1
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Bonde S, Osmani RAM, Trivedi R, Patravale V, Angolkar M, Prasad AG, Ravikumar AA. Harnessing DNA origami's therapeutic potential for revolutionizing cardiovascular disease treatment: A comprehensive review. Int J Biol Macromol 2024; 270:132246. [PMID: 38735608 DOI: 10.1016/j.ijbiomac.2024.132246] [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: 12/05/2023] [Revised: 03/25/2024] [Accepted: 05/07/2024] [Indexed: 05/14/2024]
Abstract
DNA origami is a cutting-edge nanotechnology approach that creates precise and detailed 2D and 3D nanostructures. The crucial feature of DNA origami is how it is created, which enables precise control over its size and shape. Biocompatibility, targetability, programmability, and stability are further advantages that make it a potentially beneficial technique for a variety of applications. The preclinical studies of sophisticated programmable nanomedicines and nanodevices that can precisely respond to particular disease-associated triggers and microenvironments have been made possible by recent developments in DNA origami. These stimuli, which are endogenous to the targeted disorders, include protein upregulation, pH, redox status, and small chemicals. Oncology has traditionally been the focus of the majority of past and current research on this subject. Therefore, in this comprehensive review, we delve into the intricate world of DNA origami, exploring its defining features and capabilities. This review covers the fundamental characteristics of DNA origami, targeting DNA origami to cells, cellular uptake, and subcellular localization. Throughout the review, we emphasised on elucidating the imperative for such a therapeutic platform, especially in addressing the complexities of cardiovascular disease (CVD). Moreover, we explore the vast potential inherent in DNA origami technology, envisioning its promising role in the realm of CVD treatment and beyond.
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Affiliation(s)
- Smita Bonde
- Department of Pharmaceutics, SSR College of Pharmacy, Silvassa 396230, UT of Dadra and Nagar Haveli, India.
| | - Riyaz Ali M Osmani
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education and Research (JSS AHER), Mysuru 570015, Karnataka, India.
| | - Rashmi Trivedi
- Department of Pharmaceutics, Smt. Kishoritai Bhoyar College of Pharmacy, Kamptee, Nagpur 441002, Maharashtra, India.
| | - Vandana Patravale
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga (E), Mumbai 400019, Maharashtra, India.
| | - Mohit Angolkar
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education and Research (JSS AHER), Mysuru 570015, Karnataka, India.
| | - Aprameya Ganesh Prasad
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Akhila Akkihebbal Ravikumar
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education and Research (JSS AHER), Mysuru 570015, Karnataka, India.
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2
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Mariconti M, Dechamboux L, Heckmann M, Gros J, Morel M, Escriou V, Baigl D, Hoffmann C, Rudiuk S. Intracellular Delivery of Functional Proteins with DNA-Protein Nanogels-Lipids Complex. J Am Chem Soc 2024; 146:5118-5127. [PMID: 38363821 PMCID: PMC10910493 DOI: 10.1021/jacs.3c08000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/18/2024]
Abstract
Using functional proteins for therapeutic purposes due to their high selectivity and/or catalytic properties can enable the control of various cellular processes; however, the transport of active proteins inside living cells remains a major challenge. In contrast, intracellular delivery of nucleic acids has become a routine method for a number of applications in gene therapy, genome editing, or immunization. Here we report a functionalizable platform constituting of DNA-protein nanogel carriers cross-linked through streptavidin-biotin or streptactin-biotin interactions and demonstrate its applicability for intracellular delivery of active proteins. We show that the nanogels can be loaded with proteins bearing either biotin, streptavidin, or strep-tag, and the resulting functionalized nanogels can be delivered into living cells after complexation with cationic lipid vectors. We use this approach for delivery of alkaline phosphatase enzyme, which is shown to keep its catalytic activity after internalization by mouse melanoma B16 cells, as demonstrated by the DDAO-phosphate assay. The resulting functionalized nanogels have dimensions on the order of 100 nm, contain around 100 enzyme molecules, and are shown to be transfectable at low lipid concentrations (charge ratio R± = 0.75). This ensures the low toxicity of our system, which in combination with high local enzyme concentration (∼100 μM) underlines potential interest of this nanoplatform for biomedical applications.
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Affiliation(s)
- Marina Mariconti
- PASTEUR,
UMR8640, Department of Chemistry, PSL University,
Sorbonne Université, CNRS, Ecole Normale Supérieure, Paris 75005 France
| | | | - Marion Heckmann
- Université
Paris Cité, CNRS, INSERM, UTCBS, Paris 75006, France
| | - Julien Gros
- PASTEUR,
UMR8640, Department of Chemistry, PSL University,
Sorbonne Université, CNRS, Ecole Normale Supérieure, Paris 75005 France
| | - Mathieu Morel
- PASTEUR,
UMR8640, Department of Chemistry, PSL University,
Sorbonne Université, CNRS, Ecole Normale Supérieure, Paris 75005 France
| | | | - Damien Baigl
- PASTEUR,
UMR8640, Department of Chemistry, PSL University,
Sorbonne Université, CNRS, Ecole Normale Supérieure, Paris 75005 France
| | - Céline Hoffmann
- Université
Paris Cité, CNRS, INSERM, UTCBS, Paris 75006, France
| | - Sergii Rudiuk
- PASTEUR,
UMR8640, Department of Chemistry, PSL University,
Sorbonne Université, CNRS, Ecole Normale Supérieure, Paris 75005 France
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3
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Kannappan S, Jo K, Kim KK, Lee JH. Utilizing peptide-anchored DNA templates for novel programmable nanoparticle assemblies in biological macromolecules: A review. Int J Biol Macromol 2024; 256:128427. [PMID: 38016615 DOI: 10.1016/j.ijbiomac.2023.128427] [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: 10/19/2023] [Revised: 11/23/2023] [Accepted: 11/23/2023] [Indexed: 11/30/2023]
Abstract
Biological macromolecules such as proteins and DNA are known to self-assemble into various structural moieties with distinct functions. While nucleic acids are the structural building blocks, peptides exemplify diversity as tailorable biochemical units. Thus, combining the scaffold properties of the biomacromolecule DNA and the functionality of peptides could evolve into a powerful method to obtain tailorable nano assemblies. In this review, we discuss the assembly of non-DNA-coated colloidal NPs on DNA/peptide templates using functional anchors. We begin with strategies for directly attaching metallic NPs to DNA templates to ascertain the functional role of DNA as a scaffold. Followed by methods to assemble peptides onto DNA templates to emphasize the functional versatility of biologically abundant DNA-binding peptides. Next, we focus on studies corroborating peptide self-assembling into macromolecular templates onto which NPs can attach to emphasize the properties of NP-binding peptides. Finally, we discuss the assembly of NPs on a DNA template with a focus on the bifunctional DNA-binding peptides with NP-binding affinity (peptide anchors). This review aims to highlight the immense potential of combining the functional power of DNA scaffolds and tailorable functionalities of peptides for NP assembly and the need to utilize them effectively to obtain tailorable hierarchical NP assemblies.
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Affiliation(s)
- Shrute Kannappan
- Department of Precision Medicine, School of Medicine, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea; Research Center for Advanced Materials Technology, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Kyubong Jo
- Department of Chemistry, Sogang University, Mapo-gu, Seoul 04107, Republic of Korea.
| | - Kyeong Kyu Kim
- Department of Precision Medicine, School of Medicine, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea; Department of Metabiohealth, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea.
| | - Jung Heon Lee
- Research Center for Advanced Materials Technology, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea; Department of Metabiohealth, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea; School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea.
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4
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Oh CY, Henderson ER. In vitro transcription of self-assembling DNA nanoparticles. Sci Rep 2023; 13:12961. [PMID: 37563161 PMCID: PMC10415316 DOI: 10.1038/s41598-023-39777-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023] Open
Abstract
Nucleic acid nanoparticles are playing an increasingly important role in biomolecular diagnostics and therapeutics as well as a variety of other areas. The unique attributes of self-assembling DNA nanoparticles provide a potentially valuable addition or alternative to the lipid-based nanoparticles that are currently used to ferry nucleic acids in living systems. To explore this possibility, we have assessed the ability of self-assembling DNA nanoparticles to be constructed from complete gene cassettes that are capable of gene expression in vitro. In the current report, we describe the somewhat counter-intuitive result that despite extensive crossovers (the stereochemical analogs of Holliday junctions) and variations in architecture, these DNA nanoparticles are amenable to gene expression as evidenced by T7 RNA polymerase-driven transcription of a reporter gene in vitro. These findings, coupled with the vastly malleable architecture and chemistry of self-assembling DNA nanoparticles, warrant further investigation of their utility in biomedical genetics.
