1
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Sajjadi S, Wu SJ, Rabbani Y, Zubkovs V, Ahmadzadeh H, K. Goharshadi E, Boghossian AA. Micropreparative Gel Electrophoresis for Purification of Nanoscale Bioconjugates. Bioconjug Chem 2024; 35:154-163. [PMID: 38320084 PMCID: PMC10885001 DOI: 10.1021/acs.bioconjchem.3c00388] [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: 08/29/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 02/08/2024]
Abstract
Conventional techniques for purifying macromolecular conjugates often require complex and costly installments that are inaccessible to most laboratories. In this work, we develop a one-step micropreparative method based on a trilayered polyacrylamide gel electrophoresis (MP-PAGE) setup to purify biological samples, synthetic nanoparticles, as well as biohybrid complexes. We apply this method to recover DNA from a ladder mixture with yields of up to 90%, compared to the 58% yield obtained using the conventional crush-and-soak method. MP-PAGE was also able to isolate enhanced yellow fluorescence protein (EYFP) from crude cell extract with 90% purity, which is comparable to purities achieved through a more complex two-step purification procedure involving size exclusion and immobilized metal-ion affinity chromatography. This technique was further extended to demonstrate size-dependent separation of a commercial mixture of graphene quantum dots (GQDs) into three different fractions with distinct optical properties. Finally, MP-PAGE was used to isolate DNA-EYFP and DNA-GQD bioconjugates from their reaction mixture of DNA and EYFP and GQD precursors, samples that otherwise could not be effectively purified by conventional chromatography. MP-PAGE thus offers a rapid and versatile means of purifying biological and synthetic nanomaterials without the need for specialized equipment.
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Affiliation(s)
- Sayyed
Hashem Sajjadi
- Ecole
Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
- Chemistry
Department, Faculty of Science, Ferdowsi
University of Mashhad, Mashhad 9177948974, Iran
| | - Shang-Jung Wu
- Ecole
Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Yahya Rabbani
- Ecole
Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Vitalijs Zubkovs
- Ecole
Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Hossein Ahmadzadeh
- Chemistry
Department, Faculty of Science, Ferdowsi
University of Mashhad, Mashhad 9177948974, Iran
| | - Elaheh K. Goharshadi
- Chemistry
Department, Faculty of Science, Ferdowsi
University of Mashhad, Mashhad 9177948974, Iran
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2
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Kröll S, Niemeyer CM. Nucleic Acid-based Enzyme Cascades-Current Trends and Future Perspectives. Angew Chem Int Ed Engl 2024; 63:e202314452. [PMID: 37870888 DOI: 10.1002/anie.202314452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/23/2023] [Accepted: 10/23/2023] [Indexed: 10/24/2023]
Abstract
The natural micro- and nanoscale organization of biomacromolecules is a remarkable principle within living cells, allowing for the control of cellular functions by compartmentalization, dimensional diffusion and substrate channeling. In order to explore these biological mechanisms and harness their potential for applications such as sensing and catalysis, molecular scaffolding has emerged as a promising approach. In the case of synthetic enzyme cascades, developments in DNA nanotechnology have produced particularly powerful scaffolds whose addressability can be programmed with nanometer precision. In this minireview, we summarize recent developments in the field of biomimetic multicatalytic cascade reactions organized on DNA nanostructures. We emphasize the impact of the underlying design principles like DNA origami, efficient strategies for enzyme immobilization, as well as the importance of experimental design parameters and theoretical modeling. We show how DNA nanostructures have enabled a better understanding of diffusion and compartmentalization effects at the nanometer length scale, and discuss the challenges and future potential for commercial applications.
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Affiliation(s)
- Sandra Kröll
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces 1, Hermann-von-Helmholtz-Platz 1, 76344, Karlsruhe, Germany
| | - Christof M Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces 1, Hermann-von-Helmholtz-Platz 1, 76344, Karlsruhe, Germany
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3
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Chen K, Jiang M, Liu J, Huang D, Yang YR. DNA nanostructures as biomolecular scaffolds for antigen display. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2024; 16:e1921. [PMID: 37562787 DOI: 10.1002/wnan.1921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/12/2023]
Abstract
Nanoparticle-based vaccines offer a multivalent approach for antigen display, efficiently activating T and B cells in the lymph nodes. Among various nanoparticle design strategies, DNA nanotechnology offers an innovative alternative platform, featuring high modularity, spatial addressing, nanoscale regulation, high functional group density, and lower self-antigenicity. This review delves into the potential of DNA nanostructures as biomolecular scaffolds for antigen display, addressing: (1) immunological mechanisms behind nanovaccines and commonly used nanoparticles in their design, (2) techniques for characterizing protein NP-antigen complexes, (3) advancements in DNA nanotechnology and DNA-protein assembly approach, (4) strategies for precise antigen presentation on DNA scaffolds, and (5) current applications and future possibilities of DNA scaffolds in antigen display. This analysis aims to highlight the transformative potential of DNA nanoscaffolds in immunology and vaccinology. This article is categorized under: Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.
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Affiliation(s)
- Kun Chen
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China
- Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Ming Jiang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China
| | - Jin Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China
- Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Deli Huang
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Yuhe R Yang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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4
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Mathur D, Díaz SA, Hildebrandt N, Pensack RD, Yurke B, Biaggne A, Li L, Melinger JS, Ancona MG, Knowlton WB, Medintz IL. Pursuing excitonic energy transfer with programmable DNA-based optical breadboards. Chem Soc Rev 2023; 52:7848-7948. [PMID: 37872857 PMCID: PMC10642627 DOI: 10.1039/d0cs00936a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Indexed: 10/25/2023]
Abstract
DNA nanotechnology has now enabled the self-assembly of almost any prescribed 3-dimensional nanoscale structure in large numbers and with high fidelity. These structures are also amenable to site-specific modification with a variety of small molecules ranging from drugs to reporter dyes. Beyond obvious application in biotechnology, such DNA structures are being pursued as programmable nanoscale optical breadboards where multiple different/identical fluorophores can be positioned with sub-nanometer resolution in a manner designed to allow them to engage in multistep excitonic energy-transfer (ET) via Förster resonance energy transfer (FRET) or other related processes. Not only is the ability to create such complex optical structures unique, more importantly, the ability to rapidly redesign and prototype almost all structural and optical analogues in a massively parallel format allows for deep insight into the underlying photophysical processes. Dynamic DNA structures further provide the unparalleled capability to reconfigure a DNA scaffold on the fly in situ and thus switch between ET pathways within a given assembly, actively change its properties, and even repeatedly toggle between two states such as on/off. Here, we review progress in developing these composite materials for potential applications that include artificial light harvesting, smart sensors, nanoactuators, optical barcoding, bioprobes, cryptography, computing, charge conversion, and theranostics to even new forms of optical data storage. Along with an introduction into the DNA scaffolding itself, the diverse fluorophores utilized in these structures, their incorporation chemistry, and the photophysical processes they are designed to exploit, we highlight the evolution of DNA architectures implemented in the pursuit of increased transfer efficiency and the key lessons about ET learned from each iteration. We also focus on recent and growing efforts to exploit DNA as a scaffold for assembling molecular dye aggregates that host delocalized excitons as a test bed for creating excitonic circuits and accessing other quantum-like optical phenomena. We conclude with an outlook on what is still required to transition these materials from a research pursuit to application specific prototypes and beyond.
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Affiliation(s)
- Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland OH 44106, USA
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, USA.
| | - Niko Hildebrandt
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
- Department of Engineering Physics, McMaster University, Hamilton, L8S 4L7, Canada
| | - Ryan D Pensack
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Bernard Yurke
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Austin Biaggne
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Lan Li
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
- Center for Advanced Energy Studies, Idaho Falls, ID 83401, USA
| | - Joseph S Melinger
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Mario G Ancona
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA
- Department of Electrical and Computer Engineering, Florida State University, Tallahassee, FL 32310, USA
| | - William B Knowlton
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, USA.
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5
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Winer L, Motiei L, Margulies D. Fluorescent Investigation of Proteins Using DNA-Synthetic Ligand Conjugates. Bioconjug Chem 2023; 34:1509-1522. [PMID: 37556353 PMCID: PMC10515487 DOI: 10.1021/acs.bioconjchem.3c00203] [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: 05/07/2023] [Revised: 06/27/2023] [Indexed: 08/11/2023]
Abstract
The unfathomable role that fluorescence detection plays in the life sciences has prompted the development of countless fluorescent labels, sensors, and analytical techniques that can be used to detect and image proteins or investigate their properties. Motivated by the demand for simple-to-produce, modular, and versatile fluorescent tools to study proteins, many research groups have harnessed the advantages of oligodeoxynucleotides (ODNs) for scaffolding such probes. Tight control over the valency and position of protein binders and fluorescent dyes decorating the polynucleotide chain and the ability to predict molecular architectures through self-assembly, inherent solubility, and stability are, in a nutshell, the important properties of DNA probes. This paper reviews the progress in developing DNA-based, fluorescent sensors or labels that navigate toward their protein targets through small-molecule (SM) or peptide ligands. By describing the design, operating principles, and applications of such systems, we aim to highlight the versatility and modularity of this approach and the ability to use ODN-SM or ODN-peptide conjugates for various applications such as protein modification, labeling, and imaging, as well as for biomarker detection, protein surface characterization, and the investigation of multivalency.
