1
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Bennett ID, Burns JR, Ryadnov MG, Howorka S, Pyne ALB. Lipidated DNA Nanostructures Target and Rupture Bacterial Membranes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2207585. [PMID: 38840451 DOI: 10.1002/smll.202207585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/01/2024] [Indexed: 06/07/2024]
Abstract
Chemistry has the power to endow supramolecular nanostructures with new biomedically relevant functions. Here it is reported that DNA nanostructures modified with cholesterol tags disrupt bacterial membranes to cause microbial cell death. The lipidated DNA nanostructures bind more readily to cholesterol-free bacterial membranes than to cholesterol-rich, eukaryotic membranes. These highly negatively charged, lipidated DNA nanostructures cause bacterial cell death by rupturing membranes. Strikingly, killing is mediated by clusters of barrel-shaped nanostructures that adhere to the membrane without the involvement of expected bilayer-puncturing barrels. These DNA nanomaterials may inspire the development of polymeric or small-molecule antibacterial agents that mimic the principles of selective binding and rupturing to help combat antimicrobial resistance.
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Affiliation(s)
- Isabel D Bennett
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London, WC1H 0AH, United Kingdom
- Division of Medicine, University College London, Cruciform Building, Gower Street, London, WC1E 6BT, United Kingdom
| | - Jonathan R Burns
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London, WC1H 0AJ, United Kingdom
| | - Maxim G Ryadnov
- National Physical Laboratory, Teddington, TW11 0LW, United Kingdom
- Department of Physics, King's College London, Strand Lane, London, WC2R 2LS, United Kingdom
| | - Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London, WC1H 0AJ, United Kingdom
| | - Alice L B Pyne
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London, WC1H 0AH, United Kingdom
- Department of Materials Science and Engineering, University of Sheffield, Sir Robert Hadfield Building, Sheffield, S1 3JD, United Kingdom
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2
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Zhang S, Gan Y, Wang H, Qi X, Su P, Song J, Yang Y. Enhancing Chymotrypsin Activity and Stability of Capillary Immobilized Enzyme Microreactors Using Zeolitic Imidazolate Frameworks as Encapsulation Materials. Anal Chem 2024; 96:9228-9235. [PMID: 38779801 DOI: 10.1021/acs.analchem.4c01425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Open-tubular immobilized enzyme microreactors (OT-IMERs) are some of the most widely used enzyme reaction devices due to the advantages of simple preparation and fast sample processing. However, the traditional approaches for OT-IMERs preparation had some defects such as limited enzyme loading amount, susceptibility to complex sample interference, and less stability. Here, we report a strategy for the preparation of highly active and stable OT-IMERs, in which the single-stranded DNA-enzyme composites were immobilized in capillaries and then encapsulated in situ in the capillaries via zeolitic imidazolate frameworks (ZIF-L). The phosphate groups of the DNA adjusted the surface potential of the enzyme to negative values, which could attract cations, such as Zn2+, to promote the formation of ZIF-L for enzyme encapsulation. Using chymotrypsin (ChT) as a model enzyme, the prepared ChT@ZIF-L-IMER has higher activity and better affinity than the free enzyme and ChT-IMER. Moreover, the thermal stability, pH stability, and organic solvent stability of ChT@ZIF-L-IMER were much higher than those of free enzyme and ChT-IMER. Furthermore, the activity of ChT@ZIF-L-IMER was much higher than that of ChT-IMER after ten consecutive reactions. To demonstrate the versatility of this preparation method, we replaced ChT with glucose oxidase (GOx). The stability of GOx@ZIF-L-IMER was also experimentally demonstrated to be superior to that of GOx and GOx-IMER. Finally, ChT@ZIF-L-IMER was used for proteolytic digestion analysis. The results showed that ChT@ZIF-L-IMER had a short digestion time and high digestive efficiency compared with the free enzyme. The present study broadened the synthesis method of OT-IMERs, effectively integrating the advantages of metal-organic frameworks and IMER, and the prepared OT-IMERs significantly improved enzyme stability. All of the results indicated that the IMER prepared by this method had a broad application prospect in capillary electrophoresis-based high-performance enzyme analysis.
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Affiliation(s)
- Shuyi Zhang
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Yijia Gan
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Han Wang
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Xingyi Qi
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Ping Su
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Jiayi Song
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Yi Yang
- Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, College of Chemistry, Beijing University of Chemical Technology, Beijing 100029, P. R. China
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3
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Hatami H, Rahiman N, Mohammadi M. Oligonucleotide based nanogels for cancer therapeutics. Int J Biol Macromol 2024; 267:131401. [PMID: 38582467 DOI: 10.1016/j.ijbiomac.2024.131401] [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: 02/03/2024] [Revised: 03/17/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024]
Abstract
Oligonucleotide-based nanogels, as nascent biomaterials, possess several unique functional, structural, and physicochemical features with excellent drug-loading capacity and high potential for cancer gene therapy. Ongoing studies utilizing oligonucleotide-based nanogels hold great promise, as these cutting-edge nanoplatforms can be elegantly developed with predesigned oligonucleotide sequences and complementary strands which are self-assembled or chemically crosslinked leading to the development of nanogels with predictable shape and tunable size with the desired functional properties. Current paper provides a summary of the properties, preparation methods, and applications of oligonucleotide-based nanogels in cancer therapy. The review is focused on both conventional and modified forms of oligonucleotide-based nanogels, including targeted nanogels, smart release nanogels (responsive to stimuli such as pH, temperature, and enzymes), as well as nanogels used for gene delivery. Their application in cancer immunotherapy and vaccination, photodynamic therapy, and diagnostic applications when combined with other nanoparticles is further discussed. Despite emerging designs in the development of oligonucleotide based nanogels, this field of study is still in its infancy, and clinical translation of these versatile nano-vehicles might face challenges. Hence, extensive research must be performed on in vivo behavior of such platforms determining their biodistribution, biological fate, and acute/subacute toxicity.
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Affiliation(s)
- Hooman Hatami
- Department of pharmaceutics, School of pharmacy, Mashhad University of Medical sciences, Mashhad, Iran
| | - Niloufar Rahiman
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Nanotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Marzieh Mohammadi
- Department of pharmaceutics, School of pharmacy, Mashhad University of Medical sciences, Mashhad, Iran; Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
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4
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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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5
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Alexander S, Moghadam MG, Rothenbroker M, Y T Chou L. Addressing the in vivo delivery of nucleic-acid nanostructure therapeutics. Adv Drug Deliv Rev 2023; 199:114898. [PMID: 37230305 DOI: 10.1016/j.addr.2023.114898] [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: 02/24/2023] [Revised: 05/02/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023]
Abstract
DNA and RNA nanostructures are being investigated as therapeutics, vaccines, and drug delivery systems. These nanostructures can be functionalized with guests ranging from small molecules to proteins with precise spatial and stoichiometric control. This has enabled new strategies to manipulate drug activity and to engineer devices with novel therapeutic functionalities. Although existing studies have offered encouraging in vitro or pre-clinical proof-of-concepts, establishing mechanisms of in vivo delivery is the new frontier for nucleic-acid nanotechnologies. In this review, we first provide a summary of existing literature on the in vivo uses of DNA and RNA nanostructures. Based on their application areas, we discuss current models of nanoparticle delivery, and thereby highlight knowledge gaps on the in vivo interactions of nucleic-acid nanostructures. Finally, we describe techniques and strategies for investigating and engineering these interactions. Together, we propose a framework to establish in vivo design principles and advance the in vivo translation of nucleic-acid nanotechnologies.
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Affiliation(s)
- Shana Alexander
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | | | - Meghan Rothenbroker
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | - Leo Y T Chou
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada.
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6
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Oktay E, Alem F, Hernandez K, Girgis M, Green C, Mathur D, Medintz IL, Narayanan A, Veneziano R. DNA origami presenting the receptor binding domain of SARS-CoV-2 elicit robust protective immune response. Commun Biol 2023; 6:308. [PMID: 36959304 PMCID: PMC10034259 DOI: 10.1038/s42003-023-04689-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/10/2023] [Indexed: 03/25/2023] Open
Abstract
Effective and safe vaccines are invaluable tools in the arsenal to fight infectious diseases. The rapid spreading of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible for the coronavirus disease 2019 pandemic has highlighted the need to develop methods for rapid and efficient vaccine development. DNA origami nanoparticles (DNA-NPs) presenting multiple antigens in prescribed nanoscale patterns have recently emerged as a safe, efficient, and easily scalable alternative for rational design of vaccines. Here, we are leveraging the unique properties of these DNA-NPs and demonstrate that precisely patterning ten copies of a reconstituted trimer of the receptor binding domain (RBD) of SARS-CoV-2 along with CpG adjuvants on the DNA-NPs is able to elicit a robust protective immunity against SARS-CoV-2 in a mouse model. Our results demonstrate the potential of our DNA-NP-based approach for developing safe and effective nanovaccines against infectious diseases with prolonged antibody response and effective protection in the context of a viral challenge.