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Affiliation(s)
- Chang Yong Oh
- Department of Biochemistry and Molecular Biology, Iowa State University, Ames, IA, 50011, USA.
| | - Eric R Henderson
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011, USA
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5
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Ghosal S, Bag S, Bhowmik S. Unravelling the Drug Encapsulation Ability of Functional DNA Origami Nanostructures: Current Understanding and Future Prospects on Targeted Drug Delivery. Polymers (Basel) 2023; 15:1850. [PMID: 37111997 PMCID: PMC10144338 DOI: 10.3390/polym15081850] [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: 02/23/2023] [Revised: 03/10/2023] [Accepted: 03/16/2023] [Indexed: 04/29/2023] Open
Abstract
Rapid breakthroughs in nucleic acid nanotechnology have always driven the creation of nano-assemblies with programmable design, potent functionality, good biocompatibility, and remarkable biosafety during the last few decades. Researchers are constantly looking for more powerful techniques that provide enhanced accuracy with greater resolution. The self-assembly of rationally designed nanostructures is now possible because of bottom-up structural nucleic acid (DNA and RNA) nanotechnology, notably DNA origami. Because DNA origami nanostructures can be organized precisely with nanoscale accuracy, they serve as a solid foundation for the exact arrangement of other functional materials for use in a number of applications in structural biology, biophysics, renewable energy, photonics, electronics, medicine, etc. DNA origami facilitates the creation of next-generation drug vectors to help in the solving of the rising demand on disease detection and therapy, as well as other biomedicine-related strategies in the real world. These DNA nanostructures, generated using Watson-Crick base pairing, exhibit a wide variety of properties, including great adaptability, precise programmability, and exceptionally low cytotoxicity in vitro and in vivo. This paper summarizes the synthesis of DNA origami and the drug encapsulation ability of functionalized DNA origami nanostructures. Finally, the remaining obstacles and prospects for DNA origami nanostructures in biomedical sciences are also highlighted.
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Affiliation(s)
- Souvik Ghosal
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to Be University), Pondy-Cuddalore Main Road, Pillayarkuppam, Pondicherry 607402, India
| | - Sagar Bag
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
| | - Sudipta Bhowmik
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to Be University), Pondy-Cuddalore Main Road, Pillayarkuppam, Pondicherry 607402, India
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
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6
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Knappe GA, Wamhoff EC, Bathe M. Functionalizing DNA origami to investigate and interact with biological systems. NATURE REVIEWS. MATERIALS 2023; 8:123-138. [PMID: 37206669 PMCID: PMC10191391 DOI: 10.1038/s41578-022-00517-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/11/2022] [Indexed: 05/21/2023]
Abstract
DNA origami has emerged as a powerful method to generate DNA nanostructures with dynamic properties and nanoscale control. These nanostructures enable complex biophysical studies and the fabrication of next-generation therapeutic devices. For these applications, DNA origami typically needs to be functionalized with bioactive ligands and biomacromolecular cargos. Here, we review methods developed to functionalize, purify, and characterize DNA origami nanostructures. We identify remaining challenges, such as limitations in functionalization efficiency and characterization. We then discuss where researchers can contribute to further advance the fabrication of functionalized DNA origami.
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Affiliation(s)
- Grant A. Knappe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Address correspondence to or
| | - Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Address correspondence to or
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7
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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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8
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Xu Z, Huang Y, Yin H, Zhu X, Tian Y, Min Q. DNA origami-based protein manipulation systems: From function regulation to biological application. Chembiochem 2021; 23:e202100597. [PMID: 34958167 DOI: 10.1002/cbic.202100597] [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: 10/31/2021] [Revised: 12/18/2021] [Indexed: 11/07/2022]
Abstract
Proteins directly participate in tremendous physiological processes and mediate a variety of cellular functions. However, precise manipulation of proteins with predefined relative position and stoichiometry for understanding protein-protein interactions and guiding cellular behaviors are still challenging. With superior programmability of DNA molecules, DNA origami technology is able to construct arbitrary nanostructures that can accurately control the arrangement of proteins with various functionalities to solve these problems. Herein, starting from the classification of DNA origami nanostructures and the category of assembled proteins, we summarize the existing DNA origami-based protein manipulation systems (PMSs), review the advances on the regulation of their functions, and discuss their applications in cellular behavior modulation and disease therapy. Moreover, the limitations and potential directions of DNA origami-based PMSs are also presented, which may offer guidance for rational construction and ingenious application.
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Affiliation(s)
- Ziqi Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Yide Huang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Hao Yin
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Xurong Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Ye Tian
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Qianhao Min
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
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9
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Henry SJ, Stephanopoulos N. Functionalizing DNA nanostructures for therapeutic applications. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2021; 13:e1729. [PMID: 34008347 PMCID: PMC8526372 DOI: 10.1002/wnan.1729] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/29/2021] [Accepted: 04/26/2021] [Indexed: 12/29/2022]
Abstract
Recent advances in nanotechnology have enabled rapid progress in many areas of biomedical research, including drug delivery, targeted therapies, imaging, and sensing. The emerging field of DNA nanotechnology, in which oligonucleotides are designed to self-assemble into programmable 2D and 3D nanostructures, offers great promise for further advancements in biomedicine. DNA nanostructures present highly addressable and functionally diverse platforms for biological applications due to their ease of construction, controllable architecture and size/shape, and multiple avenues for chemical modification. Both supramolecular and covalent modification with small molecules and polymers have been shown to expand or enhance the functions of DNA nanostructures in biological contexts. These alterations include the addition of small molecule, protein, or nucleic acid moieties that enable structural stability under physiological conditions, more efficient cellular uptake and targeting, delivery of various molecular cargos, stimulus-responsive behaviors, or modulation of a host immune response. Herein, various types of DNA nanostructure modifications and their functional consequences are examined, followed by a brief discussion of the future opportunities for functionalized DNA nanostructures as well as the barriers that must be overcome before their translational use. This article is categorized under: Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Therapeutic Approaches and Drug Discovery > Emerging Technologies Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures.
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Affiliation(s)
- Skylar J.W. Henry
- School of Molecular Sciences, Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe AZ
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe AZ
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10
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Knappe GA, Wamhoff EC, Read BJ, Irvine DJ, Bathe M. In Situ Covalent Functionalization of DNA Origami Virus-like Particles. ACS NANO 2021; 15:14316-14322. [PMID: 34490781 PMCID: PMC8628367 DOI: 10.1021/acsnano.1c03158] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
DNA origami is a powerful nanomaterial for biomedical applications due in part to its capacity for programmable, site-specific functionalization. To realize these applications, scalable and efficient conjugation protocols are needed for diverse moieties ranging from small molecules to biomacromolecules. Currently, there are no facile and general methods for in situ covalent modification and label-free quantification of reaction conversion. Here, we investigate the postassembly functionalization of DNA origami and the subsequent high-performance liquid chromatography-based characterization of these nanomaterials. Following this approach, we developed a versatile DNA origami functionalization and characterization platform. We observed quantitative in situ conversion using widely accessible click chemistry for carbohydrates, small molecules, peptides, polymers, and proteins. This platform should provide broader access to covalently functionalized DNA origami, as illustrated here by PEGylation for passivation and HIV antigen decoration to construct virus-like particle vaccines.
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Affiliation(s)
- Grant A. Knappe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Benjamin J. Read
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Darrell J. Irvine
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, United States of America
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, United States of America
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Address correspondence to
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11
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Zhang M, Wang S, Li L, Li M, Cheng X, Shi Y, Wu Y. Digital Numbers Constructed by Fine Patterned Polydopamine on DNA Templates. Macromol Rapid Commun 2021; 42:e2100441. [PMID: 34431573 DOI: 10.1002/marc.202100441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/05/2021] [Indexed: 01/12/2023]
Abstract
Using DNA nanostructures as templates to synthesize shape-controlled polydopamine (PDA) is a promising strategy to realize the fabrication of exquisite PDA nanomaterials. However, previous studies using small DNA tiles as templates could only afford very simple structures such as lines and crosses due to the limited space on the template and the relatively low resolution of the PDA nanopatterns. Therefore, the best resolution of the PDA nanostructures that can be achieved by this technique is carefully investigated. And by connecting several DNA tiles together, larger DNA templates are built up and achieve the synthesis of complicated digital nanopatterned PDA structures.
