1
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Fan G, Corbin N, Chung M, Gill TM, Moore EB, Karbelkar AA, Furst AL. Highly Efficient Carbon Dioxide Electroreduction via DNA-Directed Catalyst Immobilization. JACS AU 2024; 4:1413-1421. [PMID: 38665653 PMCID: PMC11040669 DOI: 10.1021/jacsau.3c00823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 03/03/2024] [Accepted: 03/04/2024] [Indexed: 04/28/2024]
Abstract
Electrochemical reduction of carbon dioxide (CO2) is a promising route to up-convert this industrial byproduct. However, to perform this reaction with a small-molecule catalyst, the catalyst must be proximal to an electrode surface. Efforts to immobilize molecular catalysts on electrodes have been stymied by the need to optimize the immobilization chemistries on a case-by-case basis. Taking inspiration from nature, we applied DNA as a molecular-scale "Velcro" to investigate the tethering of three porphyrin-based catalysts to electrodes. This tethering strategy improved both the stability of the catalysts and their Faradaic efficiencies (FEs). DNA-catalyst conjugates were immobilized on screen-printed carbon and carbon paper electrodes via DNA hybridization with nearly 100% efficiency. Following immobilization, a higher catalyst stability at relevant potentials is observed. Additionally, lower overpotentials are required for the generation of carbon monoxide (CO). Finally, high FE for CO generation was observed with the DNA-immobilized catalysts as compared to the unmodified small-molecule systems, as high as 79.1% FE for CO at -0.95 V vs SHE using a DNA-tethered catalyst. This work demonstrates the potential of DNA "Velcro" as a powerful strategy for catalyst immobilization. Here, we demonstrated improved catalytic characteristics of molecular catalysts for CO2 valorization, but this strategy is anticipated to be generalizable to any reaction that proceeds in aqueous solutions.
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Affiliation(s)
- Gang Fan
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Nathan Corbin
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Minju Chung
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Thomas M. Gill
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Evan B. Moore
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Amruta A. Karbelkar
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Ariel L. Furst
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
- Center
for Environmental Health Sciences, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
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2
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Qin C, Wang Y, Hu J, Wang T, Liu D, Dong J, Lu Y. Artificial Olfactory Biohybrid System: An Evolving Sense of Smell. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2204726. [PMID: 36529960 PMCID: PMC9929144 DOI: 10.1002/advs.202204726] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/29/2022] [Indexed: 06/17/2023]
Abstract
The olfactory system can detect and recognize tens of thousands of volatile organic compounds (VOCs) at low concentrations in complex environments. Bioelectronic nose (B-EN), which mimics olfactory systems, is becoming an emerging sensing technology for identifying VOCs with sensitivity and specificity. B-ENs integrate electronic sensors with bioreceptors and pattern recognition technologies to enable medical diagnosis, public security, environmental monitoring, and food safety. However, there is currently no commercially available B-EN on the market. Apart from the high selectivity and sensitivity necessary for volatile organic compound analysis, commercial B-ENs must overcome issues impacting sensor operation and other problems associated with odor localization. The emergence of nanotechnology has provided a novel research concept for addressing these problems. In this work, the structure and operational mechanisms of biomimetic olfactory systems are discussed, with an emphasis on the development and immobilization of materials. Various biosensor applications and current developments are reviewed. Challenges and opportunities for fulfilling the potential of artificial olfactory biohybrid systems in fundamental and practical research are investigated in greater depth.
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Affiliation(s)
- Chuanting Qin
- Key Laboratory of Industrial BiocatalysisMinistry of EducationDepartment of Chemical EngineeringTsinghua UniversityBeijing100084China
- Tianjin Industrial Microbiology Key LaboratoryCollege of BiotechnologyTianjin University of Science and TechnologyTianjin300457China
| | - Yi Wang
- Key Laboratory of Industrial BiocatalysisMinistry of EducationDepartment of Chemical EngineeringTsinghua UniversityBeijing100084China
- Tianjin Industrial Microbiology Key LaboratoryCollege of BiotechnologyTianjin University of Science and TechnologyTianjin300457China
| | - Jiawang Hu
- Key Laboratory of Industrial BiocatalysisMinistry of EducationDepartment of Chemical EngineeringTsinghua UniversityBeijing100084China
| | - Ting Wang
- Key Laboratory of Industrial BiocatalysisMinistry of EducationDepartment of Chemical EngineeringTsinghua UniversityBeijing100084China
| | - Dong Liu
- Key Laboratory of Industrial BiocatalysisMinistry of EducationDepartment of Chemical EngineeringTsinghua UniversityBeijing100084China
| | - Jian Dong
- Tianjin Industrial Microbiology Key LaboratoryCollege of BiotechnologyTianjin University of Science and TechnologyTianjin300457China
| | - Yuan Lu
- Key Laboratory of Industrial BiocatalysisMinistry of EducationDepartment of Chemical EngineeringTsinghua UniversityBeijing100084China
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3
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Tomás RMF, Gibson MI. 100th Anniversary of Macromolecular Science Viewpoint: Re-Engineering Cellular Interfaces with Synthetic Macromolecules Using Metabolic Glycan Labeling. ACS Macro Lett 2020; 9:991-1003. [PMID: 32714634 PMCID: PMC7377358 DOI: 10.1021/acsmacrolett.0c00317] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/15/2020] [Indexed: 01/08/2023]
Abstract
Cell-surface functionality is largely programmed by genetically encoded information through modulation of protein expression levels, including glycosylation enzymes. Genetic tools enable control over protein-based functionality, but are not easily adapted to recruit non-native functionality such as synthetic polymers and nanomaterials to tune biological responses and attach therapeutic or imaging payloads. Similar to how polymer-protein conjugation evolved from nonspecific PEGylation to site-selective bioconjugates, the same evolution is now occurring for polymer-cell conjugation. This Viewpoint discusses the potential of using metabolic glycan labeling to install bio-orthogonal reactive cell-surface anchors for the recruitment of synthetic polymers and nanomaterials to cell surfaces, exploring the expanding therapeutic and diagnostic potential. Comparisons to conventional approaches that target endogenous membrane components, such as hydrophobic, protein coupling and electrostatic conjugation, as well as enzymatic and genetic tools, have been made to highlight the huge potential of this approach in the emerging cellular engineering field.
