trigger the degradation of abundant probe DNA, Exo III-assisted target recycling would led to the amplification of the signal. The detection limit for DNA was 5 pM, which was 20 times lower than that without Exo III. And the assay time was largely shortened due to the faster signal recovery kinetics. What is more, this target recycling strategy was also applied to conduct an aptamer-based biosensing platform. The fluorescence intensity was also enhanced for the assay of adenosine triphosphate (ATP). For the Exo III-assisted target recycling amplification, DNA and ATP were fast detected with high sensitivity and selectivity. This work provides opportunities to develop simple, rapid, economical, and sensitive biosensing platforms for biomedical diagnostics.
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22
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Pu Y, Liu Z, Lu Y, Yuan P, Liu J, Yu B, Wang G, Yang C, Liu H, Tan W. Using DNA aptamer probe for immunostaining of cancer frozen tissues. Anal Chem 2015; 87:1919-24. [PMID: 25536018 PMCID: PMC4318623 DOI: 10.1021/ac504175h] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Accepted: 12/23/2014] [Indexed: 01/09/2023]
Abstract
Tissue immunostaining is critically important in clinical applications, and antibodies have been used extensively as the molecular probes. Recently, aptamer, as a new class of probes, have attracted much attention for their potential clinical and research value. Epithelial cell adhesion molecule (EpCAM) is a specific biomarker which is overexpressed in many cancers of epithelial origin. Here, a DNA-based EpCAM aptamer SYL3C is reported as a probe for the immunostaining of frozen and paraffin-embedded sections of colorectal cancer tissues. Commercialized EpCAM antibodies were also used as a standard control. EpCAM aptamer SYL3C specifically recognized and immunostained cancer nests of colorectal tumor sections, but it neither reacted with background cells within tumor sites nor exhibited cross-reaction to the benign lesions or inflammation of colorectal tissues. No cross-linking to EpCAM-negative malignant tumor sections occurred. Compared with standard antibody staining, our EpCAM aptamer SYL3C protocol is simpler to implement with a shorter reaction time. Moreover, SYL3C can specifically bind with either frozen or paraffin-embedded tissue sections. Since the histopathology of frozen tissue is closer to that of fresh tissue and since frozen sections can be produced more quickly than paraffin-embedded sections, SYL3C immunostaining of frozen sections is a quick protocol that is easy to implement.
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Affiliation(s)
- Ying Pu
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhenxu Liu
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yi Lu
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Peng Yuan
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jun Liu
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Bo Yu
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Guodong Wang
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Chaoyong
James Yang
- State Key
Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory
for Chemical Biology of Fujian Province, Key Laboratory of Analytical
Chemistry, and Department of Chemical Biology, College of Chemistry
and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Huixia Liu
- Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Weihong Tan
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio-Sensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, and Collaborative Research Center of Molecular Engineering
for Theranostics, Hunan University, Changsha, Hunan 410082, China
- Department of Chemistry and Physiology
and Functional Genomics, Center for Research at the Bio/Nano Interface,
Shands Cancer Center, University of Florida, Gainesville, Florida 32611-7200, United States
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