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Affiliation(s)
- Lulu Winer
- Department of Chemical and
Structural Biology, Weizmann Institute of
Science, Rehovot, 76100, Israel
| | - Leila Motiei
- Department of Chemical and
Structural Biology, Weizmann Institute of
Science, Rehovot, 76100, Israel
| | - David Margulies
- Department of Chemical and
Structural Biology, Weizmann Institute of
Science, Rehovot, 76100, Israel
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6
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Sha Y, Tang T, Zhao Y, Li M, Rao Y, Zhuang W, Ying H. Construction of co-immobilized multienzyme systems using DNA-directed immobilization technology and multifunctionalized nanoparticles. Colloids Surf B Biointerfaces 2023; 229:113443. [PMID: 37437412 DOI: 10.1016/j.colsurfb.2023.113443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 06/14/2023] [Accepted: 07/05/2023] [Indexed: 07/14/2023]
Abstract
The multienzyme co-immobilization systems with high cascade catalytic efficiency and selectivity have attracted considerable attention. In this study, through DNA-directed immobilization (DDI) technology, two model enzymes, glucose oxidase (GOD) and horseradish peroxide (HRP) were co-immobilized on the multifunctional silica nanoparticles (DDI enzyme). In addition to the directional distribution promoted by DNA complementary chains, the multienzyme system allowed the control of the stoichiometric ratio of the enzymes by adjusting the ratio of amino/carboxyl groups. The optimal mole ratio of GOD/HRP was 1:2, while the protein loading amount could reach 8.06 mg·g-1. Compared with the conventional direct adsorption, the catalytic activity of the DDI enzyme was 2.49 times higher. Moreover, with the enhancement of thermal and mechanical stability, the DDI enzyme could still retain at least 50% of its initial activity after 12 cycles. Accompanied by an excellent response and good selectivity, the constructed multienzyme systems simultaneously showed the potential as a glucose detector. Therefore, based on the DDI technology, the highly efficient multienzyme co-immobilization system could be further extended for a wider range of research fields.
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Affiliation(s)
- Yu Sha
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China
| | - Ting Tang
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Ye Zhao
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Mengyu Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China; School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Yuan Rao
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Wei Zhuang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China; State Key Laboratory of Materials-Oriented Chemical Engineering, National Engineering Technique Research Center for Biotechnology, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China.
| | - Hanjie Ying
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China; State Key Laboratory of Materials-Oriented Chemical Engineering, National Engineering Technique Research Center for Biotechnology, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China.
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7
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Ban Ž, Barišić A, Crnolatac I, Kazazić S, Škulj S, Savini F, Bertoša B, Barišić I, Piantanida I. Highly selective preparation of N-terminus Horseradish peroxidase-DNA conjugate with fully retained enzymatic activity: HRP-DNA structure - activity relation. Enzyme Microb Technol 2023; 168:110257. [PMID: 37209508 DOI: 10.1016/j.enzmictec.2023.110257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/22/2023]
Abstract
Within the last decade, the field of bio-nanoengineering has achieved significant advances allowing us to generate, e.g., nanoscaled molecular machineries with arbitrary shapes. To unleash the full potential of novel methods such as DNA origami technology, it is important to functionalise complex molecules and nanostructures precisely. Thus, considerable attention has been given to site-selective modifications of proteins allowing further incorporation of various functionalities. Here, we describe a method for the covalent attachment of oligonucleotides to the glycosylated horseradish peroxidase protein (HRP) with high N-terminus selectivity and significant yield while conserving the enzymatic activity. This two-step process includes a pH-controlled metal-free diazotransfer reaction using imidazole-1-sulfonyl azide hydrogen sulfate, which at pH 8.5 results in an N-terminal azide-functionalized protein, followed by the Cu-free click SPAAC reaction to dibenzocyclooctyne- (DBCO) modified oligonucleotides. The reaction conditions were optimised to achieve maximum yield and the best performance. The resulting protein-oligonucleotide conjugates (HRP-DNA) were characterised by electrophoresis and mass spectrometry (MS). Native-PAGE experiments demonstrated different migration patterns for HRP-DNA and the azido-modified protein allowing zymogram experiments. Structure-activity relationships of novel HRP-DNA conjugates were assessed using molecular dynamics simulations, characterising the molecular interactions that define the structural and dynamical properties of the obtained protein-oligonucleotide conjugates (POC).
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Affiliation(s)
- Željka Ban
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Antun Barišić
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Ivo Crnolatac
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia.
| | - Saša Kazazić
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Sanja Škulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | | | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia.
| | - Ivan Barišić
- AIT Austrian Institute of Technology,Vienna, Austria.
| | - Ivo Piantanida
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
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8
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Menon D, Singh R, Joshi KB, Gupta S, Bhatia D. Designer, Programmable DNA-peptide hybrid materials with emergent properties to probe and modulate biological systems. Chembiochem 2023; 24:e202200580. [PMID: 36468492 DOI: 10.1002/cbic.202200580] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/04/2022] [Accepted: 12/05/2022] [Indexed: 12/07/2022]
Abstract
The chemistry of DNA endows it with certain functional properties that facilitate the generation of self-assembled nanostructures, offering precise control over their geometry and morphology, that can be exploited for advanced biological applications. Despite the structural promise of these materials, their applications are limited owing to lack of functional capability to interact favourably with biological systems, which has been achieved by functional proteins or peptides. Herein, we outline a strategy for functionalizing DNA structures with short-peptides, leading to the formation of DNA-peptide hybrid materials. This proposition offers the opportunity to leverage the unique advantages of each of these bio-molecules, that have far reaching emergent properties in terms of better cellular interactions and uptake, better stability in biological media, an acceptable and programmable immune response and high bioactive molecule loading capacities. We discuss the synthetic strategies for the formation of these materials, namely, solid-phase functionalization and solution-coupling functionalization. We then proceed to highlight selected biological applications of these materials in the domains of cell instruction & molecular recognition, gene delivery, drug delivery and bone & tissue regeneration. We conclude with discussions shedding light on the challenges that these materials pose and offer our insights on future directions of peptide-DNA research for targeted biomedical applications.
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Affiliation(s)
- Dhruv Menon
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, CB3 0HE, United Kingdom
| | - Ramesh Singh
- Biological Engineering Discipline, Indian Institute of Technology, Gandhinagar, 382355, India
| | - Kashti B Joshi
- Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar, Madhya Pradesh, India
| | - Sharad Gupta
- Biological Engineering Discipline, Indian Institute of Technology, Gandhinagar, 382355, India
| | - Dhiraj Bhatia
- Biological Engineering Discipline, Indian Institute of Technology, Gandhinagar, 382355, India
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9
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Nakata E, Dinh H, Lin P, Morii T. Enzyme Cascade Reactions on DNA Origami Scaffold. Methods Mol Biol 2023; 2639:275-299. [PMID: 37166723 DOI: 10.1007/978-1-0716-3028-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The protocols for constructing, characterizing, and analyzing enzyme cascade reaction systems on the DNA scaffold are described. Two-step and three-step enzyme cascade reactions were adapted from the xylose metabolic pathway as the example of natural metabolic pathway and were assembled on the DNA scaffold by using the DNA binding adaptors.
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Affiliation(s)
- Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Huyen Dinh
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Peng Lin
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan.
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10
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Li L, Liu S, Zhang C, Guo Z, Shao S, Deng X, Liu Q. Recent Advances in DNA-Based Cell Surface Engineering for Biological Applications. Chemistry 2022; 28:e202202070. [PMID: 35977912 DOI: 10.1002/chem.202202070] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Indexed: 12/14/2022]
Abstract
Due to its excellent programmability and biocompatibility, DNA molecule has unique advantages in cell surface engineering. Recent progresses provide a reliable and feasible way to engineer cell surfaces with diverse DNA molecules and DNA nanostructures. The abundant form of DNA nanostructures has greatly expanded the toolbox of DNA-based cell surface engineering and gave rise to a variety of novel and fascinating applications. In this review, we summarize recent advances in DNA-based cell surface engineering and its biological applications. We first introduce some widely used methods of immobilizing DNA molecules on cell surfaces and their application features. Then we discuss the approaches of employing DNA nanostructures and dynamic DNA nanotechnology as elements for creating functional cell surfaces. Finally, we review the extensive biological applications of DNA-based cell surface engineering and discuss the challenges and prospects of DNA-based cell surface engineering.
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Affiliation(s)
- Lexun Li
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Biology, Hunan University Changsha, Hunan, 410082, People's Republic of China
| | - Shuang Liu
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Biology, Hunan University Changsha, Hunan, 410082, People's Republic of China
| | - Chunjuan Zhang
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Biology, Hunan University Changsha, Hunan, 410082, People's Republic of China
| | - Zhenzhen Guo
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Biology, Hunan University Changsha, Hunan, 410082, People's Republic of China
| | - Shuxuan Shao
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Biology, Hunan University Changsha, Hunan, 410082, People's Republic of China
| | - Xiaodan Deng
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Biology, Hunan University Changsha, Hunan, 410082, People's Republic of China
| | - Qiaoling Liu
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Biology, Hunan University Changsha, Hunan, 410082, People's Republic of China
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11
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Kröll S, Schneider L, Wadhwani P, Rabe KS, Niemeyer CM. Orthogonal protein decoration of DNA nanostructures based on SpyCatcher-SpyTag interaction. Chem Commun (Camb) 2022; 58:13471-13474. [PMID: 36383063 DOI: 10.1039/d2cc05335g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We present an efficient and readily applicable strategy for the covalent ligation of proteins to DNA origami by using the SpyCatcher-SpyTag (SC-ST) connector system. This approach showed orthogonality with other covalent connectors and has been used exemplarily for the immobilization and study of stereoselective ketoreductases to gain insight into the spatial arrangement of enzymes on DNA nanostructures.
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Affiliation(s)
- Sandra Kröll
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Karlsruhe, Germany.
| | - Leonie Schneider
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Karlsruhe, Germany.
| | - Parvesh Wadhwani
- Department of Molecular Biophysics (IBG 2), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Karlsruhe, Germany
| | - Kersten S Rabe
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Karlsruhe, Germany.
| | - Christof M Niemeyer
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Karlsruhe, Germany.