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Affiliation(s)
- Meizhou Zhang
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Luoyu Road 1037, Hongshan, Wuhan, 430074, P. R. China
| | - Shuangshuang Wang
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Luoyu Road 1037, Hongshan, Wuhan, 430074, P. R. China
| | - Longjie Li
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Luoyu Road 1037, Hongshan, Wuhan, 430074, P. R. China.,School of Life Science and Technology, Wuhan Polytechnic University, Evergreen Garden, Wuhan, 430023, P. R. China
| | - Mengran Li
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Dadao 1277, Wuhan, 430022, P. R. China
| | - Xinyi Cheng
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Luoyu Road 1037, Hongshan, Wuhan, 430074, P. R. China
| | - Yiwei Shi
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Luoyu Road 1037, Hongshan, Wuhan, 430074, P. R. China
| | - Yuzhou Wu
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Luoyu Road 1037, Hongshan, Wuhan, 430074, P. R. China
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12
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Kocabey S, Ekim Kocabey A, Schneiter R, Rüegg C. Membrane-Interacting DNA Nanotubes Induce Cancer Cell Death. NANOMATERIALS 2021; 11:nano11082003. [PMID: 34443832 PMCID: PMC8397952 DOI: 10.3390/nano11082003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/25/2021] [Accepted: 07/30/2021] [Indexed: 12/31/2022]
Abstract
DNA nanotechnology offers to build nanoscale structures with defined chemistries to precisely position biomolecules or drugs for selective cell targeting and drug delivery. Owing to the negatively charged nature of DNA, for delivery purposes, DNA is frequently conjugated with hydrophobic moieties, positively charged polymers/peptides and cell surface receptor-recognizing molecules or antibodies. Here, we designed and assembled cholesterol-modified DNA nanotubes to interact with cancer cells and conjugated them with cytochrome c to induce cancer cell apoptosis. By flow cytometry and confocal microscopy, we observed that DNA nanotubes efficiently bound to the plasma membrane as a function of the number of conjugated cholesterol moieties. The complex was taken up by the cells and localized to the endosomal compartment. Cholesterol-modified DNA nanotubes, but not unmodified ones, increased membrane permeability, caspase activation and cell death. Irreversible inhibition of caspase activity with a caspase inhibitor, however, only partially prevented cell death. Cytochrome c-conjugated DNA nanotubes were also efficiently taken up but did not increase the rate of cell death. These results demonstrate that cholesterol-modified DNA nanotubes induce cancer cell death associated with increased cell membrane permeability and are only partially dependent on caspase activity, consistent with a combined form of apoptotic and necrotic cell death. DNA nanotubes may be further developed as primary cytotoxic agents, or drug delivery vehicles, through cholesterol-mediated cellular membrane interactions and uptake.
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Affiliation(s)
- Samet Kocabey
- Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, PER17, 1700 Fribourg, Switzerland
- Correspondence: (S.K.); (C.R.)
| | - Aslihan Ekim Kocabey
- Department of Biology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 10, PER05, 1700 Fribourg, Switzerland; (A.E.K.); (R.S.)
| | - Roger Schneiter
- Department of Biology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 10, PER05, 1700 Fribourg, Switzerland; (A.E.K.); (R.S.)
| | - Curzio Rüegg
- Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, PER17, 1700 Fribourg, Switzerland
- Correspondence: (S.K.); (C.R.)
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13
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Kong G, Xiong M, Liu L, Hu L, Meng HM, Ke G, Zhang XB, Tan W. DNA origami-based protein networks: from basic construction to emerging applications. Chem Soc Rev 2021; 50:1846-1873. [PMID: 33306073 DOI: 10.1039/d0cs00255k] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Natural living systems are driven by delicate protein networks whose functions are precisely controlled by many parameters, such as number, distance, orientation, and position. Focusing on regulation rather than just imitation, the construction of artificial protein networks is important in many research areas, including biomedicine, synthetic biology and chemical biology. DNA origami, sophisticated nanostructures with rational design, can offer predictable, programmable, and addressable scaffolds for protein assembly with nanometer precision. Recently, many interdisciplinary efforts have achieved the precise construction of DNA origami-based protein networks, and their emerging application in many areas. To inspire more fantastic research and applications, herein we highlight the applicability and potentiality of DNA origami-based protein networks. After a brief introduction to the development and features of DNA origami, some important factors for the precise construction of DNA origami-based protein networks are discussed, including protein-DNA conjugation methods, networks with different patterns and the controllable parameters in the networks. The discussion then focuses on the emerging application of DNA origami-based protein networks in several areas, including enzymatic reaction regulation, sensing, bionics, biophysics, and biomedicine. Finally, current challenges and opportunities in this research field are discussed.
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Affiliation(s)
- Gezhi Kong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Mengyi Xiong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Lu Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Ling Hu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Hong-Min Meng
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou 450001, China
| | - Guoliang Ke
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Xiao-Bing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
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14
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Oerlemans RAJF, Timmermans SBPE, van Hest JCM. Artificial Organelles: Towards Adding or Restoring Intracellular Activity. Chembiochem 2021; 22:2051-2078. [PMID: 33450141 PMCID: PMC8252369 DOI: 10.1002/cbic.202000850] [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: 12/16/2020] [Revised: 01/15/2021] [Indexed: 12/15/2022]
Abstract
Compartmentalization is one of the main characteristics that define living systems. Creating a physically separated microenvironment allows nature a better control over biological processes, as is clearly specified by the role of organelles in living cells. Inspired by this phenomenon, researchers have developed a range of different approaches to create artificial organelles: compartments with catalytic activity that add new function to living cells. In this review we will discuss three complementary lines of investigation. First, orthogonal chemistry approaches are discussed, which are based on the incorporation of catalytically active transition metal-containing nanoparticles in living cells. The second approach involves the use of premade hybrid nanoreactors, which show transient function when taken up by living cells. The third approach utilizes mostly genetic engineering methods to create bio-based structures that can be ultimately integrated with the cell's genome to make them constitutively active. The current state of the art and the scope and limitations of the field will be highlighted with selected examples from the three approaches.
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Affiliation(s)
- Roy A. J. F. Oerlemans
- Bio-Organic Chemistry Research GroupInstitute for Complex Molecular SystemsEindhoven University of TechnologyP.O. Box 513 (STO3.41)5600 MBEindhovenThe Netherlands
| | - Suzanne B. P. E. Timmermans
- Bio-Organic Chemistry Research GroupInstitute for Complex Molecular SystemsEindhoven University of TechnologyP.O. Box 513 (STO3.41)5600 MBEindhovenThe Netherlands
| | - Jan C. M. van Hest
- Bio-Organic Chemistry Research GroupInstitute for Complex Molecular SystemsEindhoven University of TechnologyP.O. Box 513 (STO3.41)5600 MBEindhovenThe Netherlands
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15
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Nakata E, Hirose H, Gerelbaatar K, Arafiles JVV, Zhang Z, Futaki S, Morii T. A facile combinatorial approach to construct a ratiometric fluorescent sensor: application for the real-time sensing of cellular pH changes. Chem Sci 2021; 12:8231-8240. [PMID: 34194714 PMCID: PMC8208317 DOI: 10.1039/d1sc01575c] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/04/2021] [Indexed: 02/02/2023] Open
Abstract
Realtime monitoring of the cellular environment, such as the intracellular pH, in a defined cellular space provides a comprehensive understanding of the dynamics processes in a living cell. Considering the limitation of spatial resolution in conventional microscopy measurements, multiple types of fluorophores assembled within that space would behave as a single fluorescent probe molecule. Such a character of microscopic measurements enables a much more flexible combinatorial design strategy in developing fluorescent probes for given targets. Nanomaterials with sizes smaller than the microscopy spatial resolution provide a scaffold to assemble several types of fluorophores with a variety of optical characteristics, therefore providing a convenient strategy for designing fluorescent pH sensors. In this study, fluorescein (CF) and tetramethylrhodamine (CR) were assembled on a DNA nanostructure with controlling the number of each type of fluorophore. By taking advantage of the different responses of CF and CR emissions to the pH environment, an appropriate assembly of both CF and CR on DNA origami enabled a controlled intensity of fluorescence emission and ratiometric pH monitoring within the space defined by DNA origami. The CF and CR-assembled DNA origami was successfully applied for monitoring the intracellular pH changes.
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Affiliation(s)
- Eiji Nakata
- Institute of Advanced Energy, Kyoto University Kyoto Japan
| | - Hisaaki Hirose
- Institute for Chemical Research, Kyoto University Kyoto Japan
| | | | | | | | - Shiroh Futaki
- Institute for Chemical Research, Kyoto University Kyoto Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University Kyoto Japan
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16
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17
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Smith DM, Keller A. DNA Nanostructures in the Fight Against Infectious Diseases. ADVANCED NANOBIOMED RESEARCH 2021; 1:2000049. [PMID: 33615315 PMCID: PMC7883073 DOI: 10.1002/anbr.202000049] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/08/2020] [Indexed: 12/12/2022] Open
Abstract
Throughout history, humanity has been threatened by countless epidemic and pandemic outbreaks of infectious diseases, from the Justinianic Plague to the Spanish flu to COVID-19. While numerous antimicrobial and antiviral drugs have been developed over the last 200 years to face these threats, the globalized and highly connected world of the 21st century demands for an ever-increasing efficiency in the detection and treatment of infectious diseases. Consequently, the rapidly evolving field of nanomedicine has taken up the challenge and developed a plethora of strategies to fight infectious diseases with the help of various nanomaterials such as noble metal nanoparticles, liposomes, nanogels, and virus capsids. DNA nanotechnology represents a comparatively recent addition to the nanomedicine arsenal, which, over the past decade, has made great progress in the area of cancer diagnostics and therapy. However, the past few years have seen also an increasing number of DNA nanotechnology-related studies that particularly focus on the detection and inhibition of microbial and viral pathogens. Herein, a brief overview of this rather young research field is provided, successful concepts as well as potential challenges are identified, and promising directions for future research are highlighted.