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Affiliation(s)
- Esra Oktay
- Department of Bioengineering, George Mason University, Fairfax, VA, 22030, USA
| | - Farhang Alem
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, VA, 20110, USA
| | - Keziah Hernandez
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, VA, 20110, USA
| | - Michael Girgis
- Department of Bioengineering, George Mason University, Fairfax, VA, 22030, USA
| | - Christopher Green
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, USA
| | - Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, USA
| | - Aarthi Narayanan
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, VA, 20110, USA.
| | - Remi Veneziano
- Department of Bioengineering, George Mason University, Fairfax, VA, 22030, USA.
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7
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Huang J, Gambietz S, Saccà B. Self-Assembled Artificial DNA Nanocompartments and Their Bioapplications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2202253. [PMID: 35775957 DOI: 10.1002/smll.202202253] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Compartmentalization is the strategy evolved by nature to control reactions in space and time. The ability to emulate this strategy through synthetic compartmentalization systems has rapidly evolved in the past years, accompanied by an increasing understanding of the effects of spatial confinement on the thermodynamic and kinetic properties of the guest molecules. DNA nanotechnology has played a pivotal role in this scientific endeavor and is still one of the most promising approaches for the construction of nanocompartments with programmable structural features and nanometer-scaled addressability. In this review, the design approaches, bioapplications, and theoretical frameworks of self-assembled DNA nanocompartments are surveyed. From DNA polyhedral cages to virus-like capsules, the construction principles of such intriguing architectures are illustrated. Various applications of DNA nanocompartments, including their use for programmable enzyme scaffolding, single-molecule studies, biosensing, and as artificial nanofactories, ending with an ample description of DNA nanocages for biomedical purposes, are then reported. Finally, the theoretical hypotheses that make DNA nanocompartments, and nanosystems in general, a topic of great interest in modern science, are described and the progresses that have been done until now in the comprehension of the peculiar phenomena that occur within nanosized environments are summarized.
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Affiliation(s)
- Jing Huang
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
| | - Sabrina Gambietz
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
| | - Barbara Saccà
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
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8
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Baranda Pellejero L, Nijenhuis MAD, Ricci F, Gothelf KV. Protein-Templated Reactions Using DNA-Antibody Conjugates. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2200971. [PMID: 35344264 DOI: 10.1002/smll.202200971] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/10/2022] [Indexed: 06/14/2023]
Abstract
DNA-templated chemical reactions have found wide applications in drug discovery, programmed multistep synthesis, nucleic acid detection, and targeted drug delivery. The control of these reactions has, however, been limited to nucleic acid hybridization as a means to direct the proximity between reactants. In this work a system capable of translating protein-protein binding events into a DNA-templated reaction which leads to the covalent formation of a product is introduced. Protein-templated reactions by employing two DNA-antibody conjugates that are both able to recognize the same target protein and to colocalize a pair of reactant DNA strands able to undergo a click reaction are achieved. Two individual systems, each responsive to human serum albumin (HSA) and human IgG, are engineered and it is demonstrated that, while no reaction occurs in the absence of proteins, both protein-templated reactions can occur simultaneously in the same solution without any inter-system crosstalk.
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Affiliation(s)
- Lorena Baranda Pellejero
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, Rome, 00133, Italy
| | - Minke A D Nijenhuis
- Department of Chemistry and Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus, 8000, Denmark
| | - Francesco Ricci
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, Rome, 00133, Italy
| | - Kurt V Gothelf
- Department of Chemistry and Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus, 8000, Denmark
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9
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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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10
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Yu L, Ma Z, He Q. Dynamic DNA Nanostructures for Cell Manipulation. ACS Biomater Sci Eng 2023; 9:562-576. [PMID: 36592368 DOI: 10.1021/acsbiomaterials.2c01204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Dynamic DNA nanostructures are DNA nanostructures with reconfigurable elements that can undergo structural transformations in response to specific stimuli. Thus, anchoring dynamic DNA nanostructures on cell membranes is an attractive and promising strategy for well-controlled cell manipulation. Here, we review the latest progress in dynamic DNA nanostructures for cell manipulation. Commonly used mechanisms for dynamic DNA nanostructures are first introduced. Subsequently, we summarize the anchoring strategies for dynamic DNA nanostructures on cell membranes and list possible applications (including programming cell membrane receptors, controlling ligand activity and drug delivery, capturing and releasing cells, and assembling cells into clusters). Finally, insights into the remaining challenges are presented.
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Affiliation(s)
- Lu Yu
- Department of Endocrinology and Metabolism, The First People's Hospital of Changde City, Renmin Middle Road 818, Changde, Hunan 415000, P. R. China
| | - Zongrui Ma
- Department of Ophthalmology, The First People's Hospital of Changde City, Renmin Middle Road 818, Changde, Hunan 415000, P. R. China
| | - Qunye He
- School of Pharmacy, Shanghai Jiao Tong University, Dongchuan Road 800, Shanghai 200000, P. R. China
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11
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Ijäs H, Kostiainen MA, Linko V. Protein Coating of DNA Origami. Methods Mol Biol 2023; 2639:195-207. [PMID: 37166719 DOI: 10.1007/978-1-0716-3028-0_12] [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
DNA origami has emerged as a common technique to create custom two- (2D) and three-dimensional (3D) structures at the nanoscale. These DNA nanostructures have already proven useful in development of many biotechnological tools; however, there are still challenges that cast a shadow over the otherwise bright future of biomedical uses of these DNA objects. The rather obvious obstacles in harnessing DNA origami as drug-delivery vehicles and/or smart biodevices are related to their debatable stability in biologically relevant media, especially in physiological low-cation and endonuclease-rich conditions, relatively poor transfection rates, and, although biocompatible by nature, their unpredictable compatibility with the immune system. Here we demonstrate a technique for coating DNA origami with albumin proteins for enhancing their pharmacokinetic properties. To facilitate protective coating, a synthesized positively charged dendron was linked to bovine serum albumin (BSA) through a covalent maleimide-cysteine bonding, and then the purified dendron-protein conjugates were let to assemble on the negatively charged surface of DNA origami via electrostatic interaction. The resulted BSA-dendron conjugate-coated DNA origami showed improved transfection, high resistance against endonuclease digestion, and significantly enhanced immunocompatibility compared to bare DNA origami. Furthermore, our proposed coating strategy can be considered highly versatile as a maleimide-modified dendron serving as a synthetic DNA-binding domain can be linked to any protein with an available cysteine site.
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Affiliation(s)
- Heini Ijäs
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland
- LIBER Center of Excellence, Aalto University, Aalto, Finland
- Ludwig-Maximilians-University, Munich, Germany
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland.
- LIBER Center of Excellence, Aalto University, Aalto, Finland.
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland.
- LIBER Center of Excellence, Aalto University, Aalto, Finland.
- Institute of Technology, University of Tartu, Tartu, Estonia.
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12
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Snider DM, Pandit S, Coffin ML, Ebrahimi SB, Samanta D. DNA-Mediated Control of Protein Function in Semi-Synthetic Systems. Chembiochem 2022; 23:e202200464. [PMID: 36058885 DOI: 10.1002/cbic.202200464] [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: 08/10/2022] [Revised: 09/02/2022] [Indexed: 01/25/2023]
Abstract
The development of strategies for controlling protein function in a precise and predictable manner has the potential to revolutionize catalysis, diagnostics, and medicine. In this regard, the use of DNA has emerged as a powerful approach for modulating protein activity. The programmable nature of DNA allows for constructing sophisticated architectures wherein proteins can be placed with control over position, orientation, and stoichiometry. This ability is especially useful considering that the properties of proteins can be influenced by their local environment or their proximity to other functional molecules. Here, we chronicle the different strategies that have been developed to interface DNA with proteins in semi-synthetic systems. We further delineate the unique applications unlocked by the unprecedented level of structural control that DNA affords. We end by outlining outstanding challenges in the area and discuss future research directions towards potential solutions.