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Affiliation(s)
- Ruben M. F. Tomás
- Department of Chemistry and Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Matthew I. Gibson
- Department of Chemistry and Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom
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4
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Preparation Methods for Phospholipid Vesicle Arrays and Their Applications in Biological Analysis. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2019. [DOI: 10.1016/s1872-2040(19)61179-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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5
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Hu Y, Niemeyer CM. From DNA Nanotechnology to Material Systems Engineering. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1806294. [PMID: 30767279 DOI: 10.1002/adma.201806294] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/29/2018] [Indexed: 05/25/2023]
Abstract
In the past 35 years, DNA nanotechnology has grown to a highly innovative and vibrant field of research at the interface of chemistry, materials science, biotechnology, and nanotechnology. Herein, a short summary of the state of research in various subdisciplines of DNA nanotechnology, ranging from pure "structural DNA nanotechnology" over protein-DNA assemblies, nanoparticle-based DNA materials, and DNA polymers to DNA surface technology is given. The survey shows that these subdisciplines are growing ever closer together and suggests that this integration is essential in order to initiate the next phase of development. With the increasing implementation of machine-based approaches in microfluidics, robotics, and data-driven science, DNA-material systems will emerge that could be suitable for applications in sensor technology, photonics, as interfaces between technical systems and living organisms, or for biomimetic fabrication processes.
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Affiliation(s)
- Yong Hu
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Christof M Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
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6
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Furst AL, Klass SH, Francis MB. DNA Hybridization to Control Cellular Interactions. Trends Biochem Sci 2019; 44:342-350. [DOI: 10.1016/j.tibs.2018.10.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 10/04/2018] [Accepted: 10/10/2018] [Indexed: 12/28/2022]
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7
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Schneider A, Niemeyer CM. DNA Surface Technology: From Gene Sensors to Integrated Systems for Life and Materials Sciences. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201811713] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ann‐Kathrin Schneider
- Institute for Biological Interfaces (IBG 1) Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldshafen Germany
| | - Christof M. Niemeyer
- Institute for Biological Interfaces (IBG 1) Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldshafen Germany
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8
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Schneider A, Niemeyer CM. DNA Surface Technology: From Gene Sensors to Integrated Systems for Life and Materials Sciences. Angew Chem Int Ed Engl 2018; 57:16959-16967. [DOI: 10.1002/anie.201811713] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/15/2018] [Indexed: 01/21/2023]
Affiliation(s)
- Ann‐Kathrin Schneider
- Institute for Biological Interfaces (IBG 1) Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldshafen Germany
| | - Christof M. Niemeyer
- Institute for Biological Interfaces (IBG 1) Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldshafen Germany
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9
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Li Q, Zhang YW, Wang CF, Weitz DA, Chen S. Versatile Hydrogel Ensembles with Macroscopic Multidimensions. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1803475. [PMID: 30393968 DOI: 10.1002/adma.201803475] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/12/2018] [Indexed: 06/08/2023]
Abstract
Methods allowing construction of macroscopic programmed materials in a flexible and efficient fashion are highly desirable. However, the existing approaches are far removed from such materials. A new self-healing-driven assembly (SHDA) strategy to fabricate various programmed materials by using uniform gel beads (microsize of 212 µm or millimeter size of 4 mm) as building blocks is described here. In virtue of hydrogen bonds and host-guest interactions between gel beads, a series of linear, planar, and 3D beaded assemblies are fabricated via SHDA in microfluidic channels in a continuous and controlled manner. From the perspective of practical applications, the use of gel assemblies is exploited for tissue engineering with controlled cells coculture, as well as light conversion materials toward white-light-emitting diodes (WLEDs). The SHDA strategy developed in this study gives a new insight into the facile and rapid fabrication of various programmed materials toward biological tissue and optoelectronic device.
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Affiliation(s)
- Qing Li
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Jiangsu Key Laboratory of Fine Chemicals and Functional Polymer Materials, Nanjing Tech University, 5 Xin Mofan Road, Nanjing, 210009, P. R. China
| | - Ya-Wen Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Jiangsu Key Laboratory of Fine Chemicals and Functional Polymer Materials, Nanjing Tech University, 5 Xin Mofan Road, Nanjing, 210009, P. R. China
| | - Cai-Feng Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Jiangsu Key Laboratory of Fine Chemicals and Functional Polymer Materials, Nanjing Tech University, 5 Xin Mofan Road, Nanjing, 210009, P. R. China
| | - David A Weitz
- School of Engineering and Applied Science, Harvard University, 9 Oxford St, Cambridge, MA, 02138, USA
| | - Su Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Jiangsu Key Laboratory of Fine Chemicals and Functional Polymer Materials, Nanjing Tech University, 5 Xin Mofan Road, Nanjing, 210009, P. R. China
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10
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Yüz SG, Ricken J, Wegner SV. Independent Control over Multiple Cell Types in Space and Time Using Orthogonal Blue and Red Light Switchable Cell Interactions. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2018; 5:1800446. [PMID: 30128251 PMCID: PMC6097145 DOI: 10.1002/advs.201800446] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/27/2018] [Indexed: 05/14/2023]
Abstract
Independent control over multiple cell-material interactions with high spatiotemporal resolution is a key for many biomedical applications and understanding cell biology, as different cell types can perform different tasks in a multicellular context. In this study, the binding of two different cell types to materials is orthogonally controlled with blue and red light providing independent regulation in space and time. Cells expressing the photoswitchable protein cryptochrome 2 (CRY2) on cell surface bind to N-truncated CRY-interacting basic helix-loop-helix protein 1 (CIBN)-immobilized substrates under blue light and cells expressing the photoswitchable protein phytochrome B (PhyB ) on cell surface bind to phytochrome interaction factor 6 (PIF6)-immobilized substrates under red light, respectively. These light-switchable cell interactions provide orthogonal and noninvasive control using two wavelengths of visible light. Moreover, both cell-material interactions are dynamically switched on under light and reversible in the dark. The specificity of the CRY2/CIBN and PhyB/PIF6 interactions and their response to different wavelengths of light allow selectively activating the binding of one cell type with blue and the other cell type with red light in the presence of the other cell type.