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Affiliation(s)
- David M. Smith
- DNA Nanodevices UnitDepartment DiagnosticsFraunhofer Institute for Cell Therapy and Immunology IZI04103LeipzigGermany
- Peter Debye Institute for Soft Matter PhysicsFaculty of Physics and Earth SciencesUniversity of Leipzig04103LeipzigGermany
- Institute of Clinical ImmunologyUniversity of Leipzig Medical School04103LeipzigGermany
- Dhirubhai Ambani Institute of Information and Communication TechnologyGandhinagar382 007India
| | - Adrian Keller
- Technical and Macromolecular ChemistryPaderborn UniversityWarburger Str. 10033098PaderbornGermany
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18
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Zeng Y, Nixon RL, Liu W, Wang R. The applications of functionalized DNA nanostructures in bioimaging and cancer therapy. Biomaterials 2020; 268:120560. [PMID: 33285441 DOI: 10.1016/j.biomaterials.2020.120560] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 11/03/2020] [Accepted: 11/18/2020] [Indexed: 12/17/2022]
Abstract
Deoxyribonucleic acid (DNA) is a molecular carrier of genetic information that can be fabricated into functional nanomaterials in biochemistry and engineering fields. Those DNA nanostructures, synthesized via Watson-Crick base pairing, show a wide range of attributes along with excellent applicability, precise programmability, and extremely low cytotoxicity in vitro and in vivo. In this review, the applications of functionalized DNA nanostructures in bioimaging and tumor therapy are summarized. We focused on approaches involving DNA origami nanostructures due to their widespread use in previous and current reports. Non-DNA origami nanostructures such as DNA tetrahedrons are also covered. Finally, the remaining challenges and perspectives regarding DNA nanostructures in the biomedical arena are discussed.
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Affiliation(s)
- Yun Zeng
- Department of Chemistry, Missouri University of Science and Technology, Rolla, MO, 65409, USA; Engineering Research Center of Molecular and Neuroimaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710126, PR China.
| | - Rachel L Nixon
- Department of Chemistry, Missouri University of Science and Technology, Rolla, MO, 65409, USA
| | - Wenyan Liu
- Department of Chemistry, Missouri University of Science and Technology, Rolla, MO, 65409, USA; Center for Research in Energy and Environment, Missouri University of Science and Technology, Rolla, MO, 65409, USA
| | - Risheng Wang
- Department of Chemistry, Missouri University of Science and Technology, Rolla, MO, 65409, USA.
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Molden TA, Niccum CT, Kolpashchikov DM. Cut and Paste for Cancer Treatment: A DNA Nanodevice that Cuts Out an RNA Marker Sequence to Activate a Therapeutic Function. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Tatiana A. Molden
- Chemistry Department University of Central Florida Orlando FL 32816 USA
| | - Caitlyn T. Niccum
- Chemistry Department University of Central Florida Orlando FL 32816 USA
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20
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Molden TA, Niccum CT, Kolpashchikov DM. Cut and Paste for Cancer Treatment: A DNA Nanodevice that Cuts Out an RNA Marker Sequence to Activate a Therapeutic Function. Angew Chem Int Ed Engl 2020; 59:21190-21194. [DOI: 10.1002/anie.202006384] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 06/21/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Tatiana A. Molden
- Chemistry Department University of Central Florida Orlando FL 32816 USA
| | - Caitlyn T. Niccum
- Chemistry Department University of Central Florida Orlando FL 32816 USA
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21
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Keller A, Linko V. Challenges and Perspectives of DNA Nanostructures in Biomedicine. Angew Chem Int Ed Engl 2020; 59:15818-15833. [PMID: 32112664 PMCID: PMC7540699 DOI: 10.1002/anie.201916390] [Citation(s) in RCA: 153] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/26/2020] [Indexed: 01/12/2023]
Abstract
DNA nanotechnology holds substantial promise for future biomedical engineering and the development of novel therapies and diagnostic assays. The subnanometer-level addressability of DNA nanostructures allows for their precise and tailored modification with numerous chemical and biological entities, which makes them fit to serve as accurate diagnostic tools and multifunctional carriers for targeted drug delivery. The absolute control over shape, size, and function enables the fabrication of tailored and dynamic devices, such as DNA nanorobots that can execute programmed tasks and react to various external stimuli. Even though several studies have demonstrated the successful operation of various biomedical DNA nanostructures both in vitro and in vivo, major obstacles remain on the path to real-world applications of DNA-based nanomedicine. Here, we summarize the current status of the field and the main implementations of biomedical DNA nanostructures. In particular, we focus on open challenges and untackled issues and discuss possible solutions.
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Affiliation(s)
- Adrian Keller
- Technical and Macromolecular ChemistryPaderborn UniversityWarburger Strasse 10033098PaderbornGermany
| | - Veikko Linko
- Biohybrid MaterialsDepartment of Bioproducts and BiosystemsAalto UniversityP. O. Box 1610000076AaltoFinland
- HYBER CentreDepartment of Applied PhysicsAalto UniversityP. O. Box 1510000076AaltoFinland
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22
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Keller A, Linko V. Herausforderungen und Perspektiven von DNA‐Nanostrukturen in der Biomedizin. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916390] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Adrian Keller
- Technische und Makromolekulare Chemie Universität Paderborn Warburger Straße 100 33098 Paderborn Deutschland
| | - Veikko Linko
- Biohybrid Materials Department of Bioproducts and Biosystems Aalto University P. O. Box 16100 00076 Aalto Finnland
- HYBER Centre Department of Applied Physics Aalto University P. O. Box 15100 00076 Aalto Finnland
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23
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Zhao D, Kong Y, Zhao S, Xing H. Engineering Functional DNA–Protein Conjugates for Biosensing, Biomedical, and Nanoassembly Applications. Top Curr Chem (Cham) 2020; 378:41. [DOI: 10.1007/s41061-020-00305-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 05/05/2020] [Indexed: 12/31/2022]
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24
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Kekic T, Barisic I. In silico modelling of DNA nanostructures. Comput Struct Biotechnol J 2020; 18:1191-1201. [PMID: 32528637 PMCID: PMC7276390 DOI: 10.1016/j.csbj.2020.05.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 05/14/2020] [Accepted: 05/14/2020] [Indexed: 01/08/2023] Open
Abstract
The rise of material science and nanotechnology created a demand for a next generation of materials and procedures that can transcend the shaping of simple geometrical nano-objects. As a legacy of the technological progress made in the Human Genome Project, DNA was identified as a possible candidate. The low production costs of custom-made DNA molecules and the possibilities concerning the structural manipulation triggered significant advances in the field of DNA nanotechnology in the last decade. To facilitate the development of new DNA nanostructures and provide users an insight in less intuitive complexities and physical properties of the DNA folding, several in silico modelling tools were published. Here, we summarize the main characteristics of these specialised tools, describe the most common design principles and discuss tools and strategies used to predict the properties of DNA nanostructures.
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25
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Ge Z, Guo L, Wu G, Li J, Sun Y, Hou Y, Shi J, Song S, Wang L, Fan C, Lu H, Li Q. DNA Origami-Enabled Engineering of Ligand-Drug Conjugates for Targeted Drug Delivery. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1904857. [PMID: 32191376 DOI: 10.1002/smll.201904857] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 02/23/2020] [Accepted: 02/26/2020] [Indexed: 06/10/2023]
Abstract
Effective drug delivery systems that can systematically and selectively transport payloads to disease cells remain a challenge. Here, a targeting ligand-modified DNA origami nanostructure (DON) as an antibody-drug conjugate (ADC)-like carrier for targeted prostate cancer therapy is reported. Specifically, DON of six helical bundles is modified with a ligand 2-[3-(1,3-dicarboxy propyl)-ureido] pentanedioic acid (DUPA) against prostate-specific membrane antigen (PSMA), to serve as the antibody for drug conjugation in ADC. Doxorubicin (Dox) is then loaded to DON through intercalation to dsDNA. This platform features in spatially controllable organization of targeting ligands and high drug loading capacity. With this nanocomposite, selective delivery of Dox to the PSMA+ cancer cell line LNCaP is readily achieved. The consequent therapeutic efficacy is critically dependent on the numbers of targeting ligand assembled on DON. This target-specific and biocompatible drug delivery platform with high maximum tolerated doses shows immense potential for developing novel nanomedicine.