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12
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Winegar PH, Figg CA, Teplensky MH, Ramani N, Mirkin CA. Modular Nucleic Acid Scaffolds for Synthesizing Monodisperse and Sequence-Encoded Antibody Oligomers. Chem 2022; 8:3018-3030. [PMID: 36405374 PMCID: PMC9674055 DOI: 10.1016/j.chempr.2022.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Synthesizing protein oligomers that contain exact numbers of multiple different proteins in defined architectures is challenging. DNA-DNA interactions can be used to program protein assembly into oligomers; however, existing methods require changes to DNA design to achieve different numbers and oligomeric sequences of proteins. Herein, we develop a modular DNA scaffold that uses only six synthetic oligonucleotides to organize proteins into defined oligomers. As a proof-of-concept, model proteins (antibodies) are oligomerized into dimers and trimers, where antibody function is retained. Illustrating the modularity of this technique, dimer and trimer building blocks are then assembled into pentamers containing three different antibodies in an exact stoichiometry and oligomeric sequence. In sum, this report describes a generalizable method for organizing proteins into monodisperse, sequence-encoded oligomers using DNA. This advance will enable studies into how oligomeric protein sequences affect material properties in areas spanning pharmaceutical development, cascade catalysis, synthetic photosynthesis, and membrane transport.
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Affiliation(s)
- Peter H. Winegar
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- These authors contributed equally
| | - C. Adrian Figg
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- These authors contributed equally
| | - Michelle H. Teplensky
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Namrata Ramani
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Department of Materials Science and Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Chad A. Mirkin
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Department of Materials Science and Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Lead contact
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13
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Watson EE, Winssinger N. Synthesis of Protein-Oligonucleotide Conjugates. Biomolecules 2022; 12:biom12101523. [PMID: 36291732 PMCID: PMC9599799 DOI: 10.3390/biom12101523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
Nucleic acids and proteins form two of the key classes of functional biomolecules. Through the ability to access specific protein-oligonucleotide conjugates, a broader range of functional molecules becomes accessible which leverages both the programmability and recognition potential of nucleic acids and the structural, chemical and functional diversity of proteins. Herein, we summarize the available conjugation strategies to access such chimeric molecules and highlight some key case study examples within the field to showcase the power and utility of such technology.
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Affiliation(s)
- Emma E. Watson
- Department of Chemistry, School of Physical Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
- Correspondence: (E.E.W.); (N.W.)
| | - Nicolas Winssinger
- Department of Organic Chemistry, Faculty of Science, NCCR Chemical Biology, CH-1205 Geneva, Switzerland
- Correspondence: (E.E.W.); (N.W.)
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14
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Sheng J, Pi Y, Zhao S, Wang B, Chen M, Chang K. Novel DNA nanoflower biosensing technologies towards next-generation molecular diagnostics. Trends Biotechnol 2022; 41:653-668. [PMID: 36117022 DOI: 10.1016/j.tibtech.2022.08.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 07/29/2022] [Accepted: 08/23/2022] [Indexed: 11/26/2022]
Abstract
DNA nanoflowers (DNFs) are topological flower-like nanostructures based on ultralong-strand DNA and inorganic metal-ion frameworks. Because of their programmability, biocompatibility, and controllable assembly size for specific responses to molecular recognition stimuli, DNFs are powerful biosensing tools for detecting biomolecules. Here, we review the current state of DNF-based biosensing strategies for in vivo and in vitro detection, with a view of how the field has evolved towards molecular diagnostics. We also provide a detailed classification of DNF-based biosensing strategies and propose their future utility. Particularly as transduction elements, DNFs can accelerate biosensing engineering by signal amplification. Finally, we discuss the key challenges and further prospects of DNF-based biosensing technologies in developing applications of a broader scope.
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Affiliation(s)
- Jing Sheng
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China
| | - Yan Pi
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, China
| | - Shuang Zhao
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China
| | - Binpan Wang
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China
| | - Ming Chen
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China; College of Pharmacy and Laboratory Medicine, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China; State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China.
| | - Kai Chang
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China.
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15
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Zhang Z, Nakata E, Shibano Y, Morii T. FRET-based cathepsin probes for simultaneous detection of cathepsin B and D activities. Chembiochem 2022; 23:e202200319. [PMID: 35929606 DOI: 10.1002/cbic.202200319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/05/2022] [Indexed: 11/09/2022]
Abstract
Fluorescent cathepsin probes were prepared by modification of peptidic substrates for cathepsin B (CTSB) and cathepsin D (CTSD) with FRET pairs. Fluorophores with distinguishable emission characteristics were applied to CTSB and CTSD probes with their appropriate quenchers to simultaneously monitor the activity of CTSB and/or CTSD. Conjugation of both the CTSB and CTSD probes with short single-stranded DNA drastically increased their reactivity to cathepsins over the parent probes possibly by improving their solubility. The activity of CTSB and CTSD were simultaneously detected by using these orthogonal FRET-based cathepsin probes.
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Affiliation(s)
- Zhengxiao Zhang
- Kyoto University: Kyoto Daigaku, Institute of Advanced Energy, Gokasyo, 611-0011, Uji, JAPAN
| | - Eiji Nakata
- Kyoto University: Kyoto Daigaku, Institute of Advanced Energy, Gokasyo, 611-0011, Uji, JAPAN
| | - Yuya Shibano
- Kyoto University - Uji Campus: Kyoto Daigaku - Uji Campus, Institute of Advanced energy, Gokasyo, 6110011, Uji, JAPAN
| | - Takashi Morii
- Kyoto University: Kyoto Daigaku, Institute of Advanced Energy, Gokasyo, 611-0011, Uji, JAPAN
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16
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Lu Z, Liu Y, Deng Y, Jia B, Ding X, Zheng P, Li Z. OaAEP1-mediated PNA-protein conjugation enables erasable imaging of membrane proteins. Chem Commun (Camb) 2022; 58:8448-8451. [PMID: 35797663 DOI: 10.1039/d2cc02153f] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the use of a protein ligase to covalently ligate a protein to a peptide nucleic acid (PNA). The rapid ligation demands only an N-terminal GL dipeptide in the target protein and a C-terminal NGL tripeptide in the PNA. We demonstrate the versatility of this approach by attaching a PNA strand to three different proteins. Lastly, we show that erasable imaging of EGFR on HEK293 cell membranes is achieved with DNA origami nanostructures and toehold-mediated strand displacement.
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Affiliation(s)
- Zhangwei Lu
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China. .,State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Yutong Liu
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing, 210023, P. R. China.
| | - Yibing Deng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing, 210023, P. R. China.
| | - Bin Jia
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China. .,State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Xuan Ding
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China. .,State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing, 210023, P. R. China.
| | - Zhe Li
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China. .,State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
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17
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Koga MM, Comberlato A, Rodríguez-Franco HJ, Bastings MMC. Strategic Insights into Engineering Parameters Affecting Cell Type-Specific Uptake of DNA-Based Nanomaterials. Biomacromolecules 2022; 23:2586-2594. [PMID: 35641881 PMCID: PMC9198982 DOI: 10.1021/acs.biomac.2c00282] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
DNA-based nanomaterials are gaining popularity as uniform and programmable bioengineering tools as a result of recent solutions to their weak stability under biological conditions. The DNA nanotechnology platform uniquely allows decoupling of engineering parameters to comprehensively study the effect of each upon cellular encounter. We here present a systematic analysis of the effect of surface parameters of DNA-based nanoparticles on uptake in three different cell models: tumor cells, macrophages, and dendritic cells. The influence of surface charge, stabilizing coating, fluorophore types, functionalization technique, and particle concentration employed is found to cause significant differences in material uptake among these cell types. We therefore provide new insights into the large variance in cell type-specific uptake, highlighting the necessity of proper engineering and careful assay development when DNA-based materials are used as tools in bioengineering and as future nanotherapeutic agents.
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Affiliation(s)
- Marianna M Koga
- Programmable Biomaterials Laboratory, Institute of Materials/Interfaculty Bioengineering Institute, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne 1015, Switzerland
| | - Alice Comberlato
- Programmable Biomaterials Laboratory, Institute of Materials/Interfaculty Bioengineering Institute, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne 1015, Switzerland
| | - Hugo J Rodríguez-Franco
- Programmable Biomaterials Laboratory, Institute of Materials/Interfaculty Bioengineering Institute, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne 1015, Switzerland
| | - Maartje M C Bastings
- Programmable Biomaterials Laboratory, Institute of Materials/Interfaculty Bioengineering Institute, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne 1015, Switzerland
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18
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Zheng Y, Vaissier Welborn V. Tuning the Catalytic Activity of Synthetic Enzyme KE15 with DNA. J Phys Chem B 2022; 126:3407-3413. [PMID: 35483007 DOI: 10.1021/acs.jpcb.2c00765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Efficiency improvement of synthetic enzymes through scaffold modifications suffers from limitations in terms of effectiveness, cost, and potential devastating consequences for protein structural stability. Here, we propose an alternative to scaffold modification, within electrostatic preorganization theory, where the enzyme's greater environment is designed to support the evolution of the reaction in the active site. We demonstrate the feasibility of such an approach by placing a (polar) DNA fragment in the surroundings of the Kemp eliminase enzyme KE15 (structure from Houk's group) and computing the resulting change in catalytic activity. We find that the introduction of a DNA fragment magnifies the contribution of protein residues to the stabilization of the transition state, estimated from electric field calculations with polarizable molecular dynamics. Our randomly generated test systems reveal a 2.0 kcal/mol reduction in activation energy, suggesting that even more significant catalytic improvements could be made by optimizing DNA size, sequence, and orientation with respect to the enzyme, validating our approach.
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Affiliation(s)
- Yi Zheng
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24060, United States
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19
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Dey S, Dorey A, Abraham L, Xing Y, Zhang I, Zhang F, Howorka S, Yan H. A reversibly gated protein-transporting membrane channel made of DNA. Nat Commun 2022; 13:2271. [PMID: 35484117 PMCID: PMC9051096 DOI: 10.1038/s41467-022-28522-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 01/14/2022] [Indexed: 01/14/2023] Open
Abstract
Controlled transport of biomolecules across lipid bilayer membranes is of profound significance in biological processes. In cells, cargo exchange is mediated by dedicated channels that respond to triggers, undergo a nanomechanical change to reversibly open, and thus regulate cargo flux. Replicating these processes with simple yet programmable chemical means is of fundamental scientific interest. Artificial systems that go beyond nature's remit in transport control and cargo are also of considerable interest for biotechnological applications but challenging to build. Here, we describe a synthetic channel that allows precisely timed, stimulus-controlled transport of folded and functional proteins across bilayer membranes. The channel is made via DNA nanotechnology design principles and features a 416 nm2 opening cross-section and a nanomechanical lid which can be controllably closed and re-opened via a lock-and-key mechanism. We envision that the functional DNA device may be used in highly sensitive biosensing, drug delivery of proteins, and the creation of artificial cell networks.