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Affiliation(s)
- Dylan M Snider
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Austin, TX, 78712, USA
| | - Subrata Pandit
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Austin, TX, 78712, USA
| | - Mackenzie L Coffin
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Austin, TX, 78712, USA
| | - Sasha B Ebrahimi
- Drug Product Development - Steriles, GlaxoSmithKline 1250 S Collegeville Rd, Collegeville, PA 19426, USA
| | - Devleena Samanta
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Austin, TX, 78712, USA
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13
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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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14
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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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15
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Mathew SS, Ahamed AAS, Abraham I, Prabhu DD, John F, George J. Self‐Assemblies of DNA ‐ Amphiphiles Nanostructures for New Design Strategies of Varied Morphologies. ChemistrySelect 2022. [DOI: 10.1002/slct.202202146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - A A Subuhan Ahamed
- School of Chemistry University of Hyderabad Hyderabad 500046 Telangana India
| | - Ignatious Abraham
- Department of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala India 682013
| | - Deepak D Prabhu
- Department of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala India 682013
| | - Franklin John
- Department of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala India 682013
| | - Jinu George
- Department of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala India 682013
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16
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Buchberger A, Riker K, Bernal-Chanchavac J, Narayanan RP, Simmons CR, Fahmi NE, Freeman R, Stephanopoulos N. Bioactive Fibronectin-III 10-DNA Origami Nanofibers Promote Cell Adhesion and Spreading. ACS APPLIED BIO MATERIALS 2022; 5:10.1021/acsabm.2c00303. [PMID: 36108278 PMCID: PMC10014493 DOI: 10.1021/acsabm.2c00303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The integration of proteins with DNA nanotechnology would enable materials with diverse applications in biology, medicine, and engineering. Here, we describe a method for the incorporation of bioactive fibronectin domain proteins with DNA nanostructures using two orthogonal coiled-coil peptides. One peptide from each coiled-coil pair is attached to a DNA origami cuboid in a multivalent fashion by attaching the peptides to DNA handles. These structures can then be assembled into one-dimensional arrays through the addition of a fibronectin domain linker genetically fused with the complementary peptides to those on the origami. We validate array formation using two different self-assembly protocols and characterize the fibers by atomic force and electron microscopy. Finally, we demonstrate that surfaces coated with the protein-DNA nanofibers can serve as biomaterial substrates for fibroblast adhesion and spreading with the nanofibers showing enhanced bioactivity compared to that of the monomeric protein.
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Affiliation(s)
- Alex Buchberger
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Kyle Riker
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, North Carolina 27514, United States
| | - Julio Bernal-Chanchavac
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Raghu Pradeep Narayanan
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Chad R Simmons
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Nour Eddine Fahmi
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Ronit Freeman
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, North Carolina 27514, United States
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
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17
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Xiong Y, Tsitkov S, Hess H, Gang O, Zhang Y. Microscale Colocalization of Cascade Enzymes Yields Activity Enhancement. ACS NANO 2022; 16:10383-10391. [PMID: 35549238 DOI: 10.1021/acsnano.2c00475] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Colocalization of cascade enzymes is broadly discussed as a phenomenon that can boost the cascade reaction throughput, although a direct experimental verification is often challenging. This is mainly due to difficulties in establishing proper size regimes and in the analytical quantification of colocalization effect with adequate experimental systems and simulations. In this study, by taking advantage of reversible DNA-directed colocalization of enzymes on microspheres, we established a cascade system that can be used to directly evaluate the colocalization effect with exactly the same experimental settings except for the state of enzyme dispersion. In the regime of highly dilute microspheres of particular sizes, the colocalized cascade shows enhanced activity compared with the freely diffusing cascade, as evidenced by a shortened lag phase in the time-course production. Reaction-diffusion modeling reveals that the enhancement can be ascribed to the initial accumulation of intermediate substrate around the colocalized enzymes and is found to be carrier-size-dependent. This work demonstrates the dependence of the colocalization effect of enzyme cascades on an interplay of nano- and microscales, lending theoretical support to the rational design of highly efficient multienzyme catalysts.
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Affiliation(s)
- Yan Xiong
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Stanislav Tsitkov
- Department of Biomedical Engineering, Columbia University, New York, New York 10027, United States
| | - Henry Hess
- Department of Biomedical Engineering, Columbia University, New York, New York 10027, United States
| | - Oleg Gang
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Yifei Zhang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
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18
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Shiu SCC, Whitehouse WL, Tanner JA. Designing aptamer-enabled DNA polyhedra using paper origami. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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19
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Bej S, Ghosh M, Das R, Banerjee P. Evaluation of nanomaterials-grafted enzymes for application in contaminants degradation: Need of the hour with proposed IoT synchronized nanosensor fit sustainable clean water technology in en masse. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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20
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Chakraborty B, Das S, Gupta A, Xiong Y, Vyshnavi TV, Kizer ME, Duan J, Chandrasekaran AR, Wang X. Aptamers for Viral Detection and Inhibition. ACS Infect Dis 2022; 8:667-692. [PMID: 35220716 PMCID: PMC8905934 DOI: 10.1021/acsinfecdis.1c00546] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Indexed: 02/07/2023]
Abstract
Recent times have experienced more than ever the impact of viral infections in humans. Viral infections are known to cause diseases not only in humans but also in plants and animals. Here, we have compiled the literature review of aptamers selected and used for detection and inhibition of viral infections in all three categories: humans, animals, and plants. This review gives an in-depth introduction to aptamers, different types of aptamer selection (SELEX) methodologies, the benefits of using aptamers over commonly used antibody-based strategies, and the structural and functional mechanism of aptasensors for viral detection and therapy. The review is organized based on the different characterization and read-out tools used to detect virus-aptasensor interactions with a detailed index of existing virus-targeting aptamers. Along with addressing recent developments, we also discuss a way forward with aptamers for DNA nanotechnology-based detection and treatment of viral diseases. Overall, this review will serve as a comprehensive resource for aptamer-based strategies in viral diagnostics and treatment.
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Affiliation(s)
- Banani Chakraborty
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Sreyashi Das
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, Uttar Pradesh 208016, India
| | - Arushi Gupta
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Yanyu Xiong
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory (HMNTL), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - T-V Vyshnavi
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Megan E. Kizer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jinwei Duan
- Department of Chemistry and Materials Science, Chang’an University, Xi’an, Shaanxi 710064, China
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Xing Wang
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory (HMNTL), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology (IGB), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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21
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Wang C, Chen X, Su Y, Wang H, Li D. Precise Regulating T Cell Activation Signaling with Spatial Controllable Positioning of Receptors on DNA Origami. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1016/j.cjac.2022.100091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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22
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Zhu CY, Li FL, Zhang YW, Gupta RK, Patel SKS, Lee JK. Recent Strategies for the Immobilization of Therapeutic Enzymes. Polymers (Basel) 2022; 14:polym14071409. [PMID: 35406282 PMCID: PMC9003532 DOI: 10.3390/polym14071409] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/18/2022] [Accepted: 03/23/2022] [Indexed: 02/04/2023] Open
Abstract
Therapeutic enzymes play important roles in modern medicine due to their high affinity and specificity. However, it is very expensive to use them in clinical medicine because of their low stability and bioavailability. To improve the stability and effectiveness of therapeutic enzymes, immobilization techniques have been employed to enhance the applications of therapeutic enzymes in the past few years. Reported immobilization techniques include entrapment, adsorption, and covalent attachment. In addition, protein engineering is often used to improve enzyme properties; however, all methods present certain advantages and limitations. For carrier-bound immobilization, the delivery and release of the immobilized enzyme depend on the properties of the carrier and enzyme. In this review, we summarize the advantages and challenges of the current strategies developed to deliver therapeutic enzymes and provide a future perspective on the immobilization technologies used for therapeutic enzyme delivery.
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Affiliation(s)
- Chen-Yuan Zhu
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, China; (C.-Y.Z.); (F.-L.L.)
| | - Fei-Long Li
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, China; (C.-Y.Z.); (F.-L.L.)
| | - Ye-Wang Zhang
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, China; (C.-Y.Z.); (F.-L.L.)