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Affiliation(s)
- Zhilei Ge
- School of Chemistry and Chemical Engineering and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Linjie Guo
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Guangqi Wu
- Beijing National Laboratory for Molecular Sciences, Center for Soft Matter Science and Engineering, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Jiang Li
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Yunlong Sun
- Beijing National Laboratory for Molecular Sciences, Center for Soft Matter Science and Engineering, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Yingqin Hou
- Beijing National Laboratory for Molecular Sciences, Center for Soft Matter Science and Engineering, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Jiye Shi
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Shiping Song
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hua Lu
- Beijing National Laboratory for Molecular Sciences, Center for Soft Matter Science and Engineering, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Qian Li
- School of Chemistry and Chemical Engineering and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
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26
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McCluskey JB, Clark DS, Glover DJ. Functional Applications of Nucleic Acid-Protein Hybrid Nanostructures. Trends Biotechnol 2020; 38:976-989. [PMID: 32818445 DOI: 10.1016/j.tibtech.2020.02.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 02/14/2020] [Accepted: 02/18/2020] [Indexed: 01/09/2023]
Abstract
Combining the diverse chemical functionality of proteins with the predictable structural assembly of nucleic acids has enabled the creation of hybrid nanostructures for a range of biotechnology applications. Through the attachment of proteins onto or within nucleic acid nanostructures, materials with dynamic capabilities can be created that include switchable enzyme activity, targeted drug delivery, and multienzyme cascades for biocatalysis. Investigations of difficult-to-study biological mechanisms have also been aided by using DNA-protein assemblies that mimic natural processes in a controllable manner. Furthermore, advances that enable the recombinant production and intracellular assembly of hybrid nanostructures have the potential to overcome the significant manufacturing cost that has limited the use of DNA and RNA nanotechnology.
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Affiliation(s)
- Joshua B McCluskey
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Douglas S Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Dominic J Glover
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
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27
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DNA origami protection and molecular interfacing through engineered sequence-defined peptoids. Proc Natl Acad Sci U S A 2020; 117:6339-6348. [PMID: 32165539 PMCID: PMC7104344 DOI: 10.1073/pnas.1919749117] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
DNA nanotechnology provides a structural toolkit for the fabrication of programmable DNA nano-constructs; however, their use in biomedical applications is challenging due the limited structural integrity in complex biological fluids. Here, we report a class of tailorable molecular coatings, peptoids, which can efficiently stabilize three-dimensional wireframed DNA constructs under a variety of biomedically relevant conditions, including magnesium-ion depletion and presence of degrading nuclease. Furthermore, we show that peptoid-coated DNA constructs offer a controllable anticancer drug release and an ability to display functional biomolecules on the DNA surfaces. Our study demonstrates an approach for building multifunctional and environmentally robust DNA-based molecular structures for nanomedicine and biosensing. DNA nanotechnology has established approaches for designing programmable and precisely controlled nanoscale architectures through specific Watson−Crick base-pairing, molecular plasticity, and intermolecular connectivity. In particular, superior control over DNA origami structures could be beneficial for biomedical applications, including biosensing, in vivo imaging, and drug and gene delivery. However, protecting DNA origami structures in complex biological fluids while preserving their structural characteristics remains a major challenge for enabling these applications. Here, we developed a class of structurally well-defined peptoids to protect DNA origamis in ionic and bioactive conditions and systematically explored the effects of peptoid architecture and sequence dependency on DNA origami stability. The applicability of this approach for drug delivery, bioimaging, and cell targeting was also demonstrated. A series of peptoids (PE1–9) with two types of architectures, termed as “brush” and “block,” were built from positively charged monomers and neutral oligo-ethyleneoxy monomers, where certain designs were found to greatly enhance the stability of DNA origami. Through experimental and molecular dynamics studies, we demonstrated the role of sequence-dependent electrostatic interactions of peptoids with the DNA backbone. We showed that octahedral DNA origamis coated with peptoid (PE2) can be used as carriers for anticancer drug and protein, where the peptoid modulated the rate of drug release and prolonged protein stability against proteolytic hydrolysis. Finally, we synthesized two alkyne-modified peptoids (PE8 and PE9), conjugated with fluorophore and antibody, to make stable DNA origamis with imaging and cell-targeting capabilities. Our results demonstrate an approach toward functional and physiologically stable DNA origami for biomedical applications.
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28
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Sahle FF, Lowe TL. Design strategies for programmable oligonucleotide nanotherapeutics. Drug Discov Today 2020; 25:73-88. [PMID: 31525462 PMCID: PMC6980509 DOI: 10.1016/j.drudis.2019.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 08/02/2019] [Accepted: 09/09/2019] [Indexed: 01/08/2023]
Abstract
A systematic review on how to design different programmable nanotherapeutics using oligonucleotides as building blocks or as surface and matrix modifiers for controlled and targeted delivery of various therapeutic agents in presented.
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Affiliation(s)
- Fitsum Feleke Sahle
- Department of Pharmaceutical Sciences, University of Tennessee Health Sciences Center, Memphis, TN 38163, USA
| | - Tao L Lowe
- Department of Pharmaceutical Sciences, University of Tennessee Health Sciences Center, Memphis, TN 38163, USA.
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29
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Jahanban-Esfahlan R, Seidi K, Jahanban-Esfahlan A, Jaymand M, Alizadeh E, Majdi H, Najjar R, Javaheri T, Zare P. Static DNA Nanostructures For Cancer Theranostics: Recent Progress In Design And Applications. Nanotechnol Sci Appl 2019; 12:25-46. [PMID: 31686793 PMCID: PMC6800557 DOI: 10.2147/nsa.s227193] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 09/13/2019] [Indexed: 12/13/2022] Open
Abstract
Among the various nano/biomaterials used in cancer treatment, the beauty and benefits of DNA nanocomposites are outstanding. The specificity and programmability of the base pairing of DNA strands, together with their ability to conjugate with different types of functionalities have realized unsurpassed potential for the production of two- and three-dimensional nano-sized structures in any shape, size, surface chemistry and functionality. This review aims to provide an insight into the diversity of static DNA nanodevices, including DNA origami, DNA polyhedra, DNA origami arrays and bioreactors, DNA nanoswitch, DNA nanoflower, hydrogel and dendrimer as young but promising platforms for cancer theranostics. The utility and potential of the individual formats in biomedical science and especially in cancer therapy will be discussed.
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Affiliation(s)
- Rana Jahanban-Esfahlan
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz9841, Iran
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz9841, Iran
| | - Khaled Seidi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz9841, Iran
| | | | - Mehdi Jaymand
- Nano Drug Delivery Research Center (NDDRC), Kermanshah University of Medical Sciences, Kermanshah9883, Iran
| | - Effat Alizadeh
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz9841, Iran
| | - Hasan Majdi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz9841, Iran
| | - Reza Najjar
- Polymer Research Laboratory, Faculty of Chemistry, University of Tabriz, Tabriz9841, Iran
| | - Tahereh Javaheri
- Ludwig Boltzmann Institute for Cancer Research, Vienna1090, Austria
| | - Peyman Zare
- Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw01-938, Poland
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30
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Su LJ, Lin HH, Wu MS, Pan L, Yadav K, Hsu HH, Ling TY, Chen YT, Chang HC. Intracellular Delivery of Luciferase with Fluorescent Nanodiamonds for Dual-Modality Imaging of Human Stem Cells. Bioconjug Chem 2019; 30:2228-2237. [PMID: 31268690 DOI: 10.1021/acs.bioconjchem.9b00458] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Delivering functional proteins (such as enzymes) into cells is important in various biological studies and is often accomplished indirectly by transfection with DNA or mRNA encoding recombinant proteins. However, the transfection efficiency of conventional plasmid methods is low for primary cells, which are crucial sources of cell therapy. Here, we present a new platform based on the use of fluorescent nanodiamond (FND) as a biocompatible nanocarrier to enable rapid, effective, and homogeneous labeling of human mesenchymal stem cells (MSCs) with luciferase for multiplex assays and ultrasensitive detection. More than 100 pg of FND and 100 million copies of firefly luciferase can be delivered into each MSC through endocytosis. Moreover, these endocytic luciferase molecules are catalytically active for hours, allowing the cells to be imaged and tracked in vitro as well as in vivo by both fluorescence and bioluminescence imaging. Our results demonstrate that luciferase-conjugated FNDs are useful as multifunctional labels of human stem cells for diverse theranostic applications.
