1
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Du J, Kong Y, Wen Y, Shen E, Xing H. HUH Endonuclease: A Sequence-specific Fusion Protein Tag for Precise DNA-Protein Conjugation. Bioorg Chem 2024; 144:107118. [PMID: 38330720 DOI: 10.1016/j.bioorg.2024.107118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 01/01/2024] [Accepted: 01/09/2024] [Indexed: 02/10/2024]
Abstract
Synthetic DNA-protein conjugates have found widespread applications in diagnostics and therapeutics, prompting a growing interest in developing chemical biology methodologies for the precise and site-specific preparation of covalent DNA-protein conjugates. In this review article, we concentrate on techniques to achieve precise control over the structural and site-specific aspects of DNA-protein conjugates. We summarize conventional methods involving unnatural amino acids and self-labeling proteins, accompanied by a discussion of their potential limitations. Our primary focus is on introducing HUH endonuclease as a novel generation of fusion protein tags for DNA-protein conjugate preparation. The detailed conjugation mechanisms and structures of representative endonucleases are surveyed, showcasing their advantages as fusion protein tag in sequence selectivity, biological orthogonality, and no requirement for DNA modification. Additionally, we present the burgeoning applications of HUH-tag-based DNA-protein conjugates in protein assembly, biosensing, and gene editing. Furthermore, we delve into the future research directions of the HUH-tag, highlighting its significant potential for applications in the biomedical and DNA nanotechnology fields.
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Affiliation(s)
- Jiajun Du
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, School of Chemistry and Chemical Engineering Hunan University Changsha, Hunan 410082, PR China
| | - Yuhan Kong
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, School of Chemistry and Chemical Engineering Hunan University Changsha, Hunan 410082, PR China
| | - Yujian Wen
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, School of Chemistry and Chemical Engineering Hunan University Changsha, Hunan 410082, PR China
| | - Enxi Shen
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, School of Chemistry and Chemical Engineering Hunan University Changsha, Hunan 410082, PR China
| | - Hang Xing
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, School of Chemistry and Chemical Engineering Hunan University Changsha, Hunan 410082, PR China.
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2
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Komiya E, Takamatsu S, Miura D, Tsukakoshi K, Tsugawa W, Sode K, Ikebukuro K, Asano R. Exploration and Application of DNA-Binding Proteins to Make a Versatile DNA-Protein Covalent-Linking Patch (D-Pclip): The Case of a Biosensing Element. J Am Chem Soc 2024; 146:4087-4097. [PMID: 38295327 PMCID: PMC10870700 DOI: 10.1021/jacs.3c12668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/06/2024] [Accepted: 01/08/2024] [Indexed: 02/02/2024]
Abstract
DNA-protein complexes are attractive components with broad applications in various research fields, such as DNA aptamer-enzyme complexes as biosensing elements. However, noncovalent DNA-protein complexes often decrease detection sensitivity because they are highly susceptible to environmental conditions. In this study, we developed a versatile DNA-protein covalent-linking patch (D-Pclip) for fabricating covalent and stoichiometric DNA-protein complexes. We comprehensively explored the database to determine the DNA-binding ability of the candidates and selected UdgX as the only uracil-DNA glycosylase known to form covalent bonds with DNA via uracil, with a binding efficiency >90%. We integrated a SpyTag/SpyCatcher protein-coupling system into UdgX to create a universal and convenient D-Pclip. The usability of D-Pclip was shown by preparing a stoichiometric model complex of a hemoglobin (Hb)-binding aptamer and glucose oxidase (GOx) by mixing at 4 °C. The prepared aptamer-GOx complexes detected Hb in a dose-dependent manner within the clinically required detection range in buffer and human serum without any washing procedures. D-Pclip covalently connects any uracil-inserted DNA sequence and any SpyCatcher-fused protein stoichiometrically; therefore, it has a high potential for various applications.
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Affiliation(s)
- Erika Komiya
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Shouhei Takamatsu
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Daimei Miura
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kaori Tsukakoshi
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Wakako Tsugawa
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Koji Sode
- Joint
Department of Biomedical Engineering, University
of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, North Carolina 27599, United States
- Institute
of Global Innovation Research, Tokyo University
of Agriculture and Technology, 3-8-1 Harumi-cho, Fuchu, Tokyo 183-8509, Japan
| | - Kazunori Ikebukuro
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Ryutaro Asano
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
- Institute
of Global Innovation Research, Tokyo University
of Agriculture and Technology, 3-8-1 Harumi-cho, Fuchu, Tokyo 183-8509, Japan
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3
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Feng L, Li J, Sun J, Wang L, Fan C, Shen J. Recent Advances of DNA Nanostructure-Based Cell Membrane Engineering. Adv Healthc Mater 2021; 10:e2001718. [PMID: 33458966 DOI: 10.1002/adhm.202001718] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/20/2020] [Indexed: 01/30/2023]
Abstract
Materials that can regulate the composition and structure of the cell membrane to fabricate engineered cells with defined functions are in high demand. Compared with other biomolecules, DNA has unique advantages in cell membrane engineering due to its excellent programmability and biocompatibility. Especially, the near-atomic scale precision of DNA nanostructures facilitates the investigation of structure-property relations on the cell membrane. In this review, first the state of the art of functional DNA nanostructures is summarized, and then the overview of the use of DNA nanostructures to engineer the cell membrane is presented. Subsequently, applications of DNA nanostructures in modifying cell membrane morphology, controlling ions transport, and synthesizing high precise liposomes are highlighted. Finally, the challenges and outlook on using DNA nanostructures for cell membrane engineering are discussed.
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Affiliation(s)
- Lingyu Feng
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Jiang Li
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
- University of Chinese Academy of Sciences Beijing 100049 China
- Bioimaging Center Shanghai Synchrotron Radiation Facility Zhangjiang Laboratory Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai 201210 China
| | - Jielin Sun
- Key Laboratory of Systems Biomedicine (Ministry of Education) Shanghai Center for Systems Biomedicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Lihua Wang
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
- University of Chinese Academy of Sciences Beijing 100049 China
- Bioimaging Center Shanghai Synchrotron Radiation Facility Zhangjiang Laboratory Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai 201210 China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Jianlei Shen
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
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4
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Zhao D, Kong Y, Zhao S, Xing H. Engineering Functional DNA–Protein Conjugates for Biosensing, Biomedical, and Nanoassembly Applications. Top Curr Chem (Cham) 2020; 378:41. [DOI: 10.1007/s41061-020-00305-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 05/05/2020] [Indexed: 12/31/2022]
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5
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Stasińska AR, Putaj P, Chmielewski MK. Disulfide bridge as a linker in nucleic acids' bioconjugation. Part II: A summary of practical applications. Bioorg Chem 2019; 95:103518. [PMID: 31911308 DOI: 10.1016/j.bioorg.2019.103518] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/11/2019] [Accepted: 12/16/2019] [Indexed: 12/15/2022]
Abstract
Disulfide conjugation invariably remains a key tool in research on nucleic acids. This versatile and cost-effective method plays a crucial role in structural studies of DNA and RNA as well as their interactions with other macromolecules in a variety of biological systems. In this article we review applications of disulfide-bridged conjugates of oligonucleotides with other (bio)molecules such as peptides, proteins etc. and present key findings obtained with their help.