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Affiliation(s)
- Simge G. Yüz
- Max Planck Institute of Polymer ResearchAckermannweg 1055128MainzGermany
- Department of Biophysical ChemistryUniversity of HeidelbergIm Neuenheimer Feld 25369120HeidelbergGermany
| | - Julia Ricken
- Max Planck Institute of Polymer ResearchAckermannweg 1055128MainzGermany
- Department of Biophysical ChemistryUniversity of HeidelbergIm Neuenheimer Feld 25369120HeidelbergGermany
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11
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Gentile SD, Griebel ME, Anderson EW, Underhill GH. Click Chemistry-Based DNA Labeling of Cells for Barcoding Applications. Bioconjug Chem 2018; 29:2846-2854. [DOI: 10.1021/acs.bioconjchem.8b00435] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Stefan D. Gentile
- Department of Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Megan E. Griebel
- Department of Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Erik W. Anderson
- Department of Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Gregory H. Underhill
- Department of Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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12
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Cavatorta E, Voskuhl J, Wasserberg D, Brinkmann J, Huskens J, Jonkheijm P. Targeting protein-loaded CB[8]-mediated supramolecular nanocarriers to cells. RSC Adv 2017; 7:54341-54346. [PMID: 29568508 PMCID: PMC5819385 DOI: 10.1039/c7ra10980f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 11/21/2017] [Indexed: 11/21/2022] Open
Abstract
Supramolecular amphiphiles, consisting of ternary complexes of cucurbit[8]uril (CB[8]), an alkylated paraquat derivative and a tetraethylene glycol-functionalized azobenzene, self-assemble into vesicles of about 200 nm in diameter. The outer surface of the vesicles was functionalized with cell-targeting ligands. These vesicles were employed for loading and delivery of proteins into cells. Supramolecular amphiphile-derived vesicles show great promise as nanocarriers of functional molecules to be transferred into cells.
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Affiliation(s)
- Emanuela Cavatorta
- Molecular Nanofabrication Group, MESA+ Institute for Nanotechnology, Department of Science and Technology, University of Twente, P. O. Box 217, 7500 AE, Enschede, The Netherlands. ;
| | - Jens Voskuhl
- Molecular Nanofabrication Group, MESA+ Institute for Nanotechnology, Department of Science and Technology, University of Twente, P. O. Box 217, 7500 AE, Enschede, The Netherlands. ;
| | - Dorothee Wasserberg
- Medical Cell BioPhysics Group, MIRA Biomedical Technology and Technical Medicine, Department of Science and Technology, University of Twente, Enschede, The Netherlands
| | - Jenny Brinkmann
- Molecular Nanofabrication Group, MESA+ Institute for Nanotechnology, Department of Science and Technology, University of Twente, P. O. Box 217, 7500 AE, Enschede, The Netherlands. ;
| | - Jurriaan Huskens
- Molecular Nanofabrication Group, MESA+ Institute for Nanotechnology, Department of Science and Technology, University of Twente, P. O. Box 217, 7500 AE, Enschede, The Netherlands. ;
| | - Pascal Jonkheijm
- Molecular Nanofabrication Group, MESA+ Institute for Nanotechnology, Department of Science and Technology, University of Twente, P. O. Box 217, 7500 AE, Enschede, The Netherlands. ;
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13
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Furst AL, Smith MJ, Francis MB. Direct Electrochemical Bioconjugation on Metal Surfaces. J Am Chem Soc 2017; 139:12610-12616. [DOI: 10.1021/jacs.7b06385] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ariel L. Furst
- Department
of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460, United States
| | - Matthew J. Smith
- Department
of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460, United States
| | - Matthew B. Francis
- Department
of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460, United States
- Materials
Sciences Division, Lawrence Berkeley National Laboratories, Berkeley, California 94720-1460, United States
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14
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Abstract
Being a natural polymer, DNA attracts extensive attention and possesses great potential to open a new way for researches of biomedical or material science. In the past few decades, approaches have been developed to bring DNA into the realm of bulk materials. In this review, we discussed the progresses achieved for fabrication of novel materials with a large physical dimension from the DNA polymer.
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Affiliation(s)
- Yanmin Gao
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China e-mail:
| | - Hao Qi
- Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University)
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China e-mails:
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15
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Yang Y, Su P, Zheng K, Wang T, Song J, Yang Y. A self-directed and reconstructible immobilization strategy: DNA directed immobilization of alkaline phosphatase for enzyme inhibition assays. RSC Adv 2016. [DOI: 10.1039/c6ra01621a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A DNA-directed immobilization technique is used to develop a common method for the reversible and self-directed immobilization of enzymes.
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Affiliation(s)
- Ye Yang
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis
- College of Science
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
| | - Ping Su
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis
- College of Science
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
| | - Kangle Zheng
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis
- College of Science
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
| | - Ting Wang
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis
- College of Science
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
| | - Jiayi Song
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis
- College of Science
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
| | - Yi Yang
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis
- College of Science
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
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16
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Glavan AC, Niu J, Chen Z, Güder F, Cheng CM, Liu D, Whitesides GM. Analytical Devices Based on Direct Synthesis of DNA on Paper. Anal Chem 2015; 88:725-31. [DOI: 10.1021/acs.analchem.5b02822] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Ana C. Glavan
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Jia Niu
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Zhen Chen
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Firat Güder
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Chao-Min Cheng
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - David Liu
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - George M. Whitesides
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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17
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18
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Affiliation(s)
- Yuhe R. Yang
- Center for Molecular Design
and Biomimetics, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Yan Liu
- Center for Molecular Design
and Biomimetics, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Hao Yan
- Center for Molecular Design
and Biomimetics, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
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19
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El Muslemany KM, Twite AA, ElSohly AM, Obermeyer AC, Mathies RA, Francis MB. Photoactivated bioconjugation between ortho-azidophenols and anilines: a facile approach to biomolecular photopatterning. J Am Chem Soc 2014; 136:12600-6. [PMID: 25171554 DOI: 10.1021/ja503056x] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Methods for the surface patterning of small molecules and biomolecules can yield useful platforms for drug screening, synthetic biology applications, diagnostics, and the immobilization of live cells. However, new techniques are needed to achieve the ease, feature sizes, reliability, and patterning speed necessary for widespread adoption. Herein, we report an easily accessible and operationally simple photoinitiated reaction that can achieve patterned bioconjugation in a highly chemoselective manner. The reaction involves the photolysis of 2-azidophenols to generate iminoquinone intermediates that couple rapidly to aniline groups. We demonstrate the broad functional group compatibility of this reaction for the modification of proteins, polymers, oligonucleotides, peptides, and small molecules. As a specific application, the reaction was adapted for the photolithographic patterning of azidophenol DNA on aniline glass substrates. The presence of the DNA was confirmed by the ability of the surface to capture living cells bearing the sequence complement on their cell walls or cytoplasmic membranes. Compared to other light-based DNA patterning methods, this reaction offers higher speed and does not require the use of a photoresist or other blocking material.