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Affiliation(s)
- Swarup Dey
- Biodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, AZ, 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Adam Dorey
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK
| | - Leeza Abraham
- Biodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, AZ, 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Yongzheng Xing
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK
| | - Irene Zhang
- Biodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, AZ, 85287, USA
| | - Fei Zhang
- Department of Chemistry, Rutgers University, Newark, NJ, 07102, USA
| | - Stefan Howorka
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK.
| | - Hao Yan
- Biodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, AZ, 85287, USA.
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.
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20
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Chang X, Yang Q, Lee J, Zhang F. Self-Assembled Nucleic Acid Nanostructures for Biomedical Applications. Curr Top Med Chem 2022; 22:652-667. [PMID: 35319373 DOI: 10.2174/1568026622666220321140729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 01/20/2022] [Accepted: 01/30/2022] [Indexed: 11/22/2022]
Abstract
Structural DNA nanotechnology has been developed into a powerful method for creating self-assembled nanomaterials. Their compatibility with biosystems, nanoscale addressability, and programmable dynamic features make them appealing candidates for biomedical research. This review paper focuses on DNA self-assembly strategies and designer nanostructures with custom functions for biomedical applications. Specifically, we review the development of DNA self-assembly methods, from simple DNA motifs consisting of a few DNA strands to complex DNA architectures assembled by DNA origami. Three advantages are discussed using structural DNA nanotechnology for biomedical applications: (1) precise spatial control, (2) molding and guiding other biomolecules, and (3) using reconfigurable DNA nanodevices to overcome biomedical challenges. Finally, we discuss the challenges and opportunities of employing DNA nanotechnology for biomedical applications, emphasizing diverse assembly strategies to create a custom DNA nanostructure with desired functions.
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Affiliation(s)
- Xu Chang
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA
| | - Qi Yang
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA
| | - Jungyeon Lee
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA
| | - Fei Zhang
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA
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21
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Lanphere C, Ciccone J, Dorey A, Hagleitner-Ertuğrul N, Knyazev D, Haider S, Howorka S. Triggered Assembly of a DNA-Based Membrane Channel. J Am Chem Soc 2022; 144:4333-4344. [PMID: 35253434 PMCID: PMC8931747 DOI: 10.1021/jacs.1c06598] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Indexed: 01/01/2023]
Abstract
Chemistry is in a powerful position to synthetically replicate biomolecular structures. Adding functional complexity is key to increase the biomimetics' value for science and technology yet is difficult to achieve with poorly controlled building materials. Here, we use defined DNA blocks to rationally design a triggerable synthetic nanopore that integrates multiple functions of biological membrane proteins. Soluble triggers bind via molecular recognition to the nanopore components changing their structure and membrane position, which controls the assembly into a defined channel for efficient transmembrane cargo transport. Using ensemble, single-molecule, and simulation analysis, our activatable pore provides insight into the kinetics and structural dynamics of DNA assembly at the membrane interface. The triggered channel advances functional DNA nanotechnology and synthetic biology and will guide the design of controlled nanodevices for sensing, cell biological research, and drug delivery.
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Affiliation(s)
- Conor Lanphere
- Department
of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
| | - Jonah Ciccone
- Department
of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
| | - Adam Dorey
- Department
of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
| | | | - Denis Knyazev
- Institute
of Applied Experimental Biophysics, Johannes
Kepler University, 4040 Linz, Austria
| | - Shozeb Haider
- Department
of Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London WC1N 1AX, United Kingdom
| | - Stefan Howorka
- Department
of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
- Institute
of Applied Experimental Biophysics, Johannes
Kepler University, 4040 Linz, Austria
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22
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Sharma P, Lew TTS. Principles of Nanoparticle Design for Genome Editing in Plants. Front Genome Ed 2022; 4:846624. [PMID: 35330692 PMCID: PMC8940305 DOI: 10.3389/fgeed.2022.846624] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/15/2022] [Indexed: 12/04/2022] Open
Abstract
Precise plant genome editing technologies have provided new opportunities to accelerate crop improvement and develop more sustainable agricultural systems. In particular, the prokaryote-derived CRISPR platforms allow precise manipulation of the crop genome, enabling the generation of high-yielding and stress-tolerant crop varieties. Nanotechnology has the potential to catalyze the development of a novel molecular toolbox even further by introducing the possibility of a rapid, universal delivery method to edit the plant genome in a species-independent manner. In this Perspective, we highlight how nanoparticles can help unlock the full potential of CRISPR/Cas technology in targeted manipulation of the plant genome to improve agricultural output. We discuss current challenges hampering progress in nanoparticle-enabled plant gene-editing research and application in the field, and highlight how rational nanoparticle design can overcome them. Finally, we examine the implications of the regulatory frameworks and social acceptance for the future of nano-enabled precision breeding in the developing world.
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Affiliation(s)
- Pushkal Sharma
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Tedrick Thomas Salim Lew
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Singapore
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- *Correspondence: Tedrick Thomas Salim Lew, , orcid.org/0000-0002-4815-9921
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23
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Paiva TO, Schneider A, Bataille L, Chovin A, Anne A, Michon T, Wege C, Demaille C. Enzymatic activity of individual bioelectrocatalytic viral nanoparticles: dependence of catalysis on the viral scaffold and its length. NANOSCALE 2022; 14:875-889. [PMID: 34985473 DOI: 10.1039/d1nr07445h] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The enzymatic activity of tobacco mosaic virus (TMV) nanorod particles decorated with an integrated electro-catalytic system, comprising the quinoprotein glucose-dehydrogenase (PQQ-GDH) enzyme and ferrocenylated PEG chains as redox mediators, is probed at the individual virion scale by atomic force microscopy-scanning electrochemical atomic force microscopy (AFM-SECM). A marked dependence of the catalytic activity on the particle length is observed. This finding can be explained by electron propagation along the viral backbone, resulting from electron exchange between ferrocene moieties, coupled with enzymatic catalysis. Thus, the use of a simple 1D diffusion/reaction model allows the determination of the kinetic parameters of the virus-supported enzyme. Comparative analysis of the catalytic behavior of the Fc-PEG/PQQ-GDH system assembled on two differing viral scaffolds, TMV (this work) and bacteriophage-fd (previous work), reveals two distinct kinetic effects of scaffolding: An enhancement of catalysis that does not depend on the virus type and a modulation of substrate inhibition that depends on the virus type. AFM-SECM detection of the enzymatic activity of a few tens of PQQ-GDH molecules, decorating a 40 nm-long viral domain, is also demonstrated, a record in terms of the lowest number of enzyme molecules interrogated by an electrochemical imaging technique.
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Affiliation(s)
- Telmo O Paiva
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, CNRS UMR 7591, F-75013 Paris, France.
| | - Angela Schneider
- University of Stuttgart, Institute of Biomaterials and Biomolecular Systems, Research Unit Molecular and Synthetic Plant Virology, 70569 Stuttgart, Germany.
| | - Laure Bataille
- Université de Bordeaux, Biologie du Fruit et Pathologie, INRA UMR 1332, F-33140 Villenave d'Ornon, France.
| | - Arnaud Chovin
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, CNRS UMR 7591, F-75013 Paris, France.
| | - Agnès Anne
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, CNRS UMR 7591, F-75013 Paris, France.
| | - Thierry Michon
- Université de Bordeaux, Biologie du Fruit et Pathologie, INRA UMR 1332, F-33140 Villenave d'Ornon, France.
| | - Christina Wege
- University of Stuttgart, Institute of Biomaterials and Biomolecular Systems, Research Unit Molecular and Synthetic Plant Virology, 70569 Stuttgart, Germany.
| | - Christophe Demaille
- Université de Paris, Laboratoire d'Electrochimie Moléculaire, CNRS UMR 7591, F-75013 Paris, France.
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24
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Kondrat S, von Lieres E. Mechanisms and Effects of Substrate Channelling in Enzymatic Cascades. Methods Mol Biol 2022; 2487:27-50. [PMID: 35687228 DOI: 10.1007/978-1-0716-2269-8_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Substrate or metabolite channelling is a transfer of intermediates produced by one enzyme to the sequential enzyme of a reaction cascade or metabolic pathway, without releasing them entirely into bulk. Despite an enormous effort and more than three decades of research, substrate channelling remains the subject of continuing debates and active investigation. Herein, we review the benefits and mechanisms of substrate channelling in vivo and in vitro. We discuss critically the effects that substrate channelling can have on enzymatic cascades, including speeding up or slowing down reaction cascades and protecting intermediates from sequestration and enzymes' surroundings from toxic or otherwise detrimental intermediates. We also discuss how macromolecular crowding affects substrate channelling and point out the galore of open questions.
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Affiliation(s)
- Svyatoslav Kondrat
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland.
- Max-Planck-Institut für Intelligente Systeme, Stuttgart, Germany.