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Affiliation(s)
- Anna R Stasińska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Noskowskiego 12/14, 61-704 Poznań, Poland; FutureSynthesis sp. z o.o. ul. Rubież 46H, 61-612 Poznań, Poland
| | - Piotr Putaj
- FutureSynthesis sp. z o.o. ul. Rubież 46H, 61-612 Poznań, Poland
| | - Marcin K Chmielewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Noskowskiego 12/14, 61-704 Poznań, Poland; FutureSynthesis sp. z o.o. ul. Rubież 46H, 61-612 Poznań, Poland.
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6
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Stasińska AR, Putaj P, Chmielewski MK. Disulfide bridge as a linker in nucleic acids’ bioconjugation. Part I: An overview of synthetic strategies. Bioorg Chem 2019; 92:103223. [DOI: 10.1016/j.bioorg.2019.103223] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/26/2019] [Accepted: 08/26/2019] [Indexed: 12/23/2022]
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7
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Jaekel A, Stegemann P, Saccà B. Manipulating Enzymes Properties with DNA Nanostructures. Molecules 2019; 24:molecules24203694. [PMID: 31615123 PMCID: PMC6832416 DOI: 10.3390/molecules24203694] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/10/2019] [Accepted: 10/11/2019] [Indexed: 12/12/2022] Open
Abstract
Nucleic acids and proteins are two major classes of biopolymers in living systems. Whereas nucleic acids are characterized by robust molecular recognition properties, essential for the reliable storage and transmission of the genetic information, the variability of structures displayed by proteins and their adaptability to the environment make them ideal functional materials. One of the major goals of DNA nanotechnology-and indeed its initial motivation-is to bridge these two worlds in a rational fashion. Combining the predictable base-pairing rule of DNA with chemical conjugation strategies and modern protein engineering methods has enabled the realization of complex DNA-protein architectures with programmable structural features and intriguing functionalities. In this review, we will focus on a special class of biohybrid structures, characterized by one or many enzyme molecules linked to a DNA scaffold with nanometer-scale precision. After an initial survey of the most important methods for coupling DNA oligomers to proteins, we will report the strategies adopted until now for organizing these conjugates in a predictable spatial arrangement. The major focus of this review will be on the consequences of such manipulations on the binding and kinetic properties of single enzymes and enzyme complexes: an interesting aspect of artificial DNA-enzyme hybrids, often reported in the literature, however, not yet entirely understood and whose full comprehension may open the way to new opportunities in protein science.
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Affiliation(s)
- Andreas Jaekel
- ZMB, University Duisburg-Essen, Universitätstraße 2, 45117 Essen, Germany.
| | - Pierre Stegemann
- ZMB, University Duisburg-Essen, Universitätstraße 2, 45117 Essen, Germany.
| | - Barbara Saccà
- ZMB, University Duisburg-Essen, Universitätstraße 2, 45117 Essen, Germany.
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8
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Abstract
Proteins are a class of nanoscale building block with remarkable chemical complexity and sophistication: their diverse functions, shapes, and symmetry as well as atomically monodisperse structures far surpass the range of conventional nanoparticles that can be accessed synthetically. The chemical topologies of proteins that drive their assembly into materials are central to their functions in nature. However, despite the importance of protein materials in biology, efforts to harness these building blocks synthetically to engineer new materials have been impeded by the chemical complexity of protein surfaces, making it difficult to reliably design protein building blocks that can be robustly transformed into targeted materials. Here we describe our work aimed at exploiting a simple but important concept: if one could exchange complex protein-protein interactions with well-defined and programmable DNA-DNA interactions, one could control the assembly of proteins into structurally well-defined oligomeric and polymeric materials and three-dimensional crystals. As a class of nanoscale building block, proteins with surface DNA modifications have a vast design space that exceeds what is practically and conceptually possible with their inorganic counterparts: the sequences of the DNA and protein and the chemical nature and position of DNA attachment all play roles in dictating the assembly behavior of protein-DNA conjugates. We summarize how each of these design parameters can influence structural outcome, beginning with proteins with a single surface DNA modification, where energy barriers between protein monomers can be tuned through the sequence and secondary structure of the oligonucleotide. We then explore challenges and progress in designing directional interactions and valency on protein surfaces. The directional binding properties of protein-DNA conjugates are ultimately imposed by the amino acid sequence of the protein, which defines the spatial distribution of DNA modification sites on the protein. Through careful design and mutagenesis, bivalent building blocks that bind directionally to form one-dimensional assemblies can be realized. Finally, we discuss the assembly of proteins densely modified with DNA into crystalline superlattices. At first glance, these protein building blocks display crystallization behavior remarkably similar to that of their DNA-functionalized inorganic nanoparticle counterparts, which allows design principles elucidated for DNA-guided nanoparticle crystallization to be used as predictive tools in determining structural outcomes in protein systems. Proteins additionally offer design handles that nanoparticles do not: unlike nanoparticles, the number and spatial distribution of DNA can be controlled through the protein sequence and DNA modification chemistry. Changing the spatial distributions of DNA can drive otherwise identical proteins down distinct crystallization pathways and yield building blocks with exotic distributions of DNA that crystallize into structures that are not yet attainable using isotropically functionalized particles. We highlight challenges in accessing other classes of architectures and establishing general design rules for DNA-mediated protein assembly. Harnessing surface DNA modifications to build protein materials creates many opportunities to realize new architectures and answer fundamental questions about DNA-modified nanostructures in both materials and biological contexts. Proteins with surface DNA modifications are a powerful class of nanomaterial building blocks for which the DNA and protein sequences and the nature of their conjugation dictate the material structure.