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Affiliation(s)
- Kareem M El Muslemany
- Department of Chemistry, University of California , Berkeley, California 94720-1460, United States
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20
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Meyer R, Giselbrecht S, Rapp BE, Hirtz M, Niemeyer CM. Advances in DNA-directed immobilization. Curr Opin Chem Biol 2014; 18:8-15. [DOI: 10.1016/j.cbpa.2013.10.023] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 10/01/2013] [Indexed: 12/18/2022]
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21
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Shomorony A, Fan R. Immuno-DNA-directed Assembly of Heterotypic Multicellular Systems. CHEM LETT 2013. [DOI: 10.1246/cl.130004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | - Rong Fan
- Department of Biomedical Engineering, Yale University
- Yale Comprehensive Cancer Center
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22
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Vogel K, Glettenberg M, Schroeder H, Niemeyer CM. DNA-modification of eukaryotic cells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:255-262. [PMID: 23109119 DOI: 10.1002/smll.201201852] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Indexed: 06/01/2023]
Abstract
A novel bioorthogonal method for the modification of cells with single-stranded DNA oligomers is compared to five alternative methods with respect to labeling efficacy, specificity, and effects on cell viability. The new method is based on oxime ligation of aminooxybiotin to aldehyde groups installed by periodate cleavage of cell-surface glycans, followed by the coupling of preformed DNA-streptavidin conjugates. As compared with two literature-reported methods based on direct coupling of N-hydroxysuccinimidyl (NHS)-DNA or NHS-biotinylation as well as with techniques based on strain-promoted alkyne-azide cycloaddition, this method shows the highest labeling densities and is sufficiently mild to avoid cell damage. Functionality of the DNA tags is demonstrated by DNA-directed immobilization on solid substrates and assembly of small cell aggregates.
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Affiliation(s)
- Katrin Vogel
- Technische Universität Dortmund, Fakultät Chemie, Biologisch-Chemische Mikrostrukturtechnik, Dortmund, Germany
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23
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Onoe H, Hsiao SC, Douglas ES, Gartner ZJ, Bertozzi CR, Francis MB, Mathies RA. Cellular microfabrication: observing intercellular interactions using lithographically-defined DNA capture sequences. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:8120-8126. [PMID: 22512362 DOI: 10.1021/la204863s] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Previous reports have shown that synthetic DNA strands can be attached to the plasma membrane of living cells to equip them with artificial adhesion "receptors" that bind to complementary strands extending from material surfaces. This approach is compatible with a wide range of cell types, offers excellent capture efficiency, and can potentially be used to create complex multicellular arrangements through the use of multiple capture sequences. In this work, we apply an aluminum "lift off" lithography method to allow the efficient generation of complex patterns comprising different DNA sequences. The resulting surfaces are then demonstrated to be able to capture up to three distinct types of living cells in specific locations. The utility of this approach is demonstrated through the observation of patterned cells as they communicate by diffusion-based paracrine signaling. It is anticipated that the ability of this technique to create virtually any type of 2D heterogeneous cell pattern should prove highly useful for the examination of key questions in cell signaling, including stem cell differentiation and cancer metastasis.
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Affiliation(s)
- Hiroaki Onoe
- Department of Chemistry, University of California, Berkeley, California 94720, United States
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24
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Twite AA, Hsiao SC, Onoe H, Mathies RA, Francis MB. Direct attachment of microbial organisms to material surfaces through sequence-specific DNA hybridization. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2012; 24:2380-5. [PMID: 22431245 DOI: 10.1002/adma.201104336] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 12/12/2011] [Indexed: 05/20/2023]
Abstract
A new technique is reported for the attachment of synthetic DNA strands to the surfaces of microbial organisms. This gives algal, bacterial, and fungal cells the ability to bind to complementary strands extending from patterned surfaces that can be produced on platforms such as microfluidic devices. The ability of this method to establish complex 2- and 3-dimensional cocultures comprising multiple organism types is also presented.
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Affiliation(s)
- Amy A Twite
- Department of Chemistry, University of California, Berkeley, CA 94720-1460, USA
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25
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Bombera R, Leroy L, Livache T, Roupioz Y. DNA-directed capture of primary cells from a complex mixture and controlled orthogonal release monitored by SPR imaging. Biosens Bioelectron 2011; 33:10-6. [PMID: 22236780 DOI: 10.1016/j.bios.2011.11.034] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 10/14/2011] [Accepted: 11/21/2011] [Indexed: 01/11/2023]
Abstract
Many biological samples are composed of several cell types. Qualitative and quantitative analysis of these complex mixtures is of major interest for both diagnostic and biomedical applications. Because large amounts of biological material are often challenging to collect, tremendous efforts have been made for a decade to design miniaturized platforms-such as lab-on-a-chip or microarrays-to run sensitive and reliable analysis from tiny quantities of starting material. Although barely explored so far, the release of resolved cellular samples constitutes an exciting strategy for further cell analysis. Herein, we propose a DNA-based biochip suitable for cell-type analysis in a label-free manner. The DNA-array is firstly converted into antibody-array using antibody-DNA conjugates. These protein-DNA hybrid molecules are chemically synthesized by covalent coupling of short oligonucleotides to antibodies directed against cell-type specific markers. We show not only specific capture of primary spleen cells on protein-DNA microarray spots but also their fast and specific orthogonal release according to the antibody-DNA combinations by incorporating restriction sites in DNA. Both molecular and cellular interactions occurring on the biochip are monitored by surface plasmon resonance (SPR) imaging. This optical technique turns out to be a powerful way to monitor, in real-time, biological interactions occurring on the microarrayed features.