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Affiliation(s)
- Long-Jyun Su
- Institute of Atomic and Molecular Sciences , Academia Sinica , Taipei 106 , Taiwan.,Department of Chemistry , National Taiwan University , Taipei 106 , Taiwan
| | - Hsin-Hung Lin
- Institute of Atomic and Molecular Sciences , Academia Sinica , Taipei 106 , Taiwan
| | - Meng-Shiue Wu
- Department of Pharmacology , National Taiwan University , Taipei 100 , Taiwan
| | - Lei Pan
- Institute of Atomic and Molecular Sciences , Academia Sinica , Taipei 106 , Taiwan
| | - Kanchan Yadav
- Department of Chemistry , National Taiwan University , Taipei 106 , Taiwan
| | - Hsao-Hsun Hsu
- Department of Surgery, College of Medicine and the Hospital , National Taiwan University , Taipei 100 , Taiwan
| | - Thai-Yen Ling
- Department of Pharmacology , National Taiwan University , Taipei 100 , Taiwan
| | - Yit-Tsong Chen
- Institute of Atomic and Molecular Sciences , Academia Sinica , Taipei 106 , Taiwan.,Department of Chemistry , National Taiwan University , Taipei 106 , Taiwan
| | - Huan-Cheng Chang
- Institute of Atomic and Molecular Sciences , Academia Sinica , Taipei 106 , Taiwan.,Department of Chemical Engineering , National Taiwan University of Science and Technology , Taipei 106 , Taiwan
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31
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Fu J, Oh SW, Monckton K, Arbuckle-Keil G, Ke Y, Zhang T. Biomimetic Compartments Scaffolded by Nucleic Acid Nanostructures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900256. [PMID: 30884139 DOI: 10.1002/smll.201900256] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 02/19/2019] [Indexed: 05/28/2023]
Abstract
The behaviors of living cells are governed by a series of regulated and confined biochemical reactions. The design and successful construction of synthetic cellular reactors can be useful in a broad range of applications that will bring significant scientific and economic impact. Over the past few decades, DNA self-assembly has enabled the design and fabrication of sophisticated 1D, 2D, and 3D nanostructures, and is applied to organizing a variety of biomolecular components into prescribed 2D and 3D patterns. In this Concept, the recent and exciting progress in DNA-scaffolded compartmentalizations and their applications in enzyme encapsulation, lipid membrane assembly, artificial transmembrane nanopores, and smart drug delivery are in focus. Taking advantage of these features promises to deliver breakthroughs toward the attainment of new synthetic and biomimetic reactors.
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Affiliation(s)
- Jinglin Fu
- Department of Chemistry and Center for Computational and Integrative Biology, Rutgers University-Camden, 315 Penn Street, Camden, NJ, 08102, USA
| | - Sung Won Oh
- Department of Chemistry and Center for Computational and Integrative Biology, Rutgers University-Camden, 315 Penn Street, Camden, NJ, 08102, USA
| | - Kristin Monckton
- Department of Chemistry and Center for Computational and Integrative Biology, Rutgers University-Camden, 315 Penn Street, Camden, NJ, 08102, USA
| | - Georgia Arbuckle-Keil
- Department of Chemistry and Center for Computational and Integrative Biology, Rutgers University-Camden, 315 Penn Street, Camden, NJ, 08102, USA
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, 30322, USA
| | - Ting Zhang
- Department of Chemistry and Center for Computational and Integrative Biology, Rutgers University-Camden, 315 Penn Street, Camden, NJ, 08102, USA
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32
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Shen H, Wang Y, Wang J, Li Z, Yuan Q. Emerging Biomimetic Applications of DNA Nanotechnology. ACS APPLIED MATERIALS & INTERFACES 2019; 11:13859-13873. [PMID: 29939004 DOI: 10.1021/acsami.8b06175] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Re-engineering cellular components and biological processes has received great interest and promised compelling advantages in applications ranging from basic cell biology to biomedicine. With the advent of DNA nanotechnology, the programmable self-assembly ability makes DNA an appealing candidate for rational design of artificial components with different structures and functions. This Forum Article summarizes recent developments of DNA nanotechnology in mimicking the structures and functions of existing cellular components. We highlight key successes in the achievements of DNA-based biomimetic membrane proteins and discuss the assembly behavior of these artificial proteins. Then, we focus on the construction of higher-order structures by DNA nanotechnology to recreate cell-like structures. Finally, we explore the current challenges and speculate on future directions of DNA nanotechnology in biomimetics.
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Affiliation(s)
- Haijing Shen
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , 430072 , China
| | - Yingqian Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , 430072 , China
| | - Jie Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , 430072 , China
| | - Zhihao Li
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , 430072 , China
| | - Quan Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , 430072 , China
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33
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Palazzolo S, Hadla M, Spena CR, Bayda S, Kumar V, Lo Re F, Adeel M, Caligiuri I, Romano F, Corona G, Canzonieri V, Toffoli G, Rizzolio F. Proof-of-Concept Multistage Biomimetic Liposomal DNA Origami Nanosystem for the Remote Loading of Doxorubicin. ACS Med Chem Lett 2019; 10:517-521. [PMID: 30996789 DOI: 10.1021/acsmedchemlett.8b00557] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/31/2019] [Indexed: 12/20/2022] Open
Abstract
One of the most promising applications of DNA origami is its use as an excellent evolution of nanostructured intelligent systems for drug delivery, but short in vivo lifetime and immune-activation are still major challenges to overcome. On the contrary, stealth liposomes have long-circulation time and are well tolerated by the immune system. To overcome DNA origami limitations, we have designed and synthesized a compact short tube DNA origami (STDO) of approximately 30 nm in length and 10 nm in width. These STDO are highly stable ≥48 h in physiological conditions without any postsynthetic modifications. The compact size of STDO precisely fits inside a stealthy liposome of about 150 nm and could efficiently remotely load doxorubicin in liposomes (LSTDO) without a pH driven gradient. We demonstrated that this innovative drug delivery system (DDS) has an optimal tumoral release and high biocompatible profiles opening up new horizons to encapsulate many other hydrophobic drugs.
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Affiliation(s)
- Stefano Palazzolo
- Clinical and Experimental Pharmacology Unit, IRCCS CRO Aviano-National Cancer Institute, 33081 Aviano, Italy
- Doctoral School in Nanotechnology, University of Trieste, 34127 Trieste, Italy
- Pathology Unit, IRCCS CRO Aviano-National Cancer Institute, 33081 Aviano, Italy
| | - Mohamad Hadla
- Clinical and Experimental Pharmacology Unit, IRCCS CRO Aviano-National Cancer Institute, 33081 Aviano, Italy
| | - Concetta Russo Spena
- Clinical and Experimental Pharmacology Unit, IRCCS CRO Aviano-National Cancer Institute, 33081 Aviano, Italy
| | - Samer Bayda
- Clinical and Experimental Pharmacology Unit, IRCCS CRO Aviano-National Cancer Institute, 33081 Aviano, Italy
| | - Vinit Kumar
- Clinical and Experimental Pharmacology Unit, IRCCS CRO Aviano-National Cancer Institute, 33081 Aviano, Italy
- Amity Institute of Molecular Medicine & Stem Cell Research, 201313 Noida, India
| | - Francesco Lo Re
- Clinical and Experimental Pharmacology Unit, IRCCS CRO Aviano-National Cancer Institute, 33081 Aviano, Italy
| | - Muhammad Adeel
- Pathology Unit, IRCCS CRO Aviano-National Cancer Institute, 33081 Aviano, Italy
| | - Isabella Caligiuri
- Pathology Unit, IRCCS CRO Aviano-National Cancer Institute, 33081 Aviano, Italy
| | - Flavio Romano
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34127 Trieste, Italy
| | - Giuseppe Corona
- Clinical and Experimental Pharmacology Unit, IRCCS CRO Aviano-National Cancer Institute, 33081 Aviano, Italy
| | - Vincenzo Canzonieri
- Pathology Unit, IRCCS CRO Aviano-National Cancer Institute, 33081 Aviano, Italy
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34127 Trieste, Italy
| | - Giuseppe Toffoli
- Clinical and Experimental Pharmacology Unit, IRCCS CRO Aviano-National Cancer Institute, 33081 Aviano, Italy
| | - Flavio Rizzolio
- Clinical and Experimental Pharmacology Unit, IRCCS CRO Aviano-National Cancer Institute, 33081 Aviano, Italy
- Pathology Unit, IRCCS CRO Aviano-National Cancer Institute, 33081 Aviano, Italy
- Department of Molecular Sciences and Nanosystems, Ca’ Foscari University of Venice, 30123 Venezia, Italy
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34
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Abstract
DNA nanotechnology research has long-held promise as a means of developing functional molecules capable of delivery to cells. Recent advances in DNA origami have begun to realize this potential but is still at the earliest stage and a number of hurdles remain. This review focuses on progress in addressing these hurdles and considers some of the challenges still outstanding. These include stability of such structures necessary to reach target cells after administration; methods of cell targeting and uptake; strategies to avoid or escape endosomes and techniques for achieving specific subcellular localization. Finally, the functionality that can be expected once DNA origami structures reach their final intracellular targets will be considered.