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9
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Eradication of Human Immunodeficiency Virus Type-1 (HIV-1)-Infected Cells. Pharmaceutics 2019; 11:pharmaceutics11060255. [PMID: 31159417 PMCID: PMC6631149 DOI: 10.3390/pharmaceutics11060255] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/01/2019] [Accepted: 05/24/2019] [Indexed: 01/04/2023] Open
Abstract
Predictions made soon after the introduction of human immunodeficiency virus type-1 (HIV-1) protease inhibitors about potentially eradicating the cellular reservoirs of HIV-1 in infected individuals were too optimistic. The ability of the HIV-1 genome to remain in the chromosomes of resting CD4+ T cells and macrophages without being expressed (HIV-1 latency) has prompted studies to activate the cells in the hopes that the immune system can recognize and clear these cells. The absence of natural clearance of latently infected cells has led to the recognition that additional interventions are necessary. Here, we review the potential of utilizing suicide gene therapy to kill infected cells, excising the chromosome-integrated HIV-1 DNA, and targeting cytotoxic liposomes to latency-reversed HIV-1-infected cells.
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10
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Aviñó A, Unzueta U, Virtudes Céspedes M, Casanova I, Vázquez E, Villaverde A, Mangues R, Eritja R. Efficient bioactive oligonucleotide-protein conjugation for cell-targeted cancer therapy. ChemistryOpen 2019; 8:382-387. [PMID: 30976478 PMCID: PMC6437810 DOI: 10.1002/open.201900038] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 02/14/2019] [Indexed: 11/11/2022] Open
Abstract
Oligonucleotide-protein conjugates have important applications in biomedicine. Simple and efficient methods are described for the preparation of these conjugates. Specifically, we describe a new method in which a bifunctional linker is attached to thiol-oligonucleotide to generate a reactive intermediate that is used to link to the protein. Having similar conjugation efficacy compared with the classical method in which the bifunctional linker is attached first to the protein, this new approach produces significantly more active conjugates with higher batch to batch reproducibility. In a second approach, direct conjugation is proposed using oligonucleotides carrying carboxyl groups. These methodologies have been applied to prepare nanoconjugates of an engineered nanoparticle protein carrying a T22 peptide with affinity for the CXCR4 chemokine receptor and oligomers of the antiproliferative nucleotide 2'-deoxy-5-fluorouridine in a very efficient way. The protocols have potential uses for the functionalization of proteins, amino-containing polymers or amino-lipids in order to produce complex therapeutic nucleic acid delivery systems.
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Affiliation(s)
- Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC)Spanish Council for Scientific Research (CSIC)Jordi Girona 18–2608034BarcelonaSpain
- Networking Center on BioengineeringBiomaterials and Nanomedicine (CIBER-BBN)
| | - Ugutz Unzueta
- Networking Center on BioengineeringBiomaterials and Nanomedicine (CIBER-BBN)
- Institut d'Investigacions Biomèdiques Sant Pau and Josep Carreras Resarch InstituteHospital de Santa Creu i Sant Pau08025BarcelonaSpain
| | - María Virtudes Céspedes
- Networking Center on BioengineeringBiomaterials and Nanomedicine (CIBER-BBN)
- Institut d'Investigacions Biomèdiques Sant Pau and Josep Carreras Resarch InstituteHospital de Santa Creu i Sant Pau08025BarcelonaSpain
| | - Isolda Casanova
- Networking Center on BioengineeringBiomaterials and Nanomedicine (CIBER-BBN)
- Institut d'Investigacions Biomèdiques Sant Pau and Josep Carreras Resarch InstituteHospital de Santa Creu i Sant Pau08025BarcelonaSpain
| | - Esther Vázquez
- Networking Center on BioengineeringBiomaterials and Nanomedicine (CIBER-BBN)
- Institut de Biotecnologia i de BiomedicinaUniversitat Autònoma de Barcelona08193BellaterraSpain
- Departament de Genètica i de MicrobiologiaUniversitat Autònoma de Barcelona08193BellaterraSpain
| | - Antonio Villaverde
- Networking Center on BioengineeringBiomaterials and Nanomedicine (CIBER-BBN)
- Institut de Biotecnologia i de BiomedicinaUniversitat Autònoma de Barcelona08193BellaterraSpain
- Departament de Genètica i de MicrobiologiaUniversitat Autònoma de Barcelona08193BellaterraSpain
| | - Ramon Mangues
- Networking Center on BioengineeringBiomaterials and Nanomedicine (CIBER-BBN)
- Institut d'Investigacions Biomèdiques Sant Pau and Josep Carreras Resarch InstituteHospital de Santa Creu i Sant Pau08025BarcelonaSpain
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC)Spanish Council for Scientific Research (CSIC)Jordi Girona 18–2608034BarcelonaSpain
- Networking Center on BioengineeringBiomaterials and Nanomedicine (CIBER-BBN)
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11
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Chu CC, Silverman SK. Assessing histidine tags for recruiting deoxyribozymes to catalyze peptide and protein modification reactions. Org Biomol Chem 2018; 14:4697-703. [PMID: 27138704 DOI: 10.1039/c6ob00716c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We evaluate the ability of hexahistidine (His6) tags on peptide and protein substrates to recruit deoxyribozymes for modifying those substrates. For two different deoxyribozymes, one that creates tyrosine-RNA nucleopeptides and another that phosphorylates tyrosine side chains, we find substantial improvements in yield, kobs, and Km for peptide substrates due to recruiting by His6/Cu(2+). However, the recruiting benefits of the histidine tag are not observed for larger protein substrates, likely because the tested deoxyribozymes either cannot access the target peptide segments or cannot function when these segments are presented in a structured protein context.
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Affiliation(s)
- Chih-Chi Chu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.
| | - Scott K Silverman
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.
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12
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Bernardinelli G, Högberg B. Entirely enzymatic nanofabrication of DNA-protein conjugates. Nucleic Acids Res 2017; 45:e160. [PMID: 28977490 PMCID: PMC5737863 DOI: 10.1093/nar/gkx707] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/14/2017] [Indexed: 12/22/2022] Open
Abstract
While proteins are highly biochemically competent, DNA offers the ability to program, both reactions and the assembly of nanostructures, with a control that is unprecedented by any other molecule. Their joining: DNA–protein conjugates - offer the ability to combine the programmability of DNA with the competence of proteins to form novel tools enabling exquisite molecular control and the highest biological activity in one structure. However, in order for tools like these to become viable for biological applications, their production must be scalable, and an entirely enzymatic process is one way to achieve this. Here, we present a step in this direction: enzymatic production of DNA–protein conjugates using a new self-labeling tag derived from a truncated VirD2 protein of Agrobacterium tumefaciens. Using our previously reported MOSIC method for enzymatic ssDNA oligo production, we outline a pipeline for protein–DNA conjugates without the need for any synthetic chemistry in a one-pot reaction. Further, we validate HER2 staining using a completely enzymatically produced probe, enable the decoration of cell membranes and control of genetic expression. Establishing a method where protein–DNA conjugates can be made entirely using biological or enzymatic processing, opens a path to harvest these structures directly from bacteria and ultimately in-vivo assembly.