- IV. Institut für Theoretische Physik, Universität Stuttgart, Stuttgart, Germany.
| | - Eric von Lieres
- Forschungszentrum Jülich, IBG-1: Biotechnology, Jülich, Germany
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25
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Zhang Z, Nakata E, Dinh H, Saimura M, Rajendran A, Matsuda K, Morii T. Tuning the Reactivity of a Substrate for SNAP-Tag Expands Its Application for Recognition-Driven DNA-Protein Conjugation. Chemistry 2021; 27:18118-18128. [PMID: 34747070 DOI: 10.1002/chem.202103304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Indexed: 11/09/2022]
Abstract
Recognition-driven modification has been emerging as a novel approach to modifying biomolecular targets of interest site-specifically and efficiently. To this end, protein modular adaptors (MAs) are the ideal reaction model for recognition-driven modification of DNA as they consist of both a sequence-specific DNA-binding domain (DBD) and a self-ligating protein-tag. Coupling DNA recognition by DBD and the chemoselective reaction of the protein tag could provide a highly efficient sequence-specific reaction. However, combining an MA consisting of a reactive protein-tag and its substrate, for example, SNAP-tag and benzyl guanine (BG), revealed rather nonselective reaction with DNA. Therefore new substrates of SNAP-tag have been designed to realize sequence-selective rapid crosslinking reactions of MAs with SNAP-tag. The reactions of substrates with SNAP-tag were verified by kinetic analyses to enable the sequence-selective crosslinking reaction of MA. The new substrate enables the distinctive orthogonality of SNAP-tag against CLIP-tag to achieve orthogonal DNA-protein crosslinking by six unique MAs.
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Affiliation(s)
- Zhengxiao Zhang
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
| | - Huyen Dinh
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
| | - Masayuki Saimura
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
| | | | - Kazunari Matsuda
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
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26
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Kröll S, Rabe KS, Niemeyer CM. An Orthogonal Covalent Connector System for the Efficient Assembly of Enzyme Cascades on DNA Nanostructures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2105095. [PMID: 34825457 DOI: 10.1002/smll.202105095] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/19/2021] [Indexed: 05/06/2023]
Abstract
Combining structural DNA nanotechnology with the virtually unlimited variety of enzymes offers unique opportunities for generating novel biocatalytic devices. However, the immobilization of enzymes is still restricted by a lack of efficient covalent coupling techniques. The rational re-engineering of the genetically fusible SNAP-tag linker is reported here. By replacing five amino acids that alter the electrostatic properties of the SNAP_R5 variant, up to 11-fold increased coupling efficiency with benzylguanine-modified oligonucleotides and DNA origami nanostructures (DON) was achieved, resulting in typical occupancy densities of 75%. The novel SNAP_R5 linker can be combined with the equally efficient Halo-based oligonucleotide binding tag (HOB). Since both linkers exhibit neither cross-reactivity nor non-specific binding, they allowed orthogonal assembly of an enzyme cascade consisting of the stereoselective ketoreductase Gre2p and the cofactor-regenerating isocitrate dehydrogenase on DON. The cascade showed approximately 1.6-fold higher activity in a stereoselective cascade reaction than the corresponding free solubilized enzymes. The connector system presented here and the methods used to validate it represent important tools for further development of DON-based multienzyme systems to investigate mechanistic effects of substrate channeling and compartmentalization relevant for exploitation in biosensing and catalysis.
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Affiliation(s)
- Sandra Kröll
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Kersten S Rabe
- 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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27
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Rubio-Sánchez R, Fabrini G, Cicuta P, Di Michele L. Amphiphilic DNA nanostructures for bottom-up synthetic biology. Chem Commun (Camb) 2021; 57:12725-12740. [PMID: 34750602 PMCID: PMC8631003 DOI: 10.1039/d1cc04311k] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/28/2021] [Indexed: 12/28/2022]
Abstract
DNA nanotechnology enables the construction of sophisticated biomimetic nanomachines that are increasingly central to the growing efforts of creating complex cell-like entities from the bottom-up. DNA nanostructures have been proposed as both structural and functional elements of these artificial cells, and in many instances are decorated with hydrophobic moieties to enable interfacing with synthetic lipid bilayers or regulating bulk self-organisation. In this feature article we review recent efforts to design biomimetic membrane-anchored DNA nanostructures capable of imparting complex functionalities to cell-like objects, such as regulated adhesion, tissue formation, communication and transport. We then discuss the ability of hydrophobic modifications to enable the self-assembly of DNA-based nanostructured frameworks with prescribed morphology and functionality, and explore the relevance of these novel materials for artificial cell science and beyond. Finally, we comment on the yet mostly unexpressed potential of amphiphilic DNA-nanotechnology as a complete toolbox for bottom-up synthetic biology - a figurative and literal scaffold upon which the next generation of synthetic cells could be built.
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Affiliation(s)
- Roger Rubio-Sánchez
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Giacomo Fabrini
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Pietro Cicuta
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
| | - Lorenzo Di Michele
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
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28
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Zhu J, Avakyan N, Kakkis AA, Hoffnagle AM, Han K, Li Y, Zhang Z, Choi TS, Na Y, Yu CJ, Tezcan FA. Protein Assembly by Design. Chem Rev 2021; 121:13701-13796. [PMID: 34405992 PMCID: PMC9148388 DOI: 10.1021/acs.chemrev.1c00308] [Citation(s) in RCA: 107] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins are nature's primary building blocks for the construction of sophisticated molecular machines and dynamic materials, ranging from protein complexes such as photosystem II and nitrogenase that drive biogeochemical cycles to cytoskeletal assemblies and muscle fibers for motion. Such natural systems have inspired extensive efforts in the rational design of artificial protein assemblies in the last two decades. As molecular building blocks, proteins are highly complex, in terms of both their three-dimensional structures and chemical compositions. To enable control over the self-assembly of such complex molecules, scientists have devised many creative strategies by combining tools and principles of experimental and computational biophysics, supramolecular chemistry, inorganic chemistry, materials science, and polymer chemistry, among others. Owing to these innovative strategies, what started as a purely structure-building exercise two decades ago has, in short order, led to artificial protein assemblies with unprecedented structures and functions and protein-based materials with unusual properties. Our goal in this review is to give an overview of this exciting and highly interdisciplinary area of research, first outlining the design strategies and tools that have been devised for controlling protein self-assembly, then describing the diverse structures of artificial protein assemblies, and finally highlighting the emergent properties and functions of these assemblies.
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Affiliation(s)
| | | | - Albert A. Kakkis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Alexander M. Hoffnagle
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Kenneth Han
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Yiying Li
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Zhiyin Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Tae Su Choi
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Youjeong Na
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Chung-Jui Yu
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
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29
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Eklund A, Comberlato A, Parish IA, Jungmann R, Bastings MMC. Quantification of Strand Accessibility in Biostable DNA Origami with Single-Staple Resolution. ACS NANO 2021; 15:17668-17677. [PMID: 34613711 PMCID: PMC8613912 DOI: 10.1021/acsnano.1c05540] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/30/2021] [Indexed: 05/20/2023]
Abstract
DNA-based nanostructures are actively gaining interest as tools for biomedical and therapeutic applications following the recent development of protective coating strategies prolonging structural integrity in physiological conditions. For tailored biological action, these nanostructures are often functionalized with targeting or imaging labels using DNA base pairing. Only if these labels are accessible on the structure's surface will they be able to interact with their intended biological target. However, the accessibility of functional sites for different geometries and environments, specifically after the application of a protective coating, is currently not known. Here, we assay this accessibility on the level of single handle strands with two- and three-dimensional resolution using DNA-PAINT and show that the hybridization kinetics of top and bottom sides on the same nanostructure linked to a surface remain unaltered. We furthermore demonstrate that the functionality of the structures remains available after an oligolysine-PEG coating is applied, enabling bioassays where functionality and stability are imperative.
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Affiliation(s)
- Alexandra
S. Eklund
- Faculty
of Physics and Center for Nanoscience, Ludwig
Maximilian University, 80539, Munich, Germany
- Max
Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Alice Comberlato
- Programmable
Biomaterials Laboratory, Institute of Materials, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne, 1015, Switzerland
| | - Ian A. Parish
- Peter
MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Sir
Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3128, Australia
| | - Ralf Jungmann
- Faculty
of Physics and Center for Nanoscience, Ludwig
Maximilian University, 80539, Munich, Germany
- Max
Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Maartje M. C. Bastings
- Programmable
Biomaterials Laboratory, Institute of Materials, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne, 1015, Switzerland
- Interfaculty
Bioengineering Institute, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne, 1015, Switzerland
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30
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The biological applications of DNA nanomaterials: current challenges and future directions. Signal Transduct Target Ther 2021; 6:351. [PMID: 34620843 PMCID: PMC8497566 DOI: 10.1038/s41392-021-00727-9] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 06/24/2021] [Accepted: 07/30/2021] [Indexed: 02/08/2023] Open
Abstract
DNA, a genetic material, has been employed in different scientific directions for various biological applications as driven by DNA nanotechnology in the past decades, including tissue regeneration, disease prevention, inflammation inhibition, bioimaging, biosensing, diagnosis, antitumor drug delivery, and therapeutics. With the rapid progress in DNA nanotechnology, multitudinous DNA nanomaterials have been designed with different shape and size based on the classic Watson-Crick base-pairing for molecular self-assembly. Some DNA materials could functionally change cell biological behaviors, such as cell migration, cell proliferation, cell differentiation, autophagy, and anti-inflammatory effects. Some single-stranded DNAs (ssDNAs) or RNAs with secondary structures via self-pairing, named aptamer, possess the ability of targeting, which are selected by systematic evolution of ligands by exponential enrichment (SELEX) and applied for tumor targeted diagnosis and treatment. Some DNA nanomaterials with three-dimensional (3D) nanostructures and stable structures are investigated as drug carrier systems to delivery multiple antitumor medicine or gene therapeutic agents. While the functional DNA nanostructures have promoted the development of the DNA nanotechnology with innovative designs and preparation strategies, and also proved with great potential in the biological and medical use, there is still a long way to go for the eventual application of DNA materials in real life. Here in this review, we conducted a comprehensive survey of the structural development history of various DNA nanomaterials, introduced the principles of different DNA nanomaterials, summarized their biological applications in different fields, and discussed the current challenges and further directions that could help to achieve their applications in the future.