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Affiliation(s)
- Radoslaw Bombera
- Chemistry for Recognition & Studies of Biological Architectures Group, Institute for Nanoscience and Cryogenics, SPrAM-UMR 5819 (CEA-CNRS-UJF Grenoble 1), CEA-Grenoble, 17 rue des Martyrs, 38054 Grenoble Cedex 9, France
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26
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Staying alive: new perspectives on cell immobilization for biosensing purposes. Anal Bioanal Chem 2011; 402:1785-97. [PMID: 21922308 DOI: 10.1007/s00216-011-5364-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2011] [Revised: 08/10/2011] [Accepted: 08/24/2011] [Indexed: 01/09/2023]
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27
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Li CY, Wood DK, Hsu CM, Bhatia SN. DNA-templated assembly of droplet-derived PEG microtissues. LAB ON A CHIP 2011; 11:2967-75. [PMID: 21776518 PMCID: PMC3399244 DOI: 10.1039/c1lc20318e] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Patterning multiple cell types is a critical step for engineering functional tissues, but few methods provide three-dimensional positioning at the cellular length scale. Here, we present a "bottom-up" approach for fabricating multicellular tissue constructs that utilizes DNA-templated assembly of 3D cell-laden hydrogel microtissues. A flow focusing-generated emulsion of photopolymerizable prepolymer is used to produce 100 μm monodisperse microtissues at a rate of 100 Hz (10(5) h(-1)). Multiple cell types, including suspension and adherently cultured cells, can be encapsulated into the microtissues with high viability (~97%). We then use a DNA coding scheme to self-assemble microtissues "bottom-up" from a template that is defined using "top-down" techniques. The microtissues are derivatized with single-stranded DNA using a biotin-streptavidin linkage to the polymer network, and are assembled by sequence-specific hybridization onto spotted DNA microarrays. Using orthogonal DNA codes, we achieve multiplexed patterning of multiple microtissue types with high binding efficiency and >90% patterning specificity. Finally, we demonstrate the ability to organize multicomponent constructs composed of epithelial and mesenchymal microtissues while preserving each cell type in a 3D microenvironment. The combination of high throughput microtissue generation with scalable surface-templated assembly offers the potential to dissect mechanisms of cell-cell interaction in three dimensions in healthy and diseased states, as well as provides a framework for templated assembly of larger structures for implantation.
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Affiliation(s)
- Cheri Y Li
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA
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28
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Xu Y, Yao H, Wang L, Xing W, Cheng J. The construction of an individually addressable cell array for selective patterning and electroporation. LAB ON A CHIP 2011; 11:2417-23. [PMID: 21625729 DOI: 10.1039/c1lc20183b] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
In basic cell biology research and drug discovery, it is important to rapidly introduce genes, proteins or drug compounds into cells without permanent damage. Here, we report a three dimensional SU-8 micro-well structure sandwiched with an indium tin oxide (ITO) electrode-covered slide from the top and an individually addressable array of microelectrodes on the bottom to allow parallel delivery of exogenous molecules into various cells in a spatially specific manner. A positive dielectrophoretic force was selectively applied by energizing appropriate electrodes to capture the dispersed cells at the bottom electrode, while the micro-wells were designed to confine cells in situ when the positive dielectrophoretic force is removed. The combination of spatial positive dielectrophoresis (pDEP) and micro-wells made it possible to construct cell microarrays with specific patterns. Once the cells become attached to the electrodes, different plasmids can be introduced sequentially for selective electroporation. The present cell arraying-assisted electroporation chip integrates a pDEP-assisted cell positioning function with selective electroporation to provide a simple and efficient method for gene transfer. This platform is ideal for high throughput screening of compounds in parallel and thus holds promise for applications in cellular and molecular research.
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Affiliation(s)
- Youchun Xu
- Medical Systems Biology Research Center, Tsinghua University, Beijing, China
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29
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Abstract
In the past decade, the tendency to move from a global, one-size-fits-all treatment philosophy to personalized medicine is based, in part, on the nuanced differences and sub-classifications of disease states. Our knowledge of these varied states stems from not only the ability to diagnose, classify, and perform experiments on cell populations as a whole, but also from new technologies that allow interrogation of cell populations at the individual cell level. Such departures from conventional thinking are driven by the recognition that clonal cell populations have numerous activities that manifest as significant levels of non-genetic heterogeneity. Clonal populations by definition originate from a single genetic origin so are regarded as having a high level of homogeneity as compared to genetically distinct cell populations. However, analysis at the single cell level has revealed a different phenomenon; cells and organisms require an inherent level of non-genetic heterogeneity to function properly, and in some cases, to survive. The growing understanding of this occurrence has lead to the development of methods to monitor, analyze, and better characterize the heterogeneity in cell populations. Following the trend of DNA- and protein microarrays, platforms capable of simultaneously monitoring each cell in a population have been developed. These cellular microarray platforms and other related formats allow for continuous monitoring of single live cells and simultaneously generate individual cell and average population data that are more descriptive and information-rich than traditional bulk methods. These technological advances have helped develop a better understanding of the intricacies associated with biological processes and afforded greater insight into complex biological systems. The associated instruments, techniques, and reagents now allow for highly multiplexed analyses, which enable multiple cellular activities, processes, or pathways to be monitored simultaneously. This critical review will discuss the paradigm shift associated with cellular heterogeneity, speak to the key developments that have lead to our better understanding of systems biology, and detail the future directions of the discipline (281 references).
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Affiliation(s)
- Maureen A Walling
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave., Albany, NY 12222, USA
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30
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Frimat JP, Becker M, Chiang YY, Marggraf U, Janasek D, Hengstler JG, Franzke J, West J. A microfluidic array with cellular valving for single cell co-culture. LAB ON A CHIP 2011; 11:231-7. [PMID: 20978708 DOI: 10.1039/c0lc00172d] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
We present a highly parallel microfluidic approach for contacting single cell pairs. The approach combines a differential fluidic resistance trapping method with a novel cellular valving principle for homotypic and heterotypic single cell co-culturing. Differential fluidic resistance was used for sequential single cell arraying, with the adhesion and flattening of viable cells within the microstructured environment acting to produce valves in the open state. Reversal of the flow was used for the sequential single cell arraying of the second cell type. Plasma stencilling, along the linear path of least resistance, was required to confine the cells within the trap regions. Prime flow conditions with minimal shear stress were identified for highly efficient cell arraying (∼99%) and long term cell culture. Larger trap dimensions enabled the highest levels of cell pairing (∼70%). The single cell co-cultures were in close proximity for the formation of connexon structures and the study of contact modes of communication. The research further highlights the possibility of using the natural behaviour of cells as the working principle behind responsive microfluidic elements.
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Affiliation(s)
- Jean-Philippe Frimat
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, D-44227, Dortmund, Germany
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31
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Bally M, Bailey K, Sugihara K, Grieshaber D, Vörös J, Städler B. Liposome and lipid bilayer arrays towards biosensing applications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2010; 6:2481-97. [PMID: 20925039 DOI: 10.1002/smll.201000644] [Citation(s) in RCA: 161] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Sensitive and selective biosensors for high-throughput screening are having an increasing impact in modern medical care. The establishment of robust protein biosensing platforms however remains challenging, especially when membrane proteins are involved. Although this type of proteins is of enormous relevance since they are considered in >60% of the pharmaceutical drug targets, their fragile nature (i.e., the requirement to preserve their natural lipid environment to avoid denaturation and loss of function) puts strong additional prerequisites onto a successful biochip. In this review, the leading approaches to create lipid membrane-based arrays towards the creation of membrane protein biosensing platforms are described. Liposomes assembled in micro- and nanoarrays and the successful set-ups containing functional membrane proteins, as well as the use of liposomes in networks, are discussed in the first part. Then, the complementary approaches to create cell-mimicking supported membrane patches on a substrate in an array format will be addressed. Finally, the progress in assembling free-standing (functional) lipid bilayers over nanopore arrays for ion channel sensing will be reported. This review illustrates the rapid pace by which advances are being made towards the creation of a heterogeneous biochip for the high-throughput screening of membrane proteins for diagnostics, drug screening, or drug discovery purposes.