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Affiliation(s)
- Giulio Bernardinelli
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17 177 Stockholm, Sweden
| | - Björn Högberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17 177 Stockholm, Sweden
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13
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Schwizer F, Okamoto Y, Heinisch T, Gu Y, Pellizzoni MM, Lebrun V, Reuter R, Köhler V, Lewis JC, Ward TR. Artificial Metalloenzymes: Reaction Scope and Optimization Strategies. Chem Rev 2017; 118:142-231. [PMID: 28714313 DOI: 10.1021/acs.chemrev.7b00014] [Citation(s) in RCA: 490] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The incorporation of a synthetic, catalytically competent metallocofactor into a protein scaffold to generate an artificial metalloenzyme (ArM) has been explored since the late 1970's. Progress in the ensuing years was limited by the tools available for both organometallic synthesis and protein engineering. Advances in both of these areas, combined with increased appreciation of the potential benefits of combining attractive features of both homogeneous catalysis and enzymatic catalysis, led to a resurgence of interest in ArMs starting in the early 2000's. Perhaps the most intriguing of potential ArM properties is their ability to endow homogeneous catalysts with a genetic memory. Indeed, incorporating a homogeneous catalyst into a genetically encoded scaffold offers the opportunity to improve ArM performance by directed evolution. This capability could, in turn, lead to improvements in ArM efficiency similar to those obtained for natural enzymes, providing systems suitable for practical applications and greater insight into the role of second coordination sphere interactions in organometallic catalysis. Since its renaissance in the early 2000's, different aspects of artificial metalloenzymes have been extensively reviewed and highlighted. Our intent is to provide a comprehensive overview of all work in the field up to December 2016, organized according to reaction class. Because of the wide range of non-natural reactions catalyzed by ArMs, this was done using a functional-group transformation classification. The review begins with a summary of the proteins and the anchoring strategies used to date for the creation of ArMs, followed by a historical perspective. Then follows a summary of the reactions catalyzed by ArMs and a concluding critical outlook. This analysis allows for comparison of similar reactions catalyzed by ArMs constructed using different metallocofactor anchoring strategies, cofactors, protein scaffolds, and mutagenesis strategies. These data will be used to construct a searchable Web site on ArMs that will be updated regularly by the authors.
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Affiliation(s)
- Fabian Schwizer
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Yasunori Okamoto
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Tillmann Heinisch
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Yifan Gu
- Searle Chemistry Laboratory, University of Chicago , 5735 S. Ellis Ave., Chicago, Illinois 60637, United States
| | - Michela M Pellizzoni
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Vincent Lebrun
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Raphael Reuter
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Valentin Köhler
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
| | - Jared C Lewis
- Searle Chemistry Laboratory, University of Chicago , 5735 S. Ellis Ave., Chicago, Illinois 60637, United States
| | - Thomas R Ward
- Department of Chemistry, Spitalstrasse 51, University of Basel , CH-4056 Basel, Switzerland
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14
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Chu CC, Wong OY, Silverman SK. A generalizable DNA-catalyzed approach to peptide-nucleic acid conjugation. Chembiochem 2014; 15:1905-10. [PMID: 25056930 DOI: 10.1002/cbic.201402255] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Indexed: 01/11/2023]
Abstract
We report DNA catalysts (deoxyribozymes) that join tyrosine-containing peptides to RNA and DNA in one step and without requiring protecting groups on either the peptide or the nucleic acid. Our previous efforts towards this goal required tethering the peptide to a DNA anchor oligonucleotide. Here, we established direct in vitro selection for deoxyribozymes that use untethered, free peptide substrates. This approach enables imposition of selection pressure via reduced peptide concentration and leads to preparatively useful lower apparent Km values of ∼100 μM peptide. Use of phosphorimidazolide (Imp) rather than triphosphate as the electrophile enables reactivity of either terminus (5' or 3') of both RNA and DNA. Our findings establish a generalizable means of joining unprotected peptide to nucleic acid in one step by using DNA catalysts identified by in vitro selection.
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Affiliation(s)
- Chih-Chi Chu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801 (USA)
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15
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Template-directed covalent conjugation of DNA to native antibodies, transferrin and other metal-binding proteins. Nat Chem 2014; 6:804-9. [PMID: 25143216 DOI: 10.1038/nchem.2003] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 06/11/2014] [Indexed: 12/20/2022]
Abstract
DNA-protein conjugates are important in bioanalytical chemistry, molecular diagnostics and bionanotechnology, as the DNA provides a unique handle to identify, functionalize or otherwise manipulate proteins. To maintain protein activity, conjugation of a single DNA handle to a specific location on the protein is often needed. However, preparing such high-quality site-specific conjugates often requires genetically engineered proteins, which is a laborious and technically challenging approach. Here we demonstrate a simpler method to create site-selective DNA-protein conjugates. Using a guiding DNA strand modified with a metal-binding functionality, we directed a second DNA strand to the vicinity of a metal-binding site of His6-tagged or wild-type metal-binding proteins, such as serotransferrin, where it subsequently reacted with lysine residues at that site. This method, DNA-templated protein conjugation, facilitates the production of site-selective protein conjugates, and also conjugation to IgG1 antibodies via a histidine cluster in the constant domain.
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16
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Lu Y, Huang F, Wang J, Xia J. Affinity-Guided Covalent Conjugation Reactions Based on PDZ–Peptide and SH3–Peptide Interactions. Bioconjug Chem 2014; 25:989-99. [DOI: 10.1021/bc500134w] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Yao Lu
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Feng Huang
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Jianpeng Wang
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Jiang Xia
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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17
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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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18
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Wang J, Yu Y, Xia J. Short peptide tag for covalent protein labeling based on coiled coils. Bioconjug Chem 2013; 25:178-87. [PMID: 24341800 DOI: 10.1021/bc400498p] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
To label proteins covalently, one faces a trade-off between labeling a protein specifically and using a small tag. Often one must compromise one parameter for the other or use additional components, such as an enzyme, to satisfy both requirements. Here, we report a new reaction that covalently labels proteins by using engineered coiled-coil peptides. Harnessing the concept of "proximity-induced reactivity", the 21-amino-acid three-heptad peptides CCE/CCK were modified with a nucleophilic cysteine and an α-chloroacetyl group at selected positions. When pairs of coiled coils associated, an irreversible covalent bond spontaneously formed between the peptides. The specificity of the cross-linking reaction was characterized, the probes were improved by making them bivalent, and the system was used to label a protein in vitro and receptors on the surface of mammalian cells.