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31
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Kong G, Xiong M, Liu L, Hu L, Meng HM, Ke G, Zhang XB, Tan W. DNA origami-based protein networks: from basic construction to emerging applications. Chem Soc Rev 2021; 50:1846-1873. [PMID: 33306073 DOI: 10.1039/d0cs00255k] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Natural living systems are driven by delicate protein networks whose functions are precisely controlled by many parameters, such as number, distance, orientation, and position. Focusing on regulation rather than just imitation, the construction of artificial protein networks is important in many research areas, including biomedicine, synthetic biology and chemical biology. DNA origami, sophisticated nanostructures with rational design, can offer predictable, programmable, and addressable scaffolds for protein assembly with nanometer precision. Recently, many interdisciplinary efforts have achieved the precise construction of DNA origami-based protein networks, and their emerging application in many areas. To inspire more fantastic research and applications, herein we highlight the applicability and potentiality of DNA origami-based protein networks. After a brief introduction to the development and features of DNA origami, some important factors for the precise construction of DNA origami-based protein networks are discussed, including protein-DNA conjugation methods, networks with different patterns and the controllable parameters in the networks. The discussion then focuses on the emerging application of DNA origami-based protein networks in several areas, including enzymatic reaction regulation, sensing, bionics, biophysics, and biomedicine. Finally, current challenges and opportunities in this research field are discussed.
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Affiliation(s)
- Gezhi Kong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Mengyi Xiong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Lu Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Ling Hu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Hong-Min Meng
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou 450001, China
| | - Guoliang Ke
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Xiao-Bing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
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32
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Zhang Y, Zhang Q, Cheng F, Chang Y, Liu M, Li Y. Fast-responding functional DNA superstructures for stimuli-triggered protein release. Chem Sci 2021; 12:8282-8287. [PMID: 34221310 PMCID: PMC8221054 DOI: 10.1039/d1sc00795e] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/06/2021] [Indexed: 12/26/2022] Open
Abstract
Strategies that speed up the on-command release of proteins (e.g., enzymes) from stimuli-responsive materials are intrinsically necessary for biosensing applications, such as point-of-care testing, as they will achieve fast readouts with catalytic signal-amplification. However, current systems are challenging to work with because they usually exhibit response times on the order of hours up to days. Herein, we report on the first effort to construct a fast-responding gating system using protein-encapsulating functional DNA superstructures (denoted as protein@3D DNA). Proteins were directly embedded into 3D DNA during the one-pot rolling circle amplification process. We found that the specific DNA-DNA interaction and aptamer-ligand interaction could act as general protocols to release the loaded proteins from 3D DNA. The resulting gating system exhibits fast release kinetics on the order of minutes. Taking advantage of this finding, we designed a simple paper device by employing protein@3D DNA for colorimetric detection of toxin B (Clostridium difficile marker). This device is capable of detecting 0.1 nM toxin B within 16 minutes.
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Affiliation(s)
- Yuxin Zhang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology Dalian 116024 China
| | - Qiang Zhang
- School of Bioengineering, Dalian University of Technology Dalian 116024 China
| | - Fang Cheng
- School of Chemical Engineering, Dalian University of Technology Dalian 116024 China
| | - Yangyang Chang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology Dalian 116024 China
| | - Meng Liu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology Dalian 116024 China
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University 1280 Main Street West Hamilton Ontario L8S4K1 Canada
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33
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He L, Mu J, Gang O, Chen X. Rationally Programming Nanomaterials with DNA for Biomedical Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2003775. [PMID: 33898180 PMCID: PMC8061415 DOI: 10.1002/advs.202003775] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 11/23/2020] [Indexed: 05/05/2023]
Abstract
DNA is not only a carrier of genetic information, but also a versatile structural tool for the engineering and self-assembling of nanostructures. In this regard, the DNA template has dramatically enhanced the scalability, programmability, and functionality of the self-assembled DNA nanostructures. These capabilities provide opportunities for a wide range of biomedical applications in biosensing, bioimaging, drug delivery, and disease therapy. In this review, the importance and advantages of DNA for programming and fabricating of DNA nanostructures are first highlighted. The recent progress in design and construction of DNA nanostructures are then summarized, including DNA conjugated nanoparticle systems, DNA-based clusters and extended organizations, and DNA origami-templated assemblies. An overview on biomedical applications of the self-assembled DNA nanostructures is provided. Finally, the conclusion and perspectives on the self-assembled DNA nanostructures are presented.
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Affiliation(s)
- Liangcan He
- Yong Loo Lin School of Medicine and Faculty of EngineeringNational University of SingaporeSingapore117597Singapore
| | - Jing Mu
- Institute of Precision MedicinePeking University Shenzhen HospitalShenzhen518036China
| | - Oleg Gang
- Department of Chemical Engineering and Department of Applied Physics and Applied MathematicsColumbia UniversityNew YorkNY10027USA
- Center for Functional NanomaterialsBrookhaven National LaboratoryUptonNY11973USA
| | - Xiaoyuan Chen
- Yong Loo Lin School of Medicine and Faculty of EngineeringNational University of SingaporeSingapore117597Singapore
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34
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Weinhold E, Chakraborty B. DNA modification and visualization on an origami-based enzyme nano-factory. NANOSCALE 2021; 13:2465-2471. [PMID: 33471009 DOI: 10.1039/d0nr07618j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The past decade has seen enormous progress in DNA nanotechnology through the advent of DNA origami. Functionalizing the DNA origami for multiple applications is the recent focus of this field. Here we have constructed a novel DNA enzyme nano-factory, which modifies target DNA embedded on a DNA origami platform. The enzyme is programmed to reside in close proximity to the target DNA which enhances significantly the local concentration compared to solution-based DNA modification. To demonstrate this we have immobilized DNA methyltransferase M·TaqI next to the target DNA on the DNA origami and used this enzyme to sequence-specifically modify the target DNA with biotin using a cofactor analogue. Streptavidin binding to biotin is applied as a topographic marker to follow the machine cycle of this enzyme nano-factory using atomic force microscopy imaging. The nano-factory is demonstrated to be recyclable and holds the potential to be expanded to a multi-enzyme, multi-substrate operating system controlled by simple to complex molecules made of DNA, RNA or proteins.
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Affiliation(s)
- Elmar Weinhold
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
| | - Banani Chakraborty
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India.
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35
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36
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Affiliation(s)
- Peng Shi
- Department of Biomedical Engineering The Pennsylvania State University University Park PA 16802 USA
| | - Yong Wang
- Department of Biomedical Engineering The Pennsylvania State University University Park PA 16802 USA
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37
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Shi P, Wang Y. Synthetic DNA for Cell-Surface Engineering. Angew Chem Int Ed Engl 2021; 60:11580-11591. [PMID: 33006229 DOI: 10.1002/anie.202010278] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/29/2020] [Indexed: 12/14/2022]
Abstract
The cell membrane is not only a physical barrier, but also a functional organelle that regulates the communication between a cell and its environment. The ability to functionalize the cell membrane with synthetic molecules or nanostructures would advance cellular functions beyond what evolution has provided. The aim of this Minireview is to introduce recent progress in using synthetic DNA and DNA-based nanostructures for cell-surface engineering. We first introduce chemical conjugation and physical binding methods for monovalent and polyvalent surface engineering. We then introduce the application of these methods for either the promotion or inhibition of cell-environment communication in numerous applications, including the promotion of cell-cell recognition, regulation of intracellular pathways, protection of therapeutic cells, and sensing of the intracellular and extracellular microenvironments. Lastly, we summarize current challenges existing in this area and potential solutions to solve these challenges.
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Affiliation(s)
- Peng Shi
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Yong Wang
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
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38
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Gerrits L, Hammink R, Kouwer PHJ. Semiflexible polymer scaffolds: an overview of conjugation strategies. Polym Chem 2021. [DOI: 10.1039/d0py01662d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Semiflexible polymers are excellent scaffolds for the presentation of a wide variety of (bio)molecules. This manuscript reviews advantages and challenges of the most common conjugation strategies for the major classes of semiflexible polymers.
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Affiliation(s)
- Lotte Gerrits
- Institute for Molecules and Materials
- Radboud University
- 6525 AJ Nijmegen
- The Netherlands
| | - Roel Hammink
- Department of Tumor Immunology
- Radboud Institute for Molecular Life Sciences
- Radboud University Medical Center
- 6525 GA Nijmegen
- The Netherlands
| | - Paul H. J. Kouwer
- Institute for Molecules and Materials
- Radboud University
- 6525 AJ Nijmegen
- The Netherlands
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39
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Williams ND, Landajuela A, Kasula RK, Zhou W, Powell JT, Xi Z, Isaacs FJ, Berro J, Toomre D, Karatekin E, Lin C. DNA-Origami-Based Fluorescence Brightness Standards for Convenient and Fast Protein Counting in Live Cells. NANO LETTERS 2020; 20:8890-8896. [PMID: 33164530 PMCID: PMC7726105 DOI: 10.1021/acs.nanolett.0c03925] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Fluorescence microscopy has been one of the most discovery-rich methods in biology. In the digital age, the discipline is becoming increasingly quantitative. Virtually all biological laboratories have access to fluorescence microscopes, but abilities to quantify biomolecule copy numbers are limited by the complexity and sophistication associated with current quantification methods. Here, we present DNA-origami-based fluorescence brightness standards for counting 5-300 copies of proteins in bacterial and mammalian cells, tagged with fluorescent proteins or membrane-permeable organic dyes. Compared to conventional quantification techniques, our brightness standards are robust, straightforward to use, and compatible with nearly all fluorescence imaging applications, thereby providing a practical and versatile tool to quantify biomolecules via fluorescence microscopy.