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Affiliation(s)
- Marta Bally
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, Zurich, 8092, Switzerland
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32
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Harada A, Kobayashi R, Takashima Y, Hashidzume A, Yamaguchi H. Macroscopic self-assembly through molecular recognition. Nat Chem 2010; 3:34-7. [PMID: 21160514 DOI: 10.1038/nchem.893] [Citation(s) in RCA: 547] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Accepted: 09/22/2010] [Indexed: 01/29/2023]
Abstract
Molecular recognition plays an important role in nature, with perhaps the best known example being the complementarity exhibited by pairs of nucleobases in DNA. Studies of self-assembling and self-organizing systems based on molecular recognition are often performed at the molecular level, however, and any macroscopic implications of these processes are usually far removed from the specific molecular interactions. Here, we demonstrate that well-defined molecular-recognition events can be used to direct the assembly of macroscopic objects into larger aggregated structures. Acrylamide-based gels functionalized with either host (cyclodextrin) rings or small hydrocarbon-group guest moieties were synthesized. Pieces of host and guest gels are shown to adhere to one another through the mutual molecular recognition of the cyclodextrins and hydrocarbon groups on their surfaces. By changing the size and shape of the host and guest units, different gels can be selectively assembled and sorted into distinct macroscopic structures that are on the order of millimetres to centimetres in size.
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Affiliation(s)
- Akira Harada
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan.
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33
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Reisewitz S, Schroeder H, Tort N, Edwards KA, Baeumner AJ, Niemeyer CM. Capture and culturing of living cells on microstructured DNA substrates. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2010; 6:2162-2168. [PMID: 20730825 DOI: 10.1002/smll.201000776] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
A modular system for the DNA-directed immobilization of antibodies was applied to capture living cells on microstructured DNA surfaces. It is demonstrated in two different set-ups, static incubation and hydrodynamic flow, that this approach is well suited for specific capture and selection of cells from culture medium. The adhered cells show intact morphology and they can be cultivated to grow to dense monolayers, restricted to the lateral dimensions of DNA spots on the surface. Owing to the modularity of surface biofunctionalization, the system can readily be configured to serve as a matrix for adhesion and growth of different cells, as demonstrated by specific binding of human embryonic kidney cells (HEK293) and Hodgkin lymphoma L540cy cells onto patches bearing appropriate recognition moieties inside a microfluidic channel. We therefore anticipate that the systems described here should be useful for fundamental research in cell biology or applications in biomedical diagnostics, drug screening, and nanobiotechnology.
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Affiliation(s)
- Stephanie Reisewitz
- Technische Universität Dortmund, Fakultät Chemie, Biologisch-Chemische Mikrostrukturtechnik, Otto Hahn Str. 6, 44227 Dortmund, Germany
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34
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Shin YS, Ahmad H, Shi Q, Kim H, Pascal TA, Fan R, Goddard WA, Heath JR. Chemistries for patterning robust DNA microbarcodes enable multiplex assays of cytoplasm proteins from single cancer cells. Chemphyschem 2010; 11:3063-9. [PMID: 20715281 PMCID: PMC3681607 DOI: 10.1002/cphc.201000528] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Indexed: 11/12/2022]
Affiliation(s)
- Young Shik Shin
- Division of Chemistry and Chemical Engineering, Nanosystems Biology Cancer Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125 (USA), Fax: (+1)626-395-2355
- Division of Engineering and Applied Science, Bioengineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125 (USA)
| | - Habib Ahmad
- Division of Chemistry and Chemical Engineering, Nanosystems Biology Cancer Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125 (USA), Fax: (+1)626-395-2355
| | - Qihui Shi
- Division of Chemistry and Chemical Engineering, Nanosystems Biology Cancer Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125 (USA), Fax: (+1)626-395-2355
| | - Hyungjun Kim
- Graduate School of EEWS, Korea Advanced Institute of Science Technology, Daejeon, 305-701(Republic of Korea) and Materials and Process Simulation Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125 (USA)
| | - Tod A. Pascal
- Graduate School of EEWS, Korea Advanced Institute of Science Technology, Daejeon, 305-701(Republic of Korea) and Materials and Process Simulation Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125 (USA)
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, PO Box 208260, New Haven, CT 06520 (USA)
| | - William A. Goddard
- Graduate School of EEWS, Korea Advanced Institute of Science Technology, Daejeon, 305-701(Republic of Korea) and Materials and Process Simulation Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125 (USA)
| | - James R. Heath
- Division of Chemistry and Chemical Engineering, Nanosystems Biology Cancer Center, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125 (USA), Fax: (+1)626-395-2355
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35
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Niemeyer CM. Semisynthetic DNA-protein conjugates for biosensing and nanofabrication. Angew Chem Int Ed Engl 2010; 49:1200-16. [PMID: 20091721 DOI: 10.1002/anie.200904930] [Citation(s) in RCA: 300] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Conjugation with artificial nucleic acids allows proteins to be modified with a synthetically accessible, robust tag. This attachment is addressable in a highly specific manner by means of molecular recognition events, such as Watson-Crick hybridization. Such DNA-protein conjugates, with their combined properties, have a broad range of applications, such as in high-performance biomedical diagnostic assays, fundamental research on molecular recognition, and the synthesis of DNA nanostructures. This Review surveys current approaches to generate DNA-protein conjugates as well as recent advances in their applications. For example, DNA-protein conjugates have been assembled into model systems for the investigation of catalytic cascade reactions and light-harvesting devices. Such hybrid conjugates are also used for the biofunctionalization of planar surfaces for micro- and nanoarrays, and for decorating inorganic nanoparticles to enable applications in sensing, materials science, and catalysis.
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Affiliation(s)
- Christof M Niemeyer
- Technische Universität Dortmund, Fakultät Chemie, Biologisch-Chemische Mikrostrukturtechnik, Otto-Hahn Strasse 6, 44227 Dortmund, Germany.