- Correspondence: (Y.-W.Z.); (S.K.S.P.); (J.-K.L.); Tel.: +82-2-450-3505 (J.-K.L.)
| | - Rahul K. Gupta
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Korea;
| | - Sanjay K. S. Patel
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Korea;
- Correspondence: (Y.-W.Z.); (S.K.S.P.); (J.-K.L.); Tel.: +82-2-450-3505 (J.-K.L.)
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Korea;
- Correspondence: (Y.-W.Z.); (S.K.S.P.); (J.-K.L.); Tel.: +82-2-450-3505 (J.-K.L.)
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23
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Hua Y, Ma J, Li D, Wang R. DNA-Based Biosensors for the Biochemical Analysis: A Review. BIOSENSORS 2022; 12:bios12030183. [PMID: 35323453 PMCID: PMC8945906 DOI: 10.3390/bios12030183] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/09/2022] [Accepted: 03/16/2022] [Indexed: 05/21/2023]
Abstract
In recent years, DNA-based biosensors have shown great potential as the candidate of the next generation biomedical detection device due to their robust chemical properties and customizable biosensing functions. Compared with the conventional biosensors, the DNA-based biosensors have advantages such as wider detection targets, more durable lifetime, and lower production cost. Additionally, the ingenious DNA structures can control the signal conduction near the biosensor surface, which could significantly improve the performance of biosensors. In order to show a big picture of the DNA biosensor's advantages, this article reviews the background knowledge and recent advances of DNA-based biosensors, including the functional DNA strands-based biosensors, DNA hybridization-based biosensors, and DNA templated biosensors. Then, the challenges and future directions of DNA-based biosensors are discussed and proposed.
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24
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Wu Z, Xiao M, Lai W, Sun Y, Li L, Hu Z, Pei H. Nucleic Acid-Based Cell Surface Engineering Strategies and Their Applications. ACS APPLIED BIO MATERIALS 2022; 5:1901-1915. [DOI: 10.1021/acsabm.1c01126] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Zhongdong Wu
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Yueyang Sun
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Zongqian Hu
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
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25
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Geng J, Xia X, Teng L, Wang L, Chen L, Guo X, Belingon B, Li J, Feng X, Li X, Shang W, Wan Y, Wang H. Emerging landscape of cell-penetrating peptide-mediated nucleic acid delivery and their utility in imaging, gene-editing, and RNA-sequencing. J Control Release 2022; 341:166-183. [PMID: 34822907 DOI: 10.1016/j.jconrel.2021.11.032] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 12/11/2022]
Abstract
The safety issues like immunogenicity and unacceptable cancer risk of viral vectors for DNA/mRNA vaccine delivery necessitate the development of non-viral vectors with no toxicity. Among the non-viral strategies, cell-penetrating peptides (CPPs) have been a topic of interest recently because of their ability to cross plasma membranes and facilitate nucleic acids delivery both in vivo and in vitro. In addition to the application in the field of gene vaccine and gene therapy, CPPs based nucleic acids delivery have been proved by its potential application like gene editing, RNA-sequencing, and imaging. Here, we focus on summarizing the recent applications and progress of CPPs-mediated nucleic acids delivery and discuss the current problems and solutions in this field.
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Affiliation(s)
- Jingping Geng
- Department of Microbiology and Immunology, Medical School, China Three Gorges University, Yichang 443002, China; Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China
| | - Xuan Xia
- Department of Physiology and Pathophysiology, Medical School, China Three Gorges University, Yichang 443002, China
| | - Lin Teng
- Department of Cardiovascular Medicine, The First Clinical Medical College of China Three Gorges University, Yichang 443002, China
| | - Lidan Wang
- Department of Microbiology and Immunology, Medical School, China Three Gorges University, Yichang 443002, China; Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China
| | - Linlin Chen
- Department of Microbiology and Immunology, Medical School, China Three Gorges University, Yichang 443002, China; Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China; Affiliated Ren He Hospital of China Three Gorges University, Yichang 443002, China
| | - Xiangli Guo
- Department of Microbiology and Immunology, Medical School, China Three Gorges University, Yichang 443002, China; Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China
| | - Bonn Belingon
- Institute of Cell Engineering, Johns Hopkins University, Baltimore, MD 21210, USA
| | - Jason Li
- Department of Biology, Johns Hopkins University, Baltimore, MD 21210, USA
| | - Xuemei Feng
- Department of Microbiology and Immunology, Medical School, China Three Gorges University, Yichang 443002, China; Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China
| | - Xianghui Li
- Department of Microbiology and Immunology, Medical School, China Three Gorges University, Yichang 443002, China; Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China
| | - Wendou Shang
- Department of Microbiology and Immunology, Medical School, China Three Gorges University, Yichang 443002, China; Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China
| | - Yingying Wan
- Department of Microbiology and Immunology, Medical School, China Three Gorges University, Yichang 443002, China; Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China
| | - Hu Wang
- Department of Microbiology and Immunology, Medical School, China Three Gorges University, Yichang 443002, China.
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26
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Yan J, Zhan X, Zhang Z, Chen K, Wang M, Sun Y, He B, Liang Y. Tetrahedral DNA nanostructures for effective treatment of cancer: advances and prospects. J Nanobiotechnology 2021; 19:412. [PMID: 34876145 PMCID: PMC8650297 DOI: 10.1186/s12951-021-01164-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/24/2021] [Indexed: 11/10/2022] Open
Abstract
Recently, DNA nanostructures with vast application potential in the field of biomedicine, especially in drug delivery. Among these, tetrahedral DNA nanostructures (TDN) have attracted interest worldwide due to their high stability, excellent biocompatibility, and simplicity of modification. TDN could be synthesized easily and reproducibly to serve as carriers for, chemotherapeutic drugs, nucleic acid drugs and imaging probes. Therefore, their applications include, but are not restricted to, drug delivery, molecular diagnostics, and biological imaging. In this review, we summarize the methods of functional modification and application of TDN in cancer treatment. Also, we discuss the pressing questions that should be targeted to increase the applicability of TDN in the future.
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Affiliation(s)
- Jianqin Yan
- Department of Pharmaceutics, School of Pharmacy, Qingdao University, Qingdao, 266021, China
| | - Xiaohui Zhan
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, China
- School of Biomedical Engineering, Sichuan University, Chengdu, 610064, China
| | - Zhuangzhuang Zhang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, China
- School of Biomedical Engineering, Sichuan University, Chengdu, 610064, China
| | - Keqi Chen
- Department of Clinical Laboratory, Qingdao Special Servicemen Recuperation Centre of PLA Navy, Qingdao, 266021, China
| | - Maolong Wang
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, 266000, China
| | - Yong Sun
- Department of Pharmaceutics, School of Pharmacy, Qingdao University, Qingdao, 266021, China.
| | - Bin He
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, China
- School of Biomedical Engineering, Sichuan University, Chengdu, 610064, China
| | - Yan Liang
- Department of Pharmaceutics, School of Pharmacy, Qingdao University, Qingdao, 266021, China.
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27
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Konč J, Brown L, Whiten DR, Zuo Y, Ravn P, Klenerman D, Bernardes GJL. A Platform for Site‐Specific DNA‐Antibody Bioconjugation by Using Benzoylacrylic‐Labelled Oligonucleotides. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Juraj Konč
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Libby Brown
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Daniel R. Whiten
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Yukun Zuo
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Peter Ravn
- AstraZeneca R&D BioPharmaceuticals Unit
- Antibody Discovery & Protein Engineering (ADPE) Milstein Building, Granta Park Cambridge CB21 6GH UK
- Current address: Department of Biotherapeutic Discovery H. Lundbeck A/S Ottiliavej 9, 2500 Valby Denmark
| | - David Klenerman
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
- UK Dementia Research Institute University of Cambridge Cambridge CB2 0XY UK
| | - Gonçalo J. L. Bernardes
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
- Instituto de Medicina Molecular João Lobo Antunes Faculdade de Medicina Universidade de Lisboa Avenida Professor Egas Moniz 1649-028 Lisboa Portugal
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28
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He Q, Liu Y, Li K, Wu Y, Wang T, Tan Y, Jiang T, Liu X, Liu Z. Deoxyribonucleic acid anchored on cell membranes for biomedical application. Biomater Sci 2021; 9:6691-6717. [PMID: 34494042 DOI: 10.1039/d1bm01057c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Engineering cellular membranes with functional molecules provides an attractive strategy to manipulate cellular behaviors and functionalities. Currently, synthetic deoxyribonucleic acid (DNA) has emerged as a promising molecular tool to engineer cellular membranes for biomedical applications due to its molecular recognition and programmable properties. In this review, we summarized the recent advances in anchoring DNA on the cellular membranes and their applications. The strategies for anchoring DNA on cell membranes were summarized. Then their applications, such as immune response activation, receptor oligomerization regulation, membrane structure mimicking, cell-surface biosensing, and construction of cell clusters, were listed. The DNA-enabled intelligent systems which were able to sense stimuli such as DNA strands, light, and metal ions were highlighted. Finally, insights regarding the remaining challenges and possible future directions were provided.