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Affiliation(s)
- Nathan D. Williams
- Department of Cell Biology, Yale University School of
Medicine, New Haven, CT 06520, USA
- Nanobiology Institute, Yale University, West Haven CT
06516, USA
| | - Ane Landajuela
- Nanobiology Institute, Yale University, West Haven CT
06516, USA
- Department of Cellular and Molecular Physiology, Yale
University School of Medicine, New Haven, CT 06520, USA
| | - Ravi Kiran Kasula
- Department of Cell Biology, Yale University School of
Medicine, New Haven, CT 06520, USA
| | - Wenjiao Zhou
- Department of Cell Biology, Yale University School of
Medicine, New Haven, CT 06520, USA
- Nanobiology Institute, Yale University, West Haven CT
06516, USA
| | - John T. Powell
- Department of Cell Biology, Yale University School of
Medicine, New Haven, CT 06520, USA
- Nanobiology Institute, Yale University, West Haven CT
06516, USA
| | - Zhiqun Xi
- Department of Cell Biology, Yale University School of
Medicine, New Haven, CT 06520, USA
| | - Farren J. Isaacs
- Department of Molecular, Cellular and Developmental
Biology, Yale University, New Haven, CT 06520, USA
- Department of Biomedical Engineering, Yale University, New
Haven, CT 06520, USA
- Systems Biology Institute, Yale University, West Haven, CT
06516, USA
| | - Julien Berro
- Department of Cell Biology, Yale University School of
Medicine, New Haven, CT 06520, USA
- Nanobiology Institute, Yale University, West Haven CT
06516, USA
- Department of Molecular Biophysics and Biochemistry, New
Haven, CT 06520, USA
| | - Derek Toomre
- Department of Cell Biology, Yale University School of
Medicine, New Haven, CT 06520, USA
| | - Erdem Karatekin
- Nanobiology Institute, Yale University, West Haven CT
06516, USA
- Department of Cellular and Molecular Physiology, Yale
University School of Medicine, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, New
Haven, CT 06520, USA
- Université de Paris, SPPIN –
Saints-Pères Paris Institute for the Neurosciences, Centre National de la
Recherche Scientifique (CNRS), F-75006 Paris, France
| | - Chenxiang Lin
- Department of Cell Biology, Yale University School of
Medicine, New Haven, CT 06520, USA
- Nanobiology Institute, Yale University, West Haven CT
06516, USA
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40
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Chandrasekaran AR, Mathivanan J, Ebrahimi P, Vilcapoma J, Chen AA, Halvorsen K, Sheng J. Hybrid DNA/RNA nanostructures with 2'-5' linkages. NANOSCALE 2020; 12:21583-21590. [PMID: 33089274 PMCID: PMC7644649 DOI: 10.1039/d0nr05846g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Nucleic acid nanostructures with different chemical compositions have shown utility in biological applications as they provide additional assembly parameters and enhanced stability. The naturally occurring 2'-5' linkage in RNA is thought to be a prebiotic analogue and has potential use in antisense therapeutics. Here, we report the first instance of DNA/RNA motifs containing 2'-5' linkages. We synthesized and incorporated RNA strands with 2'-5' linkages into different DNA motifs with varying number of branch points (a duplex, four arm junction, double crossover motif and tensegrity triangle motif). Using experimental characterization and molecular dynamics simulations, we show that hybrid DNA/RNA nanostructures can accommodate interspersed 2'-5' linkages with relatively minor effect on the formation of these structures. Further, the modified nanostructures showed improved resistance to ribonuclease cleavage, indicating their potential use in the construction of robust drug delivery vehicles with prolonged stability in physiological conditions.
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Affiliation(s)
- Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
- To whom correspondence should be addressed: (ARC), (JS)
| | - Johnsi Mathivanan
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222
| | - Parisa Ebrahimi
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222
| | - Javier Vilcapoma
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
| | - Alan A. Chen
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
| | - Jia Sheng
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222
- To whom correspondence should be addressed: (ARC), (JS)
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41
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Zhou R, Hu C, Jin Y, Zhang J, Du H, Yang P, Chen J, Hou X, Cheng N. Spatially Constrained DNA Nanomachines To Accelerate Kinetics in Response to External Input: Design and Bioanalysis. Anal Chem 2020; 92:8909-8916. [PMID: 32521999 DOI: 10.1021/acs.analchem.0c00802] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Cells take advantage of the spatial organization to accelerate the reaction kinetics of diverse components within a crowded intracellular environment. Inspired by this, we hereby designed a principle of spatial constraint to overcome limitations of response kinetics in DNAzyme-powered DNA nanomachines. First, we proposed the type-1 of spatially constrained DNA nanomachines (scDN-1) by co-localizing the aptamer probe and power unit (DNAzyme), allowing the DNA nanomachines to accomplish faster cyclic cleavage of DNAzyme as intramolecular reactions. To expand the scDN into the clinical practice, Type 2 spatially constrained DNA nanomachines (scDN-2) with constrained antibody probes were then constructed through Holliday junction assembly, which increased the effective local concentration to obtain the improved kinetics. With an accelerated response kinetics, this design principle allows DNA nanomachines to accomplish the response to tumor markers in real patients' samples within 30 min, significantly broadening the bioanalytical applications of DNA nanomachines to clinical practice.
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Affiliation(s)
- Rongxing Zhou
- Biliary Surgical Department, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Changjia Hu
- Analytical & Testing Centre, Sichuan University, Chengdu, Sichuan 610064, China
| | - Yanwen Jin
- Biliary Surgical Department, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jie Zhang
- Biliary Surgical Department, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Huan Du
- Analytical & Testing Centre, Sichuan University, Chengdu, Sichuan 610064, China
| | - Peng Yang
- Analytical & Testing Centre, Sichuan University, Chengdu, Sichuan 610064, China
| | - Junbo Chen
- Analytical & Testing Centre, Sichuan University, Chengdu, Sichuan 610064, China
| | - Xiandeng Hou
- Analytical & Testing Centre, Sichuan University, Chengdu, Sichuan 610064, China
| | - Nansheng Cheng
- Biliary Surgical Department, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
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42
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Paiva TO, Torbensen K, Patel AN, Anne A, Chovin A, Demaille C, Bataille L, Michon T. Probing the Enzymatic Activity of Individual Biocatalytic fd-Viral Particles by Electrochemical-Atomic Force Microscopy. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01920] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Telmo O. Paiva
- Université de Paris, Laboratoire d’Electrochimie Moléculaire, CNRS UMR 7591, F-75006 Paris, France
| | - Kristian Torbensen
- Université de Paris, Laboratoire d’Electrochimie Moléculaire, CNRS UMR 7591, F-75006 Paris, France
| | - Anisha N. Patel
- Université de Paris, Laboratoire d’Electrochimie Moléculaire, CNRS UMR 7591, F-75006 Paris, France
| | - Agnès Anne
- Université de Paris, Laboratoire d’Electrochimie Moléculaire, CNRS UMR 7591, F-75006 Paris, France
| | - Arnaud Chovin
- Université de Paris, Laboratoire d’Electrochimie Moléculaire, CNRS UMR 7591, F-75006 Paris, France
| | - Christophe Demaille
- Université de Paris, Laboratoire d’Electrochimie Moléculaire, CNRS UMR 7591, F-75006 Paris, France
| | - Laure Bataille
- Université de Bordeaux, Biologie du Fruit et Pathologie, INRA UMR 1332, F-33140 Villenave d’Ornon, France
| | - Thierry Michon
- Université de Bordeaux, Biologie du Fruit et Pathologie, INRA UMR 1332, F-33140 Villenave d’Ornon, France
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43
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Spelkov AA, Goncharova EA, Savin AM, Kolpashchikov DM. Bifunctional RNA-Targeting Deoxyribozyme Nanodevice as a Potential Theranostic Agent. Chemistry 2020; 26:3489-3493. [PMID: 31943434 DOI: 10.1002/chem.201905528] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 01/09/2020] [Indexed: 01/14/2023]
Abstract
Theranostic approaches rely on simultaneous diagnostic of a disease and its therapy. Here, we designed a DNA nanodevice, which can simultaneously report the presence of a specific RNA target through an increase in fluorescence and cleave it. High selectivity of RNA target recognition under near physiological conditions was achieved. The proposed approach can become a basis for the design of DNA nanomachines and robots for diagnostics and therapy of viral infections, cancer, and genetic disorders.
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Affiliation(s)
- Aleksandr A Spelkov
- Laboratory of Solution Chemistry of Advanced Materials, and Technologies, ITMO University, Lomonosova St. 9, 191002, St. Petersburg, Russian Federation
| | - Ekaterina A Goncharova
- Laboratory of Solution Chemistry of Advanced Materials, and Technologies, ITMO University, Lomonosova St. 9, 191002, St. Petersburg, Russian Federation
| | - Artemii M Savin
- Laboratory of Solution Chemistry of Advanced Materials, and Technologies, ITMO University, Lomonosova St. 9, 191002, St. Petersburg, Russian Federation
| | - Dmitry M Kolpashchikov
- Laboratory of Solution Chemistry of Advanced Materials, and Technologies, ITMO University, Lomonosova St. 9, 191002, St. Petersburg, Russian Federation.,Chemistry Department, University of Central Florida, Orlando, 32816, Florida, USA.,Burnett School of Biomedical Sciences, University of Central Florida, Orlando, 32816, Florida, USA
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44
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Xiong Q, Xie C, Zhang Z, Liu L, Powell JT, Shen Q, Lin C. DNA Origami Post-Processing by CRISPR-Cas12a. Angew Chem Int Ed Engl 2020; 59:3956-3960. [PMID: 31883145 PMCID: PMC7101258 DOI: 10.1002/anie.201915555] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Indexed: 12/26/2022]
Abstract
Customizable nanostructures built through the DNA-origami technique hold tremendous promise in nanomaterial fabrication and biotechnology. Despite the cutting-edge tools for DNA-origami design and preparation, it remains challenging to separate structural components of an architecture built from-thus held together by-a continuous scaffold strand, which in turn limits the modularity and function of the DNA-origami devices. To address this challenge, here we present an enzymatic method to clean up and reconfigure DNA-origami structures. We target single-stranded (ss) regions of DNA-origami structures and remove them with CRISPR-Cas12a, a hyper-active ssDNA endonuclease without sequence specificity. We demonstrate the utility of this facile, selective post-processing method on DNA structures with various geometrical and mechanical properties, realizing intricate structures and structural transformations that were previously difficult to engineer. Given the biocompatibility of Cas12a-like enzymes, this versatile tool may be programmed in the future to operate functional nanodevices in cells.