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Affiliation(s)
- Dhanasekaran Balakrishnan
- Bionanoscience & Biochemistry Laboratory, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland.,Postgraduate School of Molecular Medicine; Żwirki i Wigury 61, 02-091 Warsaw, Poland
| | - Gerrit D Wilkens
- Bionanoscience & Biochemistry Laboratory, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland.,Postgraduate School of Molecular Medicine; Żwirki i Wigury 61, 02-091 Warsaw, Poland
| | - Jonathan G Heddle
- Bionanoscience & Biochemistry Laboratory, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland
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35
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Abstract
The predictable nature of DNA interactions enables the programmable assembly of highly advanced 2D and 3D DNA structures of nanoscale dimensions. The access to ever larger and more complex structures has been achieved through decades of work on developing structural design principles. Concurrently, an increased focus has emerged on the applications of DNA nanostructures. In its nature, DNA is chemically inert and nanostructures based on unmodified DNA mostly lack function. However, functionality can be obtained through chemical modification of DNA nanostructures and the opportunities are endless. In this review, we discuss methodology for chemical functionalization of DNA nanostructures and provide examples of how this is being used to create functional nanodevices and make DNA nanostructures more applicable. We aim to encourage researchers to adopt chemical modifications as part of their work in DNA nanotechnology and inspire chemists to address current challenges and opportunities within the field.
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Affiliation(s)
- Mikael Madsen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK - 8000 Aarhus C, Denmark
| | - Kurt V Gothelf
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK - 8000 Aarhus C, Denmark
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36
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Chen Q, Zhou S, Li C, Guo Q, Yang X, Huang J, Liu J, Wang K. DNA supersandwich assemblies as artificial receptors to mediate intracellular delivery of catalase for efficient ROS scavenging. Chem Commun (Camb) 2019; 55:4242-4245. [DOI: 10.1039/c9cc00201d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Aptamer–supersandwich nanostructures as artificial receptors to mediate catalase intracellular delivery with high transfection efficacy and a significant ROS scavenging ability.
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Affiliation(s)
- Qiaoshu Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
- Changsha 410082
| | - Shaohong Zhou
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
- Changsha 410082
| | - Chunying Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
- Changsha 410082
| | - Qiuping Guo
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
- Changsha 410082
| | - Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
- Changsha 410082
| | - Jin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
- Changsha 410082
| | - Jianbo Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
- Changsha 410082
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
- Changsha 410082
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37
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Brassat K, Ramakrishnan S, Bürger J, Hanke M, Doostdar M, Lindner JKN, Grundmeier G, Keller A. On the Adsorption of DNA Origami Nanostructures in Nanohole Arrays. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14757-14765. [PMID: 29754490 DOI: 10.1021/acs.langmuir.8b00793] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
DNA origami nanostructures are versatile substrates for the controlled arrangement of molecular capture sites with nanometer precision and thus have many promising applications in single-molecule bioanalysis. Here, we investigate the adsorption of DNA origami nanostructures in nanohole arrays which represent an important class of biosensors and may benefit from the incorporation of DNA origami-based molecular probes. Nanoholes with well-defined diameter that enable the adsorption of single DNA origami triangles are fabricated in Au films on Si wafers by nanosphere lithography. The efficiency of directed DNA origami adsorption on the exposed SiO2 areas at the bottoms of the nanoholes is evaluated in dependence of various parameters, i.e., Mg2+ and DNA origami concentrations, buffer strength, adsorption time, and nanohole diameter. We observe that the buffer strength has a surprisingly strong effect on DNA origami adsorption in the nanoholes and that multiple DNA origami triangles with 120 nm edge length can adsorb in nanoholes as small as 120 nm in diameter. We attribute the latter observation to the low lateral mobility of once adsorbed DNA origami on the SiO2 surface, in combination with parasitic adsorption to the Au film. Although parasitic adsorption can be suppressed by modifying the Au film with a hydrophobic self-assembled monolayer, the limited surface mobility of the adsorbed DNA origami still leads to poor localization accuracy in the nanoholes and results in many DNA origami crossing the boundary to the Au film even under optimized conditions. We discuss possible ways to minimize this effect by varying the composition of the adsorption buffer, employing different fabrication conditions, or using other substrate materials for nanohole array fabrication.
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38
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Shen B, Kostiainen MA, Linko V. DNA Origami Nanophotonics and Plasmonics at Interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14911-14920. [PMID: 30122051 PMCID: PMC6291805 DOI: 10.1021/acs.langmuir.8b01843] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
DNA nanotechnology provides a versatile toolbox for creating custom and accurate shapes that can serve as versatile templates for nanopatterning. These DNA templates can be used as molecular-scale precision tools in, for example, biosensing, nanometrology, and super-resolution imaging, and biocompatible scaffolds for arranging other nano-objects, for example, for drug delivery applications and molecular electronics. Recently, increasing attention has been paid to their potent use in nanophotonics since these modular templates allow a wide range of plasmonic and photonic ensembles ranging from DNA-directed nanoparticle and fluorophore arrays to entirely metallic nanostructures. This Feature Article focuses on the DNA-origami-based nanophotonics and plasmonics-especially on the methods that take advantage of various substrates and interfaces for the foreseen applications.
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Affiliation(s)
- Boxuan Shen
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Mauri A. Kostiainen
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
- HYBER
Center of Excellence, Department of Applied Physics, Aalto University, 00076 Aalto, Finland
| | - Veikko Linko
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
- E-mail:
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39
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Madhanagopal BR, Zhang S, Demirel E, Wady H, Chandrasekaran AR. DNA Nanocarriers: Programmed to Deliver. Trends Biochem Sci 2018; 43:997-1013. [DOI: 10.1016/j.tibs.2018.09.010] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 09/16/2018] [Accepted: 09/19/2018] [Indexed: 12/11/2022]
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40
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Chen Y, Wang P, Xu Y, Li X, Zhu Y, Zhang Y, Zhu J, Huang G, He D. Different Stability of DNA Origami Nanostructure between on Interface and in Bulk Solution. ACS APPLIED BIO MATERIALS 2018; 1:1424-1429. [DOI: 10.1021/acsabm.8b00379] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Yi Chen
- School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ping Wang
- National Engineering Research Center for Nanotechnology, Shanghai, 200241, China
| | - Yan Xu
- National Engineering Research Center for Nanotechnology, Shanghai, 200241, China
| | - Xiaodi Li
- Shanghai University of Medicine &Health Sciences, Shanghai, 201318, China
| | - Yuanjie Zhu
- Shanghai University of Medicine &Health Sciences, Shanghai, 201318, China
| | - Ying Zhang
- National Engineering Research Center for Nanotechnology, Shanghai, 200241, China
| | - Jun Zhu
- National Engineering Research Center for Nanotechnology, Shanghai, 200241, China
| | - Gang Huang
- Shanghai University of Medicine &Health Sciences, Shanghai, 201318, China
| | - Dannong He
- School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
- National Engineering Research Center for Nanotechnology, Shanghai, 200241, China
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41
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Loescher S, Groeer S, Walther A. 3D DNA Origami Nanoparticles: From Basic Design Principles to Emerging Applications in Soft Matter and (Bio‐)Nanosciences. Angew Chem Int Ed Engl 2018; 57:10436-10448. [DOI: 10.1002/anie.201801700] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/11/2018] [Indexed: 01/14/2023]
Affiliation(s)
- Sebastian Loescher
- Institute for Macromolecular Chemistry, Stefan-Meier-Strasse 31University of Freiburg 79104 Freiburg Germany
- Freiburg Materials Research Center, Stefan-Meier-Strasse 21University of Freiburg 79104 Freiburg Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies, Georges-Köhler-Allee 105University of Freiburg 79110 Freiburg Germany
- Freiburg Institute for Advanced Studies (FRIAS), Albertstrasse 19University of Freiburg 79104 Freiburg Germany
| | - Saskia Groeer
- Institute for Macromolecular Chemistry, Stefan-Meier-Strasse 31University of Freiburg 79104 Freiburg Germany
- Freiburg Materials Research Center, Stefan-Meier-Strasse 21University of Freiburg 79104 Freiburg Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies, Georges-Köhler-Allee 105University of Freiburg 79110 Freiburg Germany