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Affiliation(s)
- Qunye He
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, P. R. China.
| | - Yanfei Liu
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, P. R. China
| | - Ke Li
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, P. R. China.
| | - Yuwei Wu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, P. R. China.
| | - Ting Wang
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, P. R. China.
| | - Yifu Tan
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, P. R. China
| | - Ting Jiang
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, P. R. China
| | - Xiaoqin Liu
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, P. R. China
| | - Zhenbao Liu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, P. R. China. .,Molecular Imaging Research Center of Central South University, Changsha 410008, Hunan, P. R. China
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29
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Konč J, Brown L, Whiten DR, Zuo Y, Ravn P, Klenerman D, Bernardes GJL. A Platform for Site-Specific DNA-Antibody Bioconjugation by Using Benzoylacrylic-Labelled Oligonucleotides. Angew Chem Int Ed Engl 2021; 60:25905-25913. [PMID: 34555238 PMCID: PMC9297960 DOI: 10.1002/anie.202109713] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Indexed: 12/27/2022]
Abstract
Many bioconjugation strategies for DNA oligonucleotides and antibodies suffer limitations, such as site-specificity, stoichiometry and hydrolytic instability of the conjugates, which makes them unsuitable for biological applications. Here, we report a new platform for the preparation of DNA-antibody bioconjugates with a simple benzoylacrylic acid pentafluorophenyl ester reagent. Benzoylacrylic-labelled oligonucleotides prepared with this reagent can be site-specifically conjugated to a range of proteins and antibodies through accessible cysteine residues. The homogeneity of the prepared DNA-antibody bioconjugates was confirmed by a new LC-MS protocol and the bioconjugate probes were used in fluorescence or super-resolution microscopy cell imaging experiments. This work demonstrates the versatility and robustness of our bioconjugation protocol that gives site-specific, well-defined and plasma-stable DNA-antibody bioconjugates for biological applications.
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Affiliation(s)
- Juraj Konč
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Libby Brown
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Daniel R Whiten
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Yukun Zuo
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Peter Ravn
- AstraZeneca, R&D BioPharmaceuticals Unit
- Antibody Discovery & Protein Engineering (ADPE), Milstein Building, Granta Park, Cambridge, CB21 6GH, UK.,Current address: Department of Biotherapeutic Discovery, H. Lundbeck A/S, Ottiliavej 9, 2500, Valby, Denmark
| | - David Klenerman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.,UK Dementia Research Institute, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Gonçalo J L Bernardes
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.,Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
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30
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Mariconti M, Morel M, Baigl D, Rudiuk S. Enzymatically Active DNA-Protein Nanogels with Tunable Cross-Linking Density. Biomacromolecules 2021; 22:3431-3439. [PMID: 34260203 DOI: 10.1021/acs.biomac.1c00501] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Hybrid DNA-protein nanogels represent potential protein vectors and enzymatic nanoreactors for modern biotechnology. Here, we describe a new, easy, and robust method for preparation of tunable DNA-protein nanogels with controllable size and density. For this purpose, polymerase chain reaction is used to prepare highly biotinylated DNA as a soft biopolymeric backbone, which can be efficiently cross-linked via streptavidin-biotin binding. This approach enables us to control both the density and size of the resulting nanogels not only by adjusting the amount of the cross-linking streptavidin but also by using different rates of DNA biotinylation. This gives DNA-streptavidin nanogels with the size ranging from 80 nm, for the most compact state, to up to 200 nm. Furthermore, using streptavidin-enzyme conjugates allows the straightforward one-pot incorporation of enzymes during the preparation of the nanogels. Monoenzymatic and multienzymatic nanogels have been obtained in this manner, and their catalytic activities have been characterized. All tested enzymes (alkaline phosphatase (AP), horseradish peroxidase (HRP), and β-galactosidase (βGal)), incorporated individually or in a coupled manner (glucose oxidase (GOx)-HRP cascade), were shown to remain functional. The activities of AP and βGal were unchanged while that of HRP was slightly improved inside the nanogels. We demonstrate that, for HRP, it is not the DNA-to-enzyme ratio but the physical density of the functionalized DNA nanogels that is responsible for the improvement of its enzymatic activity.
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Affiliation(s)
- Marina Mariconti
- PASTEUR, Department of Chemistry, PSL University, Sorbonne Université, CNRS, Ecole Normale Supérieure, Paris 75005, France
| | - Mathieu Morel
- PASTEUR, Department of Chemistry, PSL University, Sorbonne Université, CNRS, Ecole Normale Supérieure, Paris 75005, France
| | - Damien Baigl
- PASTEUR, Department of Chemistry, PSL University, Sorbonne Université, CNRS, Ecole Normale Supérieure, Paris 75005, France
| | - Sergii Rudiuk
- PASTEUR, Department of Chemistry, PSL University, Sorbonne Université, CNRS, Ecole Normale Supérieure, Paris 75005, France
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31
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Berger RML, Weck JM, Kempe SM, Hill O, Liedl T, Rädler JO, Monzel C, Heuer-Jungemann A. Nanoscale FasL Organization on DNA Origami to Decipher Apoptosis Signal Activation in Cells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2101678. [PMID: 34057291 DOI: 10.1002/smll.202101678] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/13/2021] [Indexed: 05/27/2023]
Abstract
Cell signaling is initiated by characteristic protein patterns in the plasma membrane, but tools to decipher their molecular organization and activation are hitherto lacking. Among the well-known signaling pattern is the death inducing signaling complex with a predicted hexagonal receptor architecture. To probe this architecture, DNA origami-based nanoagents with nanometer precise arrangements of the death receptor ligand FasL are introduced and presented to cells. Mimicking different receptor geometries, these nanoagents act as signaling platforms inducing fastest time-to-death kinetics for hexagonal FasL arrangements with 10 nm inter-molecular spacing. Compared to naturally occurring soluble FasL, this trigger is faster and 100× more efficient. Nanoagents with different spacing, lower FasL number or higher coupling flexibility impede signaling. The results present DNA origami as versatile signaling scaffolds exhibiting unprecedented control over molecular number and geometry. They define molecular benchmarks in apoptosis signal initiation and constitute a new strategy to drive particular cell responses.
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Affiliation(s)
- Ricarda M L Berger
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Johann M Weck
- Max Planck Institute of Biochemistry and Center for Nanoscience (CeNS), Ludwig-Maximilians-University, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Simon M Kempe
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Oliver Hill
- Apogenix AG, University of Heidelberg, Im Neuenheimer Feld 584, 69120, Heidelberg, Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Joachim O Rädler
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Cornelia Monzel
- Experimental Medical Physics, Heinrich-Heine University, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Amelie Heuer-Jungemann
- Max Planck Institute of Biochemistry and Center for Nanoscience (CeNS), Ludwig-Maximilians-University, Am Klopferspitz 18, 82152, Martinsried, Germany
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32
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DNA Nanodevices as Mechanical Probes of Protein Structure and Function. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11062802] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA nanotechnology has reported a wide range of structurally tunable scaffolds with precise control over their size, shape and mechanical properties. One promising application of these nanodevices is as probes for protein function or determination of protein structure. In this perspective we cover several recent examples in this field, including determining the effect of ligand spacing and multivalency on cell activation, applying forces at the nanoscale, and helping to solve protein structure by cryo-EM. We also highlight some future directions in the chemistry necessary for integrating proteins with DNA nanoscaffolds, as well as opportunities for computational modeling of hybrid protein-DNA nanomaterials.