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Affiliation(s)
- Jianpeng Wang
- Department of Chemistry, The Chinese University of Hong Kong , Shatin, Hong Kong SAR, China
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19
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Khatwani SL, Mullen DG, Hast MA, Beese LS, Distefano MD, Taton TA. Covalent protein-oligonucleotide conjugates by copper-free click reaction. Bioorg Med Chem 2012; 20:4532-9. [PMID: 22682299 PMCID: PMC3682506 DOI: 10.1016/j.bmc.2012.05.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2012] [Revised: 05/03/2012] [Accepted: 05/09/2012] [Indexed: 11/18/2022]
Abstract
Covalent protein-oligodeoxynucleotide (protein-ODN) conjugates are useful in a number of biological applications, but synthesizing discrete conjugates-where the connection between the two components is at a defined location in both the protein and the ODN-under mild conditions with significant yield can be a challenge. In this article, we demonstrate a strategy for synthesizing discrete protein-ODN conjugates using strain-promoted azide-alkyne [3+2] cycloaddition (SPAAC, a copper-free 'click' reaction). Azide-functionalized proteins, prepared by enzymatic prenylation of C-terminal CVIA tags with synthetic azidoprenyl diphosphates, were 'clicked' to ODNs that had been modified with a strained dibenzocyclooctyne (DIBO-ODN). The resulting protein-ODN conjugates were purified and characterized by size-exclusion chromatography and gel electrophoresis. We find that the yields and reaction times of the SPAAC bioconjugation reactions are comparable to those previously reported for copper-catalyzed azide-alkyne [3+2] cycloaddition (CuAAC) bioconjugation, but require no catalyst. The same SPAAC chemistry was used to immobilize azide-modified proteins onto surfaces, using surface-bound DIBO-ODN as a heterobifunctional linker. Cu-free click bioconjugation of proteins to ODNs is a simple and versatile alternative to Cu-catalyzed click methods.
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Affiliation(s)
| | - Daniel G. Mullen
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Michael A. Hast
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - Lorena S. Beese
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - Mark D. Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - T. Andrew Taton
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
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20
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Abstract
Signaling cascades are managed in time and space by interactions between and among proteins. These interactions are often aided by adaptor proteins, which guide enzyme-substrate pairs into proximity. Miniature proteins are a class of small, well-folded protein domains possessing engineered binding properties. Here we made use of two miniature proteins with complementary binding properties to create a synthetic adaptor protein that effectively redirects a ubiquitous signaling event: tyrosine phosphorylation. We report that miniature-protein-based adaptor 3 uses templated catalysis to redirect the Src family kinase Hck to phosphorylate hDM2, a negative regulator of the p53 tumor suppressor and a poor Hck substrate. Phosphorylation occurs with multiple turnover and at a single site targeted by c-Abl kinase in the cell.
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Affiliation(s)
- Elissa M. Hobert
- Department of Chemistry, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8107, United States
| | - Alanna Schepartz
- Department of Chemistry, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8107, United States
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8107, United States
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21
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Radzvilavicius T, Lagunavicius A. Selective inactivation of M-MuLV RT RNase H activity by site-directed PEGylation: an improved ability to synthesize long cDNA molecules. N Biotechnol 2012; 29:285-92. [DOI: 10.1016/j.nbt.2011.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 06/27/2011] [Accepted: 07/14/2011] [Indexed: 10/18/2022]
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22
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Shimada J, Maruyama T, Kitaoka M, Kamiya N, Goto M. Microplate assay for aptamer-based thrombin detection using a DNA-enzyme conjugate based on histidine-tag chemistry. Anal Biochem 2011; 421:541-6. [PMID: 22178916 DOI: 10.1016/j.ab.2011.11.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 11/21/2011] [Accepted: 11/22/2011] [Indexed: 01/01/2023]
Abstract
We report a method to prepare a DNA-enzyme conjugate using histidine-tag (His-tag) chemistry. A DNA oligonucleotide was modified with nitrilotriacetate (NTA), whose K(d) was approximately 10⁻⁶ (M⁻¹) toward a His-tag present on a recombinant protein via the complexation of Ni²⁺. His-tagged alkaline phosphatase (His-AP) was used as the model enzyme. Enzyme immobilization on the microplate revealed the conjugation of His-AP and the NTA-modified DNA via an Ni²⁺ complex. SPR measurements also proved the conjugation of His-AP with the NTA-modified DNA via an Ni²⁺ complex. The DNA-enzyme conjugate was then used for the detection of thrombin using a DNA aptamer. The DNA-AP conjugate successfully amplified the binding signal between the DNA aptamer and the thrombin, and the signal was measured as the fluorescent intensity derived from the AP-catalyzed reaction. The detection limit was 11 nM. Finally, we studied the effect of the release of the immobilized His-AP from the microplate on the AP activity, because the present strategy used a cleavable linker for the conjugation and the enzyme immobilization. The DNase-catalyzed release of the immobilized His-AP resulted in a 1.7-fold higher AP activity than observed when the His-AP was surface-immobilized.
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Affiliation(s)
- Josui Shimada
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
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23
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Shimada J, Maruyama T, Kitaoka M, Kamiya N, Goto M. DNA-enzyme conjugate with a weak inhibitor that can specifically detect thrombin in a homogeneous medium. Anal Biochem 2011; 414:103-8. [PMID: 21371416 DOI: 10.1016/j.ab.2011.02.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 02/24/2011] [Accepted: 02/24/2011] [Indexed: 01/02/2023]
Abstract
We present the DNA-assisted control of enzymatic activity for the detection of a target protein using a new type of DNA-enzyme conjugate. The conjugate is composed of an enzyme inhibitor to regulate enzyme activity and a DNA aptamer to be responsive toward the analyte protein. Glutathione S-transferase (GST) and thrombin were selected as a model enzyme and an analyte protein. A hexahistidine tag was genetically attached to the C terminus of the GST, and the 5' end of an oligonucleotide was conjugated with nitrilotriacetic acid (NTA) for the site-specific conjugation of the DNA with the GST based on a Ni(2+) complex interaction. We found that fluorescein acted as a weak inhibitor of GST and succeeded in the regulation of GST activity by increasing the local concentration of the weak inhibitor by the hybridization of a 3'-end fluorescein-modified DNA. The catalytic activity of the DNA aptamer-enzyme conjugate showed a dose-dependent response to thrombin, indicating that the GST activity was clearly recovered by the binding of the DNA aptamer to thrombin. The current system enables the sensitive and specific detection of thrombin simply by measuring the enzymatic activity in a homogeneous medium.