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36
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Niemeyer C. Halbsynthetische DNA-Protein-Konjugate für Biosensorik und Nanofabrikation. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200904930] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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37
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Torisawa YS, Mosadegh B, Luker GD, Morell M, O'Shea KS, Takayama S. Microfluidic hydrodynamic cellular patterning for systematic formation of co-culture spheroids. Integr Biol (Camb) 2009; 1:649-54. [PMID: 20027373 DOI: 10.1039/b915965g] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This paper describes a microfluidic method to form co-culture spheroids of various geometries and compositions in order to manipulate cell-cell interaction dynamics. The cellular patterning is performed in a two-layered microfluidic device that sandwiches a semi-porous membrane so that flow occurs from the top channel through the membrane to the bottom channel. Arbitrary cellular arrangements are enabled by regulating the geometric features of the bottom channel so that as culture media drains, the flow hydrodynamically focuses (aggregates) cells onto the membrane only over the regions of the bottom channel. Furthermore, when the top channel has multiple inlets, cells can be seeded in adjacent laminar streams, allowing different cell types to be patterned simultaneously in well defined spatial arrangements. Interestingly, the initial cell positioning of certain cell types can result in two juxtaposed non-concentric "Janus" spheroids, rather than homogeneous mixtures or layered shell structures. Therefore, the initial position of cells prior to aggregation can influence the final configuration within a co-culture spheroid. When Janus spheroids were constructed from mouse embryonic stem (mES) cells and hepatocytes, the mES cells differentiated in a spatially distinct pattern dictated by the position of the hepatocytes. This contrasts with uniform mES differentiation observed when co-culture spheroids are formed by the conventional method of randomly mixing the two cell types. This cellular patterning method opens new possibilities for understanding and manipulating interactions between different cell types in 3D.
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Affiliation(s)
- Yu-suke Torisawa
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
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38
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Shi J, Ahmed D, Mao X, Lin SCS, Lawit A, Huang TJ. Acoustic tweezers: patterning cells and microparticles using standing surface acoustic waves (SSAW). LAB ON A CHIP 2009; 9:2890-5. [PMID: 19789740 DOI: 10.1039/b910595f] [Citation(s) in RCA: 346] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Here we present an active patterning technique named "acoustic tweezers" that utilizes standing surface acoustic wave (SSAW) to manipulate and pattern cells and microparticles. This technique is capable of patterning cells and microparticles regardless of shape, size, charge or polarity. Its power intensity, approximately 5x10(5) times lower than that of optical tweezers, compares favorably with those of other active patterning methods. Flow cytometry studies have revealed it to be non-invasive. The aforementioned advantages, along with this technique's simple design and ability to be miniaturized, render the "acoustic tweezers" technique a promising tool for various applications in biology, chemistry, engineering, and materials science.
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Affiliation(s)
- Jinjie Shi
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802, USA
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39
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Liu P, Mathies RA. Integrated microfluidic systems for high-performance genetic analysis. Trends Biotechnol 2009; 27:572-81. [DOI: 10.1016/j.tibtech.2009.07.002] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Revised: 06/30/2009] [Accepted: 07/02/2009] [Indexed: 01/09/2023]
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40
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Douglas ES, Hsiao SC, Onoe H, Bertozzi CR, Francis MB, Mathies RA. DNA-barcode directed capture and electrochemical metabolic analysis of single mammalian cells on a microelectrode array. LAB ON A CHIP 2009; 9:2010-5. [PMID: 19568668 PMCID: PMC2892333 DOI: 10.1039/b821690h] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
A microdevice is developed for DNA-barcode directed capture of single cells on an array of pH-sensitive microelectrodes for metabolic analysis. Cells are modified with membrane-bound single-stranded DNA, and specific single-cell capture is directed by the complementary strand bound in the sensor area of the iridium oxide pH microelectrodes within a microfluidic channel. This bifunctional microelectrode array is demonstrated for the pH monitoring and differentiation of primary T cells and Jurkat T lymphoma cells. Single Jurkat cells exhibited an extracellular acidification rate of 11 milli-pH min(-1), while primary T cells exhibited only 2 milli-pH min(-1). This system can be used to capture non-adherent cells specifically and to discriminate between visually similar healthy and cancerous cells in a heterogeneous ensemble based on their altered metabolic properties.
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Affiliation(s)
- Erik S Douglas
- UCSF/UC Berkeley Joint Graduate Group in Bioengineering, University of California, Berkeley, California 94720, USA.
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41
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Bailey K, Bally M, Leifert W, Vörös J, McMurchie T. G-protein coupled receptor array technologies: site directed immobilisation of liposomes containing the H1-histamine or M2-muscarinic receptors. Proteomics 2009; 9:2052-63. [PMID: 19337994 DOI: 10.1002/pmic.200800539] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This paper describes a novel strategy to create a microarray of G-protein coupled receptors (GPCRs), an important group of membrane proteins both physiologically and pharmacologically. The H(1)-histamine receptor and the M(2)-muscarinic receptor were both used as model GPCRs in this study. The receptor proteins were embedded in liposomes created from the cellular membrane extracts of Spodoptera frugiperda (Sf9) insect cell culture line with its accompanying baculovirus protein insert used for overexpression of the receptors. Once captured onto a surface these liposomes provide a favourable lipidic environment for the integral membrane proteins. Site directed immobilisation of these liposomes was achieved by introduction of cholesterol-modified oligonucleotides (oligos). These oligo/cholesterol conjugates incorporate within the lipid bilayer and were captured by the complementary oligo strand exposed on the surface. Sequence specific immobilisation was demonstrated using a quartz crystal microbalance with dissipation (QCM-D). Confirmatory results were also obtained by monitoring fluorescent ligand binding to GPCRs captured on a spotted oligo microarray using Confocal Laser Scanning Microscopy and the Zepto-READER microarray imaging system. Sequence specific immobilisation of such biologically important membrane proteins could lead to the development of a heterogeneous self-sorting liposome array of GPCRs which would underpin a variety of future novel applications.
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Affiliation(s)
- Kelly Bailey
- CSIRO Molecular and Health Technologies, Adelaide, SA, Australia.