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33
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Kim T, Nam K, Kim YM, Yang K, Roh YH. DNA-Assisted Smart Nanocarriers: Progress, Challenges, and Opportunities. ACS NANO 2021; 15:1942-1951. [PMID: 33492127 DOI: 10.1021/acsnano.0c08905] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Due to powerful breakthroughs in nanotechnology, smart delivery mechanisms have rapidly emerged for use in diverse applications across biomedical research and therapeutic development. Recent efforts toward understanding stimuli-responsive strategies have led to substantial improvements in their conceptual application and in vitro efficiency. Because disease targets for therapy are often localized in specific cells, organs, or tissues, an enhanced permeability and retention (EPR)-based strategy remains inadequate for accurate drug delivery and release to target regions, resulting in an insufficient drug concentration reaching the target region and undesired side effects. To address these issues, more precise and remote-controlled stimuli-responsive systems, which recognize and react to changes in the pathophysiological microenvironment, were recently elucidated as feasible on-demand drug-delivery systems. In this Perspective, we focus on progress toward stimuli-responsive drug-delivery systems that utilize dynamic DNA molecules by exploiting DNA nanotechnology. DNA structures can be precisely reconfigured by external and internal stimuli to drive the release of a loaded drug in a target region with appropriate microenvironments. We describe the chemical, physical, and biological engineering principles and strategies for constructing DNA-assisted nanocarriers. We also provide a summary of smart nanocarrier systems, organized with respect to the structural changes in the DNA strand in the microenvironment, resulting from changes in pH and temperature and the presence of intracellular oligonucleotides. To do so, we highlight recent advances in related biomedical research and applications as well as discuss major challenges and opportunities for DNA-assisted nanocarriers to guide the development of future in vivo therapies and clinical translation strategies.
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Affiliation(s)
- Taehyung Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Keonwook Nam
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Young Min Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Kyungjik Yang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Young Hoon Roh
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
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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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Lanphere C, Arnott PM, Jones SF, Korlova K, Howorka S. A Biomimetic DNA-Based Membrane Gate for Protein-Controlled Transport of Cytotoxic Drugs. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 133:1931-1936. [PMID: 38504763 PMCID: PMC10947198 DOI: 10.1002/ange.202011583] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Indexed: 12/15/2022]
Abstract
Chemistry is ideally placed to replicate biomolecular structures with tuneable building materials. Of particular interest are molecular nanopores, which transport cargo across membranes, as in DNA sequencing. Advanced nanopores control transport in response to triggers, but this cannot be easily replicated with biogenic proteins. Here we use DNA nanotechnology to build a synthetic molecular gate that opens in response to a specific protein. The gate self-assembles from six DNA strands to form a bilayer-spanning pore, and a lid strand comprising a protein-binding DNA aptamer to block the channel entrance. Addition of the trigger protein, thrombin, selectively opens the gate and enables a 330-fold increase inw the transport rate of small-molecule cargo. The molecular gate incorporates in delivery vesicles to controllably release enclosed cytotoxic drugs and kill eukaryotic cells. The generically designed gate may be applied in biomedicine, biosensing or for building synthetic cells.
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Affiliation(s)
- Conor Lanphere
- Department of ChemistryInstitute of Structural and Molecular BiologyUniversity College LondonLondonWC1H 0AJUK
| | - Patrick M. Arnott
- Department of Biochemical EngineeringUniversity College LondonLondonWC1E 7JEUK
| | - Sioned Fôn Jones
- Department of ChemistryInstitute of Structural and Molecular BiologyUniversity College LondonLondonWC1H 0AJUK
- Department of ChemistryKing's College LondonLondonSE1 1DBUK
| | - Katarina Korlova
- Department of ChemistryInstitute of Structural and Molecular BiologyUniversity College LondonLondonWC1H 0AJUK
| | - Stefan Howorka
- Department of ChemistryInstitute of Structural and Molecular BiologyUniversity College LondonLondonWC1H 0AJUK
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36
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Lim S, Kim J, Kim Y, Xu D, Clark DS. CRISPR/Cas-directed programmable assembly of multi-enzyme complexes. Chem Commun (Camb) 2020; 56:4950-4953. [PMID: 32239050 DOI: 10.1039/d0cc01174f] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe a versatile CRISPR/Cas-based strategy to construct multi-enzyme complexes scaffolded on a DNA template in programmable patterns. Catalytically inactive dCas9 nuclease was used in combination with SpyCatcher-SpyTag chemistry to assemble enzymes in a highly modular fashion. Five enzymes comprising the violacein biosynthesis pathway were precisely organized in nanometer proximity; a notable increase in violacein production demonstrated the benefits of scaffolding.
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Affiliation(s)
- Samuel Lim
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA.
| | - Jiwoo Kim
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA.
| | - Yujin Kim
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA.
| | - Dawei Xu
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA.
| | - Douglas S Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA. and Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
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37
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Lanphere C, Arnott PM, Jones SF, Korlova K, Howorka S. A Biomimetic DNA-Based Membrane Gate for Protein-Controlled Transport of Cytotoxic Drugs. Angew Chem Int Ed Engl 2020; 60:1903-1908. [PMID: 33231913 PMCID: PMC7894144 DOI: 10.1002/anie.202011583] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Indexed: 11/23/2022]
Abstract
Chemistry is ideally placed to replicate biomolecular structures with tuneable building materials. Of particular interest are molecular nanopores, which transport cargo across membranes, as in DNA sequencing. Advanced nanopores control transport in response to triggers, but this cannot be easily replicated with biogenic proteins. Here we use DNA nanotechnology to build a synthetic molecular gate that opens in response to a specific protein. The gate self‐assembles from six DNA strands to form a bilayer‐spanning pore, and a lid strand comprising a protein‐binding DNA aptamer to block the channel entrance. Addition of the trigger protein, thrombin, selectively opens the gate and enables a 330‐fold increase inw the transport rate of small‐molecule cargo. The molecular gate incorporates in delivery vesicles to controllably release enclosed cytotoxic drugs and kill eukaryotic cells. The generically designed gate may be applied in biomedicine, biosensing or for building synthetic cells.
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Affiliation(s)
- Conor Lanphere
- Department of Chemistry, Institute of Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK
| | - Patrick M Arnott
- Department of Biochemical Engineering, University College London, London, WC1E 7JE, UK
| | - Sioned Fôn Jones
- Department of Chemistry, Institute of Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK.,Department of Chemistry, King's College London, London, SE1 1DB, UK
| | - Katarina Korlova
- Department of Chemistry, Institute of Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK
| | - Stefan Howorka
- Department of Chemistry, Institute of Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK
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38
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Copp W, Wilds CJ. O 6 -Alkylguanine DNA Alkyltransferase Mediated Disassembly of a DNA Tetrahedron. Chemistry 2020; 26:14802-14806. [PMID: 32543755 DOI: 10.1002/chem.202002565] [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: 05/26/2020] [Indexed: 11/05/2022]
Abstract
Tetrahedron DNA structures were formed by the assembly of three-way junction (TWJ) oligonucleotides containing O6 -2'-deoxyguanosine-alkylene-O6 -2'-deoxyguanosine (butylene and heptylene linked) intrastrand cross-links (IaCLs) lacking a phosphodiester group between the 2'-deoxyribose residues. The DNA tetrahedra containing TWJs were shown to undergo an unhooking reaction by the human DNA repair protein O6 -alkylguanine DNA alkyltransferase (hAGT) resulting in structure disassembly. The unhooking reaction of hAGT towards the DNA tetrahedra was observed to be moderate to virtually complete depending on the protein equivalents. DNA tetrahedron structures have been explored as drug delivery platforms that release their payload in response to triggers, such as light, chemical agents or hybridization of release strands. The dismantling of DNA tetrahedron structures by a DNA repair protein contributes to the armamentarium of approaches for drug release employing DNA nanostructures.
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Affiliation(s)
- William Copp
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, H4B 1R6, Canada
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, H4B 1R6, Canada
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39
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Cai Y, Yu Q, Zhao H. Electrostatic assisted fabrication and dissociation of multi-component proteinosomes. J Colloid Interface Sci 2020; 576:90-98. [PMID: 32408164 DOI: 10.1016/j.jcis.2020.05.013] [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: 03/16/2020] [Revised: 05/03/2020] [Accepted: 05/04/2020] [Indexed: 01/17/2023]
Abstract
Self-assembly of proteins into well-organized proteinosomes has attracted great interest due to the potential medical and biological applications of the structures. Herein, a new concept of electrostatic assisted fabrication of proteinosomes is proposed. The self-assembly is performed by using multi-step dialysis approach, where negatively charged bovine serum albumin-poly(N-isopropylacrylamide) (BSA-PNIPAM) bioconjugate and positively charged enzyme (lysozyme or trypsin) are initially dissolved in phosphate buffer (PB) solution at a high salt concentration, and subsequently the protein solution is dialyzed against PB solutions at low salt concentrations, resulting in the formation of biofunctional proteinosomes. Transmission electron microscopy (TEM), cryo-TEM and light scattering results all demonstrate the formation of hollow structures. The wall of a proteinosome is composed of BSA and enzyme (lysozyme or trypsin), and PNIPAM chains of the bioconjugate are in the corona stabilizing the structure. In comparison with the native enzymes, the enzyme molecules in the assemblies basically retain their bioactivities. The proteinosomes formed by BSA-PNIPAM and lysozyme can be dissociated in the presence of trypsin, and those self-assembled by BSA-PNIPAM and trypsin are able to be self-hydrolyzed, resulting in the dissociation of the structures in aqueous solution. The size and morphology changes of the proteinosomes in the hydrolysis are studied.