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Affiliation(s)
- Josui Shimada
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, Fukuoka, Japan
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24
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Multispectral labeling of antibodies with polyfluorophores on a DNA backbone and application in cellular imaging. Proc Natl Acad Sci U S A 2011; 108:3493-8. [PMID: 21321224 DOI: 10.1073/pnas.1017349108] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Most current approaches to multiantigen fluorescent imaging require overlaying of multiple images taken with separate filter sets as a result of differing dye excitation requirements. This requirement for false-color composite imaging prevents the user from visualizing multiple species in real time and disallows imaging of rapidly moving specimens. To address this limitation, here we investigate the use of oligodeoxyfluoroside (ODF) fluorophores as labels for antibodies. ODFs are short DNA-like oligomers with fluorophores replacing the DNA bases and can be assembled in many colors with excitation at a single wavelength. A DNA synthesizer was used to construct several short ODFs carrying a terminal alkyne group and having emission maxima of 410-670 nm. We developed a new approach to antibody conjugation, using Huisgen-Sharpless cycloaddition, which was used to react the alkynes on ODFs with azide groups added to secondary antibodies. Multiple ODF-tagged secondary antibodies were then used to mark primary antibodies. The set of antibodies was tested for spectral characteristics in labeling tubulin in HeLa cells and revealed a wide spectrum of colors, ranging from violet-blue to red with excitation through a single filter (340-380 nm). Selected sets of the differently labeled secondary antibodies were then used to simultaneously mark four antigens in fixed cells, using a single image and filter set. We also imaged different surface tumor markers on two live cell lines. Experiments showed that all colors could be visualized simultaneously by eye under the microscope, yielding multicolor images of multiple cellular antigens in real time.
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25
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Saccà B, Niemeyer CM. Functionalization of DNA nanostructures with proteins. Chem Soc Rev 2011; 40:5910-21. [DOI: 10.1039/c1cs15212b] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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26
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Lee JH, Wong NY, Tan LH, Wang Z, Lu Y. Controlled alignment of multiple proteins and nanoparticles with nanometer resolution via backbone-modified phosphorothioate DNA and bifunctional linkers. J Am Chem Soc 2010; 132:8906-8. [PMID: 20536179 DOI: 10.1021/ja103739f] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Controlled alignment of streptavidin (STV), myoglobin, and nanoparticles with nanometer resolution has been achieved via backbone-modified phosphorothioate DNA and biotin- and maleimide-containing bifunctional linkers. Introducing triplet biotin modifications in three adjacent PSs significantly increased the STV conjugation yield. By placing phosphorothioate modifications at multiple positions of a double stranded DNA template, monomer, dimer, and trimer STV-DNA assemblies were formed with the STVs placed at controlled positions. The activity of the conjugated protein has been demonstrated by binding biotinylated AuNPs onto STV-DNA complexes, indicating the use of the system as a template for the formation of AuNP dimers and trimers with STVs separated by distances of 10-30 nm. Furthermore, a melting temperature experiment carried out with an STV-dsDNA assembly showed that the bifunctional-linker-modified PS-DNA system is much more stable than base-modified conjugation systems. This method allows for high yield, nanoscale-precision conjugation of multiple proteins to DNA. The linker can be designed to conjugate any proteins and nanomaterials specifically for a wide range of applications.
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Affiliation(s)
- Jung Heon Lee
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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27
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Gaidamaviciute E, Tauraite D, Gagilas J, Lagunavicius A. Site-directed chemical modification of archaeal Thermococcus litoralis Sh1B DNA polymerase: Acquired ability to read through template-strand uracils. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:1385-93. [DOI: 10.1016/j.bbapap.2010.01.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Revised: 01/20/2010] [Accepted: 01/29/2010] [Indexed: 11/27/2022]
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28
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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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29
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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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30
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Goodman RP, Erben CM, Malo J, Ho WM, McKee ML, Kapanidis AN, Turberfield AJ. A facile method for reversibly linking a recombinant protein to DNA. Chembiochem 2009; 10:1551-7. [PMID: 19449345 DOI: 10.1002/cbic.200900165] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We present a facile method for linking recombinant proteins to DNA. It is based on the nickel-mediated interaction between a hexahistidine tag (His(6)-tag) and DNA functionalized with three nitrilotriacetic acid (NTA) groups. The resulting DNA-protein linkage is site-specific. It can be broken quickly and controllably by the addition of a chelating agent that binds nickel. We have used this new linker to bind proteins to a variety of DNA motifs commonly used in the fabrication of nanostructures by DNA self-assembly.
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Affiliation(s)
- Russell P Goodman
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX13PU, UK
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31
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Dahdah DB, Morin I, Moreau MJJ, Dixon NE, Schaeffer PM. Site-specific covalent attachment of DNA to proteins using a photoactivatable Tus-Ter complex. Chem Commun (Camb) 2009:3050-2. [PMID: 19462083 DOI: 10.1039/b900905a] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Investigations into the photocrosslinking kinetics of the protein Tus with various bromodeoxyuridine-substituted Ter DNA variants highlight the potential use of this complex as a photoactivatable connector between proteins of interest and specific DNA sequences.
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Affiliation(s)
- Dahdah B Dahdah
- Comparative Genomics Centre, School of Pharmacy & Molecular Sciences, James Cook University, Townsville, QLD 4811, Australia
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32
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Abstract
Synthetic protein-DNA conjugates are valuable tools with applications in fields including nanobiotechnology, bioanalytical chemistry, and molecular diagnostics, and various synthetic methods for their production have been developed during the past three decades. The present article reviews current methodologies for the synthesis of covalent protein-DNA conjugates with particular focus on the regiospecificity and stoichiometry of these reactions.
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33
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Takeda S, Tsukiji S, Ueda H, Nagamune T. Covalent split protein fragment-DNA hybrids generated through N-terminus-specific modification of proteins by oligonucleotides. Org Biomol Chem 2008; 6:2187-94. [PMID: 18528581 DOI: 10.1039/b720013g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Semisynthetic protein-DNA hybrid molecules have recently attracted much attention as valuable tools for bioanalytical chemistry and nanobiotechnology. Here we describe a synthetic method for conjugating oligonucleotides to the N-terminus of recombinant proteins. Our strategy involves the conversion of amine-terminated oligonucleotides to thioester-functionalized oligonucleotides by using a bifunctional reagent bearing an N-hydroxysuccinimide ester and benzyl thioester group, followed by native chemical ligation with proteins containing an N-terminal cysteine. We applied this technique to construct split luciferase fragment-DNA hybrid systems in which the catalytic activity of split luciferase is restored by the re-assembly of each fragment through a specific DNA-protein or DNA-DNA interaction. Split protein fragment-DNA hybrids will offer new opportunities to explore the potential of protein-DNA conjugates for various applications.