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42
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Woodrow KA, Wood MJ, Saucier-Sawyer JK, Solbrig C, Saltzman WM. Biodegradable meshes printed with extracellular matrix proteins support micropatterned hepatocyte cultures. Tissue Eng Part A 2009; 15:1169-79. [PMID: 19072719 DOI: 10.1089/ten.tea.2008.0265] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The spatial organization of cells of different phenotypes is an important and often defining determinant of tissue function. In tissue engineering, which attempts to rebuild functional tissues from cellular and synthetic components, spatial patterning of cells onto biomaterials is likely to be equally important. We have printed combinatorial arrays of extracellular matrix (ECM) and screened them for attachment by HepG2 hepatocytes, LX-2 hepatic stellate cells, primary portal fibroblasts, and bovine aortic endothelial cells-cells selected as representative phenotypes found in adult liver. Differential cell attachment to the underlying matrix proteins allowed us to establish two-dimensional co-cultures of HepG2 with these non-parenchymal cell types. These general approaches were then translated to tissue engineering scaffolds where deposition of ECM proteins onto electrospun polylactide meshes resulted in patterned HepG2 cultures. We observed that the spatial organization of fibronectin deposits influenced HepG2 attachment and the establishment of co-cultures on our arrays. These micropatterned co-culture systems should serve as valuable tools for studying the soluble and insoluble signals involved in liver development, function, and disease.
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Affiliation(s)
- Kim A Woodrow
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, USA
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Schröder H, Hoffmann L, Müller J, Alhorn P, Fleger M, Neyer A, Niemeyer CM. Addressable microfluidic polymer chip for DNA-directed immobilization of oligonucleotide-tagged compounds. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2009; 5:1547-1552. [PMID: 19326353 DOI: 10.1002/smll.200801016] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A microfluidic polymer chip for the self-assembly of DNA conjugates through DNA-directed immobilization is developed. The chip is fabricated from two parts, one of which contains a microfluidic channel produced from poly(dimethylsiloxane) (PDMS) by replica-casting technique using a mold prepared by photolithographic techniques. The microfluidic part is sealed by covalent bonding with a chemically activated glass slide containing a DNA oligonucleotide microarray. The dimension of the PDMS-glass microfluidic chip is equivalent to standard microscope slides (76 x 26 mm(2)). The DNA microarray surface inside the microfluidic channels is configured through conventional spotting, and the resulting DNA patches can be conveniently addressed with compounds containing complementary DNA tags. To demonstrate the utility of the addressable surface within the microfluidic channel, DNA-directed immobilization (DDI) of DNA-modified gold nanoparticles (AuNPs) and DNA-conjugates of the enzymes glucose oxidase (GOx) and horseradish peroxidase (HRP) are carried out. DDI of AuNPs is used to demonstrate site selectivity and reversibility of the surface-modification process. In the case of the DNA-enzyme conjugates, the patterned assembly of the two enzymes allows the establishment and investigation of the coupled reaction of GOx and HRP, with particular emphasis on surface coverage and lateral flow rates. The results demonstrate that this addressable chip is well suited for the generation of fluidically coupled multi-enzyme microreactors.
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Affiliation(s)
- Hendrik Schröder
- Technische Universität Dortmund, Fakultät Chemie Biologisch-Chemische Mikrostrukturtechnik, Otto Hahn Str. 6, 44227 Dortmund, Germany
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Renberg B, Sato K, Mawatari K, Idota N, Tsukahara T, Kitamori T. Serial DNA immobilization in micro- and extended nanospace channels. LAB ON A CHIP 2009; 9:1517-23. [PMID: 19458857 DOI: 10.1039/b823436a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
That focused arrays, even with a small set of ligands, provide more data than single point experiments is well established in the DNA microarray research field, but microarray technology has yet to be transferred to fused silica microchips. Fused silica microchips have several attractive features such as stability to pressure, solvents, acids and bases, and can be fabricated with minute dimensions, making them good candidates for nanofluidic research. However, due to harsh bonding conditions, DNA ligands must be immobilized after fabrication, thus preventing standard microarray spotting techniques from being used. In this paper, we provide tools for serial DNA immobilization in fused silica microchips using UV. We report the synthesis of a new UV-linker which was used to covalently couple functional DNA oligos to the inside of channels in fused silica microchips. With some simple modifications to our mask aligner, we were able to transfer OHP mask patterns, which allows the creation of basically any pattern in the channels. The functionality of the oligos was measured through the binding of fluorophore-labeled complementary target oligos. We examined parameters influencing DNA immobilization, and carry-over between spots after consecutive immobilizations inside the same channel. We also report the first successful multiple immobilizations of functional DNA oligos inside single channels of extended nanospace depth (460 nm).
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Affiliation(s)
- Björn Renberg
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo, Tokyo 113-8656, Japan
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Integrated microfluidic bioprocessor for single-cell gene expression analysis. Proc Natl Acad Sci U S A 2008; 105:20173-8. [PMID: 19075237 DOI: 10.1073/pnas.0806355106] [Citation(s) in RCA: 166] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An integrated microdevice is developed for the analysis of gene expression in single cells. The system captures a single cell, transcribes and amplifies the mRNA, and quantitatively analyzes the products of interest. The key components of the microdevice include integrated nanoliter metering pumps, a 200-nL RT-PCR reactor with a single-cell capture pad, and an affinity capture matrix for the purification and concentration of products that is coupled to a microfabricated capillary electrophoresis separation channel for product analysis. Efficient microchip integration of these processes enables the sensitive and quantitative examination of gene expression variation at the single-cell level. This microdevice is used to measure siRNA knockdown of the GAPDH gene in individual Jurkat cells. Single-cell measurements suggests the presence of 2 distinct populations of cells with moderate (approximately 50%) or complete (approximately 0%) silencing. This stochastic variation in gene expression and silencing within single cells is masked by conventional bulk measurements.
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Hsiao S, Crow A, Lam W, Bertozzi C, Fletcher D, Francis M. DNA-Coated AFM Cantilevers for the Investigation of Cell Adhesion and the Patterning of Live Cells. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200802525] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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47
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Hsiao SC, Crow AK, Lam WA, Bertozzi CR, Fletcher DA, Francis MB. DNA-coated AFM cantilevers for the investigation of cell adhesion and the patterning of live cells. Angew Chem Int Ed Engl 2008; 47:8473-7. [PMID: 18798192 PMCID: PMC2748828 DOI: 10.1002/anie.200802525] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Measurement of receptor adhesion strength requires the precise manipulation of single cells on a contact surface. To attach live cells to a moveable probe, DNA sequences complementary to strands displayed on the plasma membrane are introduced onto AFM cantilevers (see picture, bp=base pairs). The strength of the resulting linkages can be tuned by varying the length of DNA strands, allowing for controlled transport of the cells
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Affiliation(s)
- Sonny C Hsiao
- Department of Chemistry, University of California, Berkeley
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