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Affiliation(s)
- Yaqian Cai
- Key Laboratory of Functional Polymer Materials, Ministry of Education, College of Chemistry, Nankai University, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300071, China
| | - Qianyu Yu
- Key Laboratory of Functional Polymer Materials, Ministry of Education, College of Chemistry, Nankai University, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300071, China
| | - Hanying Zhao
- Key Laboratory of Functional Polymer Materials, Ministry of Education, College of Chemistry, Nankai University, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300071, China.
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40
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Aghebat Rafat A, Sagredo S, Thalhammer M, Simmel FC. Barcoded DNA origami structures for multiplexed optimization and enrichment of DNA-based protein-binding cavities. Nat Chem 2020; 12:852-859. [PMID: 32661410 DOI: 10.1038/s41557-020-0504-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 06/05/2020] [Indexed: 01/15/2023]
Abstract
Simultaneous binding of molecules by multiple binding partners is known to strongly reduce the apparent dissociation constant of the corresponding molecular complexes, and can be used to achieve strong, non-covalent molecular interactions. Based on this principle, efficient binding of proteins to DNA nanostructures has been achieved previously by placing several aptamers in close proximity to each other onto DNA scaffolds. Here, we develop an approach for exploring design parameters, such as the geometric arrangement or the nanomechanical properties of the binding sites, that use two-dimensional DNA origami-based nanocavities that bear aptamers with known mechanical properties at defined distances and orientations. The origami structures are labelled with barcodes, which enables large numbers of binding cavities to be investigated in parallel and under identical conditions, and facilitates a direct and reliable quantitative comparison of their binding yields. We demonstrate that binding geometry and mechanical properties have a dramatic effect on origami-based multivalent binding sites, and that optimization of linker spacings and flexibilities can improve the effective binding strength of the sites substantially.
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Affiliation(s)
- Ali Aghebat Rafat
- Physics Department E14 and ZNN, Technical University Munich, Garching, Germany
| | - Sandra Sagredo
- Physics Department E14 and ZNN, Technical University Munich, Garching, Germany
| | - Melissa Thalhammer
- Physics Department E14 and ZNN, Technical University Munich, Garching, Germany
| | - Friedrich C Simmel
- Physics Department E14 and ZNN, Technical University Munich, Garching, Germany.
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41
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Sato Y, Sakamoto T, Takinoue M. Sequence-based engineering of dynamic functions of micrometer-sized DNA droplets. SCIENCE ADVANCES 2020; 6:eaba3471. [PMID: 32537507 PMCID: PMC7269647 DOI: 10.1126/sciadv.aba3471] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 04/01/2020] [Indexed: 05/02/2023]
Abstract
DNA has the potential to achieve a controllable macromolecular structure, such as hydrogels or droplets formed through liquid-liquid phase separation (LLPS), as the design of its base sequence can result in programmable interactions. Here, we constructed "DNA droplets" via LLPS of sequence-designed DNA nanostructures and controlled their dynamic functions by designing their sequences. Specifically, we were able to adjust the temperature required for the formation of DNA droplets by designing the sequences. In addition, the fusion, fission, and formation of Janus-shaped droplets were controlled by sequence design and enzymatic reactions. Furthermore, modifications of proteins with sequence-designed DNAs allowed for their capture into specific droplets. Overall, our results provide a platform for designing and controlling macromolecular droplets via the information encoded in component molecules and pave the way for various applications of sequence-designed DNA such as cell mimics, synthetic membraneless organelles, and artificial molecular systems.
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Affiliation(s)
| | - Tetsuro Sakamoto
- Department of Computer Science, Tokyo Institute of Technology, Kanagawa 226-8502, Japan
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42
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Lahav-Mankovski N, Prasad PK, Oppenheimer-Low N, Raviv G, Dadosh T, Unger T, Salame TM, Motiei L, Margulies D. Decorating bacteria with self-assembled synthetic receptors. Nat Commun 2020; 11:1299. [PMID: 32157077 PMCID: PMC7064574 DOI: 10.1038/s41467-020-14336-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 12/16/2019] [Indexed: 02/07/2023] Open
Abstract
The responses of cells to their surroundings are mediated by the binding of cell surface proteins (CSPs) to extracellular signals. Such processes are regulated via dynamic changes in the structure, composition, and expression levels of CSPs. In this study, we demonstrate the possibility of decorating bacteria with artificial, self-assembled receptors that imitate the dynamic features of CSPs. We show that the local concentration of these receptors on the bacterial membrane and their structure can be reversibly controlled using suitable chemical signals, in a way that resembles changes that occur with CSP expression levels or posttranslational modifications (PTMs), respectively. We also show that these modifications can endow the bacteria with programmable properties, akin to the way CSP responses can induce cellular functions. By programming the bacteria to glow, adhere to surfaces, or interact with proteins or mammalian cells, we demonstrate the potential to tailor such biomimetic systems for specific applications. Cell surface proteins mediate the interactions between cells and their extracellular environment. Here the authors design synthetic biomemetic receptor-like sensors that facilitate programmable interactions between bacteria and their target.
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Affiliation(s)
- Naama Lahav-Mankovski
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Pragati Kishore Prasad
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Noa Oppenheimer-Low
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Gal Raviv
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Tali Dadosh
- Chemical Research Support, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Tamar Unger
- Life Sciences Core Facilities, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Tomer Meir Salame
- Life Sciences Core Facilities, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Leila Motiei
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001, Rehovot, Israel.
| | - David Margulies
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001, Rehovot, Israel.
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43
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Taylor RE, Zahid M. Cell Penetrating Peptides, Novel Vectors for Gene Therapy. Pharmaceutics 2020; 12:E225. [PMID: 32138146 PMCID: PMC7150854 DOI: 10.3390/pharmaceutics12030225] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 02/27/2020] [Accepted: 03/01/2020] [Indexed: 12/31/2022] Open
Abstract
Cell penetrating peptides (CPPs), also known as protein transduction domains (PTDs), first identified ~25 years ago, are small, 6-30 amino acid long, synthetic, or naturally occurring peptides, able to carry variety of cargoes across the cellular membranes in an intact, functional form. Since their initial description and characterization, the field of cell penetrating peptides as vectors has exploded. The cargoes they can deliver range from other small peptides, full-length proteins, nucleic acids including RNA and DNA, liposomes, nanoparticles, and viral particles as well as radioisotopes and other fluorescent probes for imaging purposes. In this review, we will focus briefly on their history, classification system, and mechanism of transduction followed by a summary of the existing literature on use of CPPs as gene delivery vectors either in the form of modified viruses, plasmid DNA, small interfering RNA, oligonucleotides, full-length genes, DNA origami or peptide nucleic acids.