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Affiliation(s)
| | | | - Zhao Zhang
- Department of Cell Biology & Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516 (USA)
| | - Longfei Liu
- Department of Cell Biology & Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516 (USA)
| | - John T Powell
- Department of Cell Biology & Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516 (USA)
| | - Qi Shen
- Department of Cell Biology & Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516 (USA)
| | - Chenxiang Lin
- Department of Cell Biology & Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516 (USA)
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45
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Xiong Q, Xie C, Zhang Z, Liu L, Powell JT, Shen Q, Lin C. DNA Origami Post‐Processing by CRISPR‐Cas12a. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Qiancheng Xiong
- Department of Cell Biology & Nanobiology Institute Yale University 850 West Campus Drive West Haven CT 06516 USA
| | - Chun Xie
- Department of Cell Biology & Nanobiology Institute Yale University 850 West Campus Drive West Haven CT 06516 USA
| | - Zhao Zhang
- Department of Cell Biology & Nanobiology Institute Yale University 850 West Campus Drive West Haven CT 06516 USA
| | - Longfei Liu
- Department of Cell Biology & Nanobiology Institute Yale University 850 West Campus Drive West Haven CT 06516 USA
| | - John T Powell
- Department of Cell Biology & Nanobiology Institute Yale University 850 West Campus Drive West Haven CT 06516 USA
| | - Qi Shen
- Department of Cell Biology & Nanobiology Institute Yale University 850 West Campus Drive West Haven CT 06516 USA
| | - Chenxiang Lin
- Department of Cell Biology & Nanobiology Institute Yale University 850 West Campus Drive West Haven CT 06516 USA
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46
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Wang D, Chai Y, Yuan Y, Yuan R. Lattice-Like DNA Tetrahedron Nanostructure as Scaffold to Locate GOx and HRP Enzymes for Highly Efficient Enzyme Cascade Reaction. ACS APPLIED MATERIALS & INTERFACES 2020; 12:2871-2877. [PMID: 31849211 DOI: 10.1021/acsami.9b18702] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In this work, the array arrangement of cascade enzymes was implemented by alternately and equidistantly anchoring two model enzymes glucose oxidase (GOx) and horseradish peroxidase (HRP) to the vertexes of rigid DNA tetrahedron units in lattice-like nucleic acid scaffold, in which the distance between any adjacent cascade enzymes had been regulated to the optimum for obtaining high enzyme cascade catalytic efficiency. Compared to the enzyme cascade system with no-array arrangement of cascade enzymes, the proposed enzyme cascade system allowed the intermediate H2O2 produced by GOx catalyzing substrate glucose to concurrently and equidistantly diffuse toward the four adjacent HRP enzyme surfaces. In this case, the invalid diffusion effect of intermediate H2O2 between cascade enzymes could be effectively avoided, thereby promoting the enzyme cascade reaction with high catalytic efficiency. The specific catalytic efficiency (kcat/Km) of the cascade enzyme system with array arrangement had been evaluated, which exhibited catalytic efficiency about 3.6 times higher than that of the randomly arranged cascade enzyme system. As a result, this strategy provided a new avenue for constructing a highly efficient enzyme cascade system with ultimate applications in biosynthesis, bioanalysis, and biodiagnostics.
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Affiliation(s)
- Ding Wang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China
| | - Yaqin Chai
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China
| | - Yali Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China
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47
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Shen Q, Grome MW, Yang Y, Lin C. Engineering Lipid Membranes with Programmable DNA Nanostructures. ADVANCED BIOSYSTEMS 2020; 4:1900215. [PMID: 31934608 PMCID: PMC6957268 DOI: 10.1002/adbi.201900215] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Indexed: 12/18/2022]
Abstract
Lipid and DNA are abundant biomolecules with critical functions in cells. The water-insoluble, amphipathic lipid molecules are best known for their roles in energy storage (e.g. as triglyceride), signaling (e.g. as sphingolipid), and compartmentalization (e.g. by forming membrane-enclosed bodies). The soluble, highly negatively charged DNA, which stores cells' genetic information, has proven to be an excellent material for constructing programmable nanostructures in vitro thanks to its self-assembling capabilities. These two seemingly distant molecules make contact within cell nuclei, often via lipidated proteins, with proposed functions of modulating chromatin structures. Carefully formulated lipid/DNA complexes are promising reagents for gene therapy. The past few years saw an emerging research field of interfacing DNA nanostructures with lipid membranes, with an overarching goal of generating DNA/lipid hybrid materials that possess novel and controllable structure, dynamics, and function. An arsenal of DNA-based tools has been created to coat, mold, deform, and penetrate lipid bilayers, affording us the ability to manipulate membranes with nanoscopic precision. These membrane engineering methods not only enable quantitative biophysical studies, but also open new opportunities in synthetic biology (e.g. artificial cells) and therapeutics (e.g. drug delivery).
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Affiliation(s)
- Qi Shen
- Department of Cell Biology and Nanobiology Institute, Yale University
| | - Michael W Grome
- Department of Cell Biology and Nanobiology Institute, Yale University
| | - Yang Yang
- Department of Cell Biology and Nanobiology Institute, Yale University
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine
| | - Chenxiang Lin
- Department of Cell Biology and Nanobiology Institute, Yale University
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48
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Ngo TA, Dinh H, Nguyen TM, Liew FF, Nakata E, Morii T. Protein adaptors assemble functional proteins on DNA scaffolds. Chem Commun (Camb) 2019; 55:12428-12446. [PMID: 31576822 DOI: 10.1039/c9cc04661e] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
DNA is an attractive molecular building block to construct nanoscale structures for a variety of applications. In addition to their structure and function, modification the DNA nanostructures by other molecules opens almost unlimited possibilities for producing functional DNA-based architectures. Among the molecules to functionalize DNA nanostructures, proteins are one of the most attractive candidates due to their vast functional variations. DNA nanostructures loaded with various types of proteins hold promise for applications in the life and material sciences. When loading proteins of interest on DNA nanostructures, the nanostructures by themselves act as scaffolds to specifically control the location and number of protein molecules. The methods to arrange proteins of interest on DNA scaffolds at high yields while retaining their activity are still the most demanding task in constructing usable protein-modified DNA nanostructures. Here, we provide an overview of the existing methods applied for assembling proteins of interest on DNA scaffolds. The assembling methods were categorized into two main classes, noncovalent and covalent conjugation, with both showing pros and cons. The recent advance of DNA-binding adaptor mediated assembly of proteins on the DNA scaffolds is highlighted and discussed in connection with the future perspectives of protein assembled DNA nanoarchitectures.
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Affiliation(s)
- Tien Anh Ngo
- Vinmec Biobank, Hi-tech Center, Vinmec Healthcare System, 458 Minh Khai, Ha Noi, Vietnam
| | - Huyen Dinh
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Thang Minh Nguyen
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Fong Fong Liew
- MAHSA University, Faculty of Dentistry, Bandar Saujana Putra, 42610 Jenjarom, Selangor, Malaysia
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
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49
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Ellis GA, Klein WP, Lasarte-Aragonés G, Thakur M, Walper SA, Medintz IL. Artificial Multienzyme Scaffolds: Pursuing in Vitro Substrate Channeling with an Overview of Current Progress. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02413] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Gregory A. Ellis
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - William P. Klein
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- National Research Council, Washington, D.C. 20001, United States
| | - Guillermo Lasarte-Aragonés
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Meghna Thakur
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Scott A. Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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50
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Nguyen TM, Nakata E, Zhang Z, Saimura M, Dinh H, Morii T. Rational design of a DNA sequence-specific modular protein tag by tuning the alkylation kinetics. Chem Sci 2019; 10:9315-9325. [PMID: 32110294 PMCID: PMC7006624 DOI: 10.1039/c9sc02990g] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 08/19/2019] [Indexed: 01/03/2023] Open
Abstract
Sequence-selective chemical modification of DNA by synthetic ligands has been a long-standing challenge in the field of chemistry. Even when the ligand consists of a sequence-specific DNA binding domain and reactive group, sequence-selective reactions by these ligands are often accompanied by off-target reactions. A basic principle to design DNA modifiers that react at specific sites exclusively governed by DNA sequence recognition remains to be established. We have previously reported selective DNA modification by a self-ligating protein tag conjugated with a DNA-binding domain, termed as a modular adaptor, and orthogonal application of modular adaptors by relying on the chemoselectivity of the protein tag. The sequence-specific crosslinking reaction by the modular adaptor is thought to proceed in two steps: the first step involves the formation of a DNA-protein complex, while in the second step, a proximity-driven intermolecular crosslinking occurs. According to this scheme, the specific crosslinking reaction of a modular adaptor would be driven by the DNA recognition process only when the dissociation rate of the DNA complex is much higher than the rate constant for the alkylation reaction. In this study, as a proof of principle, a set of combinations for modular adaptors and their substrates were utilized to evaluate the reactions. Three types of modular adaptors consisting of a single type of self-ligating tag and three types of DNA binding proteins fulfill the kinetic requirements for the reaction of the self-ligating tag with a substrate and the dissociation of the DNA-protein complex. These modular adaptors actually undergo sequence-specific crosslinking reactions exclusively driven by the recognition of a specific DNA sequence. The design principle of sequence-specific modular adaptors based on the kinetic aspects of complex formation and chemical modification is applicable for developing recognition-driven selective modifiers for proteins and other biological macromolecules.
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Affiliation(s)
- Thang Minh Nguyen
- Institute of Advanced Energy , Kyoto University , Uji , Kyoto 611-0011 , Japan .
| | - Eiji Nakata
- Institute of Advanced Energy , Kyoto University , Uji , Kyoto 611-0011 , Japan .
| | - Zhengxiao Zhang
- Institute of Advanced Energy , Kyoto University , Uji , Kyoto 611-0011 , Japan .
| | - Masayuki Saimura
- Institute of Advanced Energy , Kyoto University , Uji , Kyoto 611-0011 , Japan .
| | - Huyen Dinh
- Institute of Advanced Energy , Kyoto University , Uji , Kyoto 611-0011 , Japan .
| | - Takashi Morii
- Institute of Advanced Energy , Kyoto University , Uji , Kyoto 611-0011 , Japan .
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