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Affiliation(s)
- Shuji Takeda
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
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34
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Duckworth B, Chen Y, Wollack J, Sham Y, Mueller J, Taton T, Distefano M. A Universal Method for the Preparation of Covalent Protein–DNA Conjugates for Use in Creating Protein Nanostructures. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200701942] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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35
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Duckworth B, Chen Y, Wollack J, Sham Y, Mueller J, Taton T, Distefano M. A Universal Method for the Preparation of Covalent Protein–DNA Conjugates for Use in Creating Protein Nanostructures. Angew Chem Int Ed Engl 2007; 46:8819-22. [DOI: 10.1002/anie.200701942] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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36
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Humenik M, Huang Y, Wang Y, Sprinzl M. C-terminal incorporation of bio-orthogonal azide groups into a protein and preparation of protein-oligodeoxynucleotide conjugates by Cu'-catalyzed cycloaddition. Chembiochem 2007; 8:1103-6. [PMID: 17557370 DOI: 10.1002/cbic.200700070] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Martin Humenik
- Laboratorium für Biochemie, Universität Bayreuth, Universitätstrasse 30, 95440 Bayreuth, Germany
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37
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Martin H, Kinns H, Mitchell N, Astier Y, Madathil R, Howorka S. Nanoscale Protein Pores Modified with PAMAM Dendrimers. J Am Chem Soc 2007; 129:9640-9. [PMID: 17636906 DOI: 10.1021/ja0689029] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe nanoscale protein pores modified with a single hyperbranched dendrimer molecule inside the channel lumen. Sulfhydryl-reactive polyamido amine (PAMAM) dendrimers of generations 2, 3 and 5 were synthesized, chemically characterized, and reacted with engineered cysteine residues in the transmembrane pore alpha-hemolysin. Successful coupling was monitored using an electrophoretic mobility shift assay. The results indicate that G2 and G3 but not G5 dendrimers permeated through the 2.9 nm cis entrance to couple inside the pore. The defined molecular weight cutoff for the passage of hyperbranched PAMAM polymers is in contrast to the less restricted accessibility of flexible linear poly(ethylene glycol) polymers of comparable hydrodynamic volume. Their higher compactness makes sulfhydryl-reactive PAMAM dendrimers promising research reagents to probe the structure of porous membrane proteins with wide internal diameters. The conductance properties of PAMAM-modified proteins pores were characterized with single-channel current recordings. A G3 dendrimer molecule in the channel lumen reduced the ionic current by 45%, indicating that the hyperbranched and positively charged polymer blocked the passage of ions through the pore. In line with expectations, a smaller and less dense G2 dendrimer led to a less pronounced current reduction of 25%. Comparisons to recordings of PEG-modified pores revealed striking dissimilarities, suggesting that differences in the structural dynamics of flexible linear polymers vs compact dendrimers can be observed at the single-molecule level. Current recordings also revealed that dendrimers functioned as ion-selectivity filters and molecular sieves for the controlled passage of molecules. The alteration of pore properties with charged and hyperbranched dendrimers is a new approach and might be extended to inorganic nanopores with applications in sensing and separation technology.
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Affiliation(s)
- Hugh Martin
- Department of Chemistry, University College London, London WC1H 0AJ, England, United Kingdom
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38
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Gianneschi N, Ghadiri M. Design of Molecular Logic Devices Based on a Programmable DNA-Regulated Semisynthetic Enzyme. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200700047] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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39
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40
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Huo FJ, Yin CX, Yang P. The crystal structure, self-assembly, DNA-binding and cleavage studies of the [2]pseudorotaxane composed of cucurbit[6]uril. Bioorg Med Chem Lett 2007; 17:932-6. [PMID: 17161945 DOI: 10.1016/j.bmcl.2006.11.054] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2006] [Revised: 11/14/2006] [Accepted: 11/16/2006] [Indexed: 10/23/2022]
Abstract
The [2]pseudorotaxanes of cucurbit[6]uril with guest molecule 1,6-bis(imidazol-1-yl)hexane (BIMH) were synthesized and characterized by ESI-MS spectrometry, (1)H NMR spectra, and X-ray diffraction crystallography. The influence of different anions on self-assembly in solid-state was discussed by X-ray diffraction crystallography. However, more interestingly, and to our amazement, we discovered the CB[6]/BIMH [2]pseudorotaxane exhibiting efficient cleavage of pBR322 DNA in physiological environment. The cleavage mechanism were studied by fluorescence spectra and the hydrolysis of bis(2,4-dinitrophenyl)-phosphate (BDNPP). From DNA-binding mode being electrostatic force and the first-order kinetics equation, we prove indirectly that the mechanism may be hydrolytic cleavage.
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Affiliation(s)
- Fang-Jun Huo
- Institute of Molecular Science, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, China
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41
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Gianneschi NC, Ghadiri MR. Design of molecular logic devices based on a programmable DNA-regulated semisynthetic enzyme. Angew Chem Int Ed Engl 2007; 46:3955-8. [PMID: 17427900 PMCID: PMC2790070 DOI: 10.1002/anie.200700047] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Nathan C. Gianneschi
- Dr. N. C. Gianneschi, Prof. Dr. M. R. Ghadiri, Departments of Chemistry and Molecular Biology and the, Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037 (USA), Fax: (+1) 858-784-2798
| | - M. Reza Ghadiri
- Dr. N. C. Gianneschi, Prof. Dr. M. R. Ghadiri, Departments of Chemistry and Molecular Biology and the, Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037 (USA), Fax: (+1) 858-784-2798, E-mail:
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Creus M, Ward TR. Designed evolution of artificial metalloenzymes: protein catalysts made to order. Org Biomol Chem 2007; 5:1835-44. [PMID: 17551630 DOI: 10.1039/b702068f] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Artificial metalloenzymes based on biotin-streptavidin technology, a "fusion" of chemistry and biology, illustrate how asymmetric catalysts can be improved and evolved using chemogenetic approaches.
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Affiliation(s)
- Marc Creus
- Department of Cellular and Molecular Biology, University of Neuchâtel, Rue Emile-Argand 11, C.P. 158, Neuchâtel, CH-2009, Switzerland.