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Affiliation(s)
- Rebecca E. Taylor
- Mechanical Engineering, Biomedical Engineering and Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA;
| | - Maliha Zahid
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15201, USA
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44
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Xiong M, Liu Q, Tang D, Liu L, Kong G, Fu X, Yang C, Lyu Y, Meng HM, Ke G, Zhang XB. “Apollo Program” in Nanoscale: Landing and Exploring Cell-Surface with DNA Nanotechnology. ACS APPLIED BIO MATERIALS 2020; 3:2723-2742. [DOI: 10.1021/acsabm.9b01193] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Mengyi Xiong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Qin Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Decui Tang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Lu Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Gezhi Kong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Xiaoyi Fu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Chan Yang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Yifan Lyu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Hong-Min Meng
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Guoliang Ke
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
| | - Xiao-Bing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China
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45
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46
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Ledbetter MP, Craig JM, Karadeema RJ, Noakes MT, Kim HC, Abell SJ, Huang JR, Anderson BA, Krishnamurthy R, Gundlach JH, Romesberg FE. Nanopore Sequencing of an Expanded Genetic Alphabet Reveals High-Fidelity Replication of a Predominantly Hydrophobic Unnatural Base Pair. J Am Chem Soc 2020; 142:2110-2114. [PMID: 31985216 DOI: 10.1021/jacs.9b09808] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Unnatural base pairs (UBPs) have been developed and used for a variety of in vitro applications as well as for the engineering of semisynthetic organisms (SSOs) that store and retrieve increased information. However, these applications are limited by the availability of methods to rapidly and accurately determine the sequence of unnatural DNA. Here we report the development and application of the MspA nanopore to sequence DNA containing the dTPT3-dNaM UBP. Analysis of two sequence contexts reveals that DNA containing the UBP is replicated with an efficiency and fidelity similar to that of natural DNA and sufficient for use as the basis of an SSO that produces proteins with noncanonical amino acids.
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Affiliation(s)
- Michael P Ledbetter
- Department of Chemistry , The Scripps Research Institute , La Jolla , California 92037 , United States
| | - Jonathan M Craig
- Department of Physics , University of Washington , Seattle , Washington 98195 , United States
| | - Rebekah J Karadeema
- Department of Chemistry , The Scripps Research Institute , La Jolla , California 92037 , United States
| | - Matthew T Noakes
- Department of Physics , University of Washington , Seattle , Washington 98195 , United States
| | - Hwanhee C Kim
- Department of Physics , University of Washington , Seattle , Washington 98195 , United States
| | - Sarah J Abell
- Department of Physics , University of Washington , Seattle , Washington 98195 , United States
| | - Jesse R Huang
- Department of Physics , University of Washington , Seattle , Washington 98195 , United States
| | - Brooke A Anderson
- Department of Chemistry , The Scripps Research Institute , La Jolla , California 92037 , United States
| | | | - Jens H Gundlach
- Department of Physics , University of Washington , Seattle , Washington 98195 , United States
| | - Floyd E Romesberg
- Department of Chemistry , The Scripps Research Institute , La Jolla , California 92037 , United States
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47
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Rosier BJHM, Markvoort AJ, Gumí Audenis B, Roodhuizen JAL, den Hamer A, Brunsveld L, de Greef TFA. Proximity-induced caspase-9 activation on a DNA origami-based synthetic apoptosome. Nat Catal 2020; 3:295-306. [PMID: 32190819 PMCID: PMC7080557 DOI: 10.1038/s41929-019-0403-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Living cells regulate key cellular processes by spatial organisation of catalytically active proteins in higher-order signalling complexes. These act as organising centres to facilitate proximity-induced activation and inhibition of multiple intrinsically weakly associating signalling components, which makes elucidation of the underlying protein-protein interactions challenging. Here we show that DNA origami nanostructures provide a programmable molecular platform for the systematic analysis of signalling proteins by engineering a synthetic DNA origami-based version of the apoptosome, a multi-protein complex that regulates apoptosis by co-localizing multiple caspase-9 monomers. Tethering of both wildtype and inactive caspase-9 variants to a DNA origami platform demonstrates that enzymatic activity is induced by proximity-driven dimerization with half-of-sites reactivity, and additionally, reveals a multivalent activity enhancement in oligomers of three and four enzymes. Our results offer fundamental insights in caspase-9 activity regulation and demonstrate that DNA origami-based protein assembly platforms have the potential to inform the function of other multi-enzyme complexes involved in inflammation, innate immunity and cell death.
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Affiliation(s)
- Bas J H M Rosier
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, The Netherlands
| | - Albert J Markvoort
- Institute for Complex Molecular Systems, Eindhoven University of Technology, The Netherlands.,Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, The Netherlands
| | - Berta Gumí Audenis
- Institute for Complex Molecular Systems, Eindhoven University of Technology, The Netherlands.,Laboratory of Self-Organising Soft Matter and Laboratory of Macromolecular and Organic Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, The Netherlands
| | - Job A L Roodhuizen
- Institute for Complex Molecular Systems, Eindhoven University of Technology, The Netherlands.,Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, The Netherlands
| | - Anniek den Hamer
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, The Netherlands
| | - Tom F A de Greef
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, The Netherlands.,Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, The Netherlands.,Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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48
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Graczyk A, Pawlowska R, Jedrzejczyk D, Chworos A. Gold Nanoparticles in Conjunction with Nucleic Acids as a Modern Molecular System for Cellular Delivery. Molecules 2020; 25:E204. [PMID: 31947834 PMCID: PMC6982881 DOI: 10.3390/molecules25010204] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/23/2019] [Accepted: 12/26/2019] [Indexed: 02/07/2023] Open
Abstract
Development of nanotechnology has become prominent in many fields, such as medicine, electronics, production of materials, and modern drugs. Nanomaterials and nanoparticles have gained recognition owing to the unique biochemical and physical properties. Considering cellular application, it is speculated that nanoparticles can transfer through cell membranes following different routes exclusively owing to their size (up to 100 nm) and surface functionalities. Nanoparticles have capacity to enter cells by themselves but also to carry other molecules through the lipid bilayer. This quality has been utilized in cellular delivery of substances like small chemical drugs or nucleic acids. Different nanoparticles including lipids, silica, and metal nanoparticles have been exploited in conjugation with nucleic acids. However, the noble metal nanoparticles create an alternative, out of which gold nanoparticles (AuNP) are the most common. The hybrids of DNA or RNA and metal nanoparticles can be employed for functional assemblies for variety of applications in medicine, diagnostics or nano-electronics by means of biomarkers, specific imaging probes, or gene expression regulatory function. In this review, we focus on the conjugates of gold nanoparticles and nucleic acids in the view of their potential application for cellular delivery and biomedicine. This review covers the current advances in the nanotechnology of DNA and RNA-AuNP conjugates and their potential applications. We emphasize the crucial role of metal nanoparticles in the nanotechnology of nucleic acids and explore the role of such conjugates in the biological systems. Finally, mechanisms guiding the process of cellular intake, essential for delivery of modern therapeutics, will be discussed.
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Affiliation(s)
| | | | | | - Arkadiusz Chworos
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland; (A.G.); (R.P.); (D.J.)
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49
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Klein WP, Thomsen RP, Turner KB, Walper SA, Vranish J, Kjems J, Ancona MG, Medintz IL. Enhanced Catalysis from Multienzyme Cascades Assembled on a DNA Origami Triangle. ACS NANO 2019; 13:13677-13689. [PMID: 31751123 DOI: 10.1021/acsnano.9b05746] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Developing reliable methods of constructing cell-free multienzyme biocatalytic systems is a milestone goal of synthetic biology. It would enable overcoming the limitations of current cell-based systems, which suffer from the presence of competing pathways, toxicity, and inefficient access to extracellular reactants and removal of products. DNA nanostructures have been suggested as ideal scaffolds for assembling sequential enzymatic cascades in close enough proximity to potentially allow for exploiting of channeling effects; however, initial demonstrations have provided somewhat contradictory results toward confirming this phenomenon. In this work, a three-enzyme sequential cascade was realized by site-specifically immobilizing DNA-conjugated amylase, maltase, and glucokinase on a self-assembled DNA origami triangle. The kinetics of seven different enzyme configurations were evaluated experimentally and compared to simulations of optimized activity. A 30-fold increase in the pathway's kinetic activity was observed for enzymes assembled to the DNA. Detailed kinetic analysis suggests that this catalytic enhancement originated from increased enzyme stability and a localized DNA surface affinity or hydration layer effect and not from a directed enzyme-to-enzyme channeling mechanism. Nevertheless, the approach used to construct this pathway still shows promise toward improving other more elaborate multienzymatic cascades and could potentially allow for the custom synthesis of complex (bio)molecules that cannot be realized with conventional organic chemistry approaches.
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Affiliation(s)
- William P Klein
- National Research Council , Washington , D.C. 20001 , United States
| | - Rasmus P Thomsen
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics , Aarhus University , 8000 Aarhus , Denmark
| | | | - Scott A Walper
- National Research Council , Washington , D.C. 20001 , United States
| | - James Vranish
- Ave Maria University , Ave Maria , Florida 34142 , United States
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics , Aarhus University , 8000 Aarhus , Denmark
| | | | - Igor L Medintz
- National Research Council , Washington , D.C. 20001 , United States
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50
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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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