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Liu Y, Lin C, Li H, Yan H. Aptamer-directed self-assembly of protein arrays on a DNA nanostructure. Angew Chem Int Ed Engl 2006; 44:4333-8. [PMID: 15945116 DOI: 10.1002/anie.200501089] [Citation(s) in RCA: 141] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Yan Liu
- Department of Chemistry and Biochemistry & Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
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44
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Abstract
Can proteins be used as computational devices to address difficult computational problems? In recent years there has been much interest in biological computing, that is, building a general purpose computer from biological molecules. Most of the current efforts are based on DNA because of its ability to self-hybridize. The exquisite selectivity and specificity of complex protein-based networks motivated us to suggest that similar principles can be used to devise biological systems that will be able to directly implement any logical circuit as a parallel asynchronous computation. Such devices, powered by ATP molecules, would be able to perform, for medical applications, digital computation with natural interface to biological input conditions. We discuss how to design protein molecules that would serve as the basic computational element by functioning as a NAND logical gate, utilizing DNA tags for recognition, and phosphorylation and exonuclease reactions for information processing. A solution of these elements could carry out effective computation. Finally, the model and its robustness to errors were tested in a computer simulation.
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Affiliation(s)
- Ron Unger
- Faculty of Life Science, Bar-Ilan University, Ramat-Gan, Israel.
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45
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Agafonov DE, Rabe KS, Grote M, Voertler CS, Sprinzl M. C-terminal modifications of a protein by UAG-encoded incorporation of puromycin during in vitro protein synthesis in the absence of release factor 1. Chembiochem 2006; 7:330-6. [PMID: 16444758 DOI: 10.1002/cbic.200500358] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Deactivation of release factor 1 by polyclonal antibodies in an in vitro translation system, which was used to express the esterase gene, led to the reversible elimination of naturally occurring termination. This technique allowed the antibiotic puromycin to be used as an acceptor substrate for the peptidyl residue in the peptidyl-transferase reaction. This resulted in more than 80 % yield of protein with C-terminally incorporated puromycin. pCpPuromycin that was either conjugated with the Cy3 fluorophor or biotin by N4 alkylation of cytosine, also acted as an acceptor substrate for the peptidyl-transferase reaction and was incorporated into the protein C terminus. The resulting conjugates possessed Cy3-specific fluorescence and affinity to streptavidin-coated surfaces, respectively. This left the enzymatic activity of the reporter protein unaffected. It was also shown that extension of puromycin on its 5'-hydroxyl end by up to ten deoxyoligonucleotides also allowed conjugation with the C terminus of in vitro translated protein when RF1-dependent termination was suppressed. However, the conjugation yield decreased upon addition of more than six nucleotides.
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Affiliation(s)
- Dmitry E Agafonov
- Fellow of the Alexander von Humboldt Foundation on leave from the Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
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46
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Yang Q, Xu J, Sun Y, Li Z, Li Y, Qian X. Hydrolysis of plasmid DNA and RNA by amino alkyl naphthalimide as metal-free artificial nuclease. Bioorg Med Chem Lett 2006; 16:803-6. [PMID: 16314096 DOI: 10.1016/j.bmcl.2005.11.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Revised: 10/23/2005] [Accepted: 11/08/2005] [Indexed: 10/25/2022]
Abstract
A strategy of dimethylamino alkyldiimide conjugated with an intercalator of naphthalimide for hydrolysis of DNA was suggested and evaluated. 4 can hydrolyze 4 kb plasmid DNA into 2 kb fragments with GC and GG selectivity, which represents a novel example of sequence- or site-selective metal-free DNA artificial nuclease. Results also show it could hydrolyze RNA efficiently.
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Affiliation(s)
- Qing Yang
- Department of Bioscience and Biotechnology, Dalian University of Technology, Dalian 116024, China.
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47
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Liu Y, Lin C, Li H, Yan H. Aptamer-Directed Self-Assembly of Protein Arrays on a DNA Nanostructure. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200501089] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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48
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49
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Abstract
Although chemists can synthesize virtually any small organic molecule, our ability to rationally manipulate the structures of proteins is quite limited, despite their involvement in virtually every life process. For most proteins, modifications are largely restricted to substitutions among the common 20 amino acids. Herein we describe recent advances that make it possible to add new building blocks to the genetic codes of both prokaryotic and eukaryotic organisms. Over 30 novel amino acids have been genetically encoded in response to unique triplet and quadruplet codons including fluorescent, photoreactive, and redox-active amino acids, glycosylated amino acids, and amino acids with keto, azido, acetylenic, and heavy-atom-containing side chains. By removing the limitations imposed by the existing 20 amino acid code, it should be possible to generate proteins and perhaps entire organisms with new or enhanced properties.
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Affiliation(s)
- Lei Wang
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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50
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Halpin DR, Lee JA, Wrenn SJ, Harbury PB. DNA display III. Solid-phase organic synthesis on unprotected DNA. PLoS Biol 2004; 2:E175. [PMID: 15221029 PMCID: PMC434150 DOI: 10.1371/journal.pbio.0020175] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2004] [Accepted: 04/13/2004] [Indexed: 12/02/2022] Open
Abstract
DNA-directed synthesis represents a powerful new tool for molecular discovery. Its ultimate utility, however, hinges upon the diversity of chemical reactions that can be executed in the presence of unprotected DNA. We present a solid-phase reaction format that makes possible the use of standard organic reaction conditions and common reagents to facilitate chemical transformations on unprotected DNA supports. We demonstrate the feasibility of this strategy by comprehensively adapting solid-phase 9-fluorenylmethyoxycarbonyl-based peptide synthesis to be DNA-compatible, and we describe a set of tools for the adaptation of other chemistries. Efficient peptide coupling to DNA was observed for all 33 amino acids tested, and polypeptides as long as 12 amino acids were synthesized on DNA supports. Beyond the direct implications for synthesis of peptide-DNA conjugates, the methods described offer a general strategy for organic synthesis on unprotected DNA. Their employment can facilitate the generation of chemically diverse DNA-encoded molecular populations amenable to in vitro evolution and genetic manipulation.
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Affiliation(s)
- David R Halpin
- 1Department of Biochemistry, Stanford University School of MedicineStanford, California, United States of America
| | - Juanghae A Lee
- 2Department of Chemistry, Stanford University School of Humanities and SciencesStanford, CaliforniaUnited States of America
| | - S. Jarrett Wrenn
- 1Department of Biochemistry, Stanford University School of MedicineStanford, California, United States of America
| | - Pehr B Harbury
- 1Department of Biochemistry, Stanford University School of MedicineStanford, California, United States of America
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