- Freiburg Institute for Advanced Studies (FRIAS), Albertstrasse 19University of Freiburg 79104 Freiburg Germany
| | - Andreas Walther
- Institute for Macromolecular Chemistry, Stefan-Meier-Strasse 31University of Freiburg 79104 Freiburg Germany
- Freiburg Materials Research Center, Stefan-Meier-Strasse 21University of Freiburg 79104 Freiburg Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies, Georges-Köhler-Allee 105University of Freiburg 79110 Freiburg Germany
- Freiburg Institute for Advanced Studies (FRIAS), Albertstrasse 19University of Freiburg 79104 Freiburg Germany
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42
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Loescher S, Groeer S, Walther A. 3D‐DNA‐Origami‐Nanopartikel: von grundlegenden Designprinzipien hin zu neuartigen Anwendungen in der weichen Materie und den (Bio‐)Nanowissenschaften. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801700] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Sebastian Loescher
- Institut für Makromolekulare Chemie, Stefan-Meier-Straße 31Albert-Ludwigs-Universität Freiburg 79104 Freiburg Deutschland
- Freiburger MaterialforschungszentrumAlbert-Ludwigs-Universität Freiburg Deutschland
- Freiburger Zentrum für interaktive Werkstoffe und bioinspirierte TechnologienAlbert-Ludwigs-Universität Freiburg Deutschland
- Freiburg Institute for Advanced Studies (FRIAS)Albert-Ludwigs-Universität Freiburg Deutschland
| | - Saskia Groeer
- Institut für Makromolekulare Chemie, Stefan-Meier-Straße 31Albert-Ludwigs-Universität Freiburg 79104 Freiburg Deutschland
- Freiburger MaterialforschungszentrumAlbert-Ludwigs-Universität Freiburg Deutschland
- Freiburger Zentrum für interaktive Werkstoffe und bioinspirierte TechnologienAlbert-Ludwigs-Universität Freiburg Deutschland
- Freiburg Institute for Advanced Studies (FRIAS)Albert-Ludwigs-Universität Freiburg Deutschland
| | - Andreas Walther
- Institut für Makromolekulare Chemie, Stefan-Meier-Straße 31Albert-Ludwigs-Universität Freiburg 79104 Freiburg Deutschland
- Freiburger MaterialforschungszentrumAlbert-Ludwigs-Universität Freiburg Deutschland
- Freiburger Zentrum für interaktive Werkstoffe und bioinspirierte TechnologienAlbert-Ludwigs-Universität Freiburg Deutschland
- Freiburg Institute for Advanced Studies (FRIAS)Albert-Ludwigs-Universität Freiburg Deutschland
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43
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Ijäs H, Nummelin S, Shen B, Kostiainen MA, Linko V. Dynamic DNA Origami Devices: from Strand-Displacement Reactions to External-Stimuli Responsive Systems. Int J Mol Sci 2018; 19:E2114. [PMID: 30037005 PMCID: PMC6073283 DOI: 10.3390/ijms19072114] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 07/16/2018] [Accepted: 07/18/2018] [Indexed: 12/31/2022] Open
Abstract
DNA nanotechnology provides an excellent foundation for diverse nanoscale structures that can be used in various bioapplications and materials research. Among all existing DNA assembly techniques, DNA origami proves to be the most robust one for creating custom nanoshapes. Since its invention in 2006, building from the bottom up using DNA advanced drastically, and therefore, more and more complex DNA-based systems became accessible. So far, the vast majority of the demonstrated DNA origami frameworks are static by nature; however, there also exist dynamic DNA origami devices that are increasingly coming into view. In this review, we discuss DNA origami nanostructures that exhibit controlled translational or rotational movement when triggered by predefined DNA sequences, various molecular interactions, and/or external stimuli such as light, pH, temperature, and electromagnetic fields. The rapid evolution of such dynamic DNA origami tools will undoubtedly have a significant impact on molecular-scale precision measurements, targeted drug delivery and diagnostics; however, they can also play a role in the development of optical/plasmonic sensors, nanophotonic devices, and nanorobotics for numerous different tasks.
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Affiliation(s)
- Heini Ijäs
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland.
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland.
| | - Sami Nummelin
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland.
| | - Boxuan Shen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland.
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland.
- HYBER Center of Excellence, Department of Applied Physics, Aalto University, 00076 Aalto, Finland.
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland.
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44
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Kielar C, Xin Y, Shen B, Kostiainen MA, Grundmeier G, Linko V, Keller A. On the Stability of DNA Origami Nanostructures in Low-Magnesium Buffers. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802890] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Charlotte Kielar
- Technical and Macromolecular Chemistry; Paderborn University; Warburger Str. 100 33098 Paderborn Germany
| | - Yang Xin
- Technical and Macromolecular Chemistry; Paderborn University; Warburger Str. 100 33098 Paderborn Germany
| | - Boxuan Shen
- Biohybrid Materials; Department of Bioproducts and Biosystems Aalto University; P. O. Box 16100 00076 Aalto Finland
| | - Mauri A. Kostiainen
- Biohybrid Materials; Department of Bioproducts and Biosystems Aalto University; P. O. Box 16100 00076 Aalto Finland
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry; Paderborn University; Warburger Str. 100 33098 Paderborn Germany
| | - Veikko Linko
- Technical and Macromolecular Chemistry; Paderborn University; Warburger Str. 100 33098 Paderborn Germany
- Biohybrid Materials; Department of Bioproducts and Biosystems Aalto University; P. O. Box 16100 00076 Aalto Finland
| | - Adrian Keller
- Technical and Macromolecular Chemistry; Paderborn University; Warburger Str. 100 33098 Paderborn Germany
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Kielar C, Xin Y, Shen B, Kostiainen MA, Grundmeier G, Linko V, Keller A. On the Stability of DNA Origami Nanostructures in Low-Magnesium Buffers. Angew Chem Int Ed Engl 2018; 57:9470-9474. [PMID: 29799663 DOI: 10.1002/anie.201802890] [Citation(s) in RCA: 148] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 05/17/2018] [Indexed: 12/28/2022]
Abstract
DNA origami structures have great potential as functional platforms in various biomedical applications. Many applications, however, are incompatible with the high Mg2+ concentrations commonly believed to be a prerequisite for maintaining DNA origami integrity. Herein, we investigate DNA origami stability in low-Mg2+ buffers. DNA origami stability is found to crucially depend on the availability of residual Mg2+ ions for screening electrostatic repulsion. The presence of EDTA and phosphate ions may thus facilitate DNA origami denaturation by displacing Mg2+ ions from the DNA backbone and reducing the strength of the Mg2+ -DNA interaction, respectively. Most remarkably, these buffer dependencies are affected by DNA origami superstructure. However, by rationally selecting buffer components and considering superstructure-dependent effects, the structural integrity of a given DNA origami nanostructure can be maintained in conventional buffers even at Mg2+ concentrations in the low-micromolar range.
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Affiliation(s)
- Charlotte Kielar
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Yang Xin
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Boxuan Shen
- Biohybrid Materials, Department of Bioproducts and Biosystems Aalto University, P. O. Box 16100, 00076, Aalto, Finland
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems Aalto University, P. O. Box 16100, 00076, Aalto, Finland
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Veikko Linko
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany.,Biohybrid Materials, Department of Bioproducts and Biosystems Aalto University, P. O. Box 16100, 00076, Aalto, Finland
| | - Adrian Keller
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
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Zhang Y, Tu J, Wang D, Zhu H, Maity SK, Qu X, Bogaert B, Pei H, Zhang H. Programmable and Multifunctional DNA-Based Materials for Biomedical Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1703658. [PMID: 29389041 DOI: 10.1002/adma.201703658] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/09/2017] [Indexed: 06/07/2023]
Abstract
DNA encodes the genetic information; recently, it has also become a key player in material science. Given the specific Watson-Crick base-pairing interactions between only four types of nucleotides, well-designed DNA self-assembly can be programmable and predictable. Stem-loops, sticky ends, Holliday junctions, DNA tiles, and lattices are typical motifs for forming DNA-based structures. The oligonucleotides experience thermal annealing in a near-neutral buffer containing a divalent cation (usually Mg2+ ) to produce a variety of DNA nanostructures. These structures not only show beautiful landscape, but can also be endowed with multifaceted functionalities. This Review begins with the fundamental characterization and evolutionary trajectory of DNA-based artificial structures, but concentrates on their biomedical applications. The coverage spans from controlled drug delivery to high therapeutic profile and accurate diagnosis. A variety of DNA-based materials, including aptamers, hydrogels, origamis, and tetrahedrons, are widely utilized in different biomedical fields. In addition, to achieve better performance and functionality, material hybridization is widely witnessed, and DNA nanostructure modification is also discussed. Although there are impressive advances and high expectations, the development of DNA-based structures/technologies is still hindered by several commonly recognized challenges, such as nuclease instability, lack of pharmacokinetics data, and relatively high synthesis cost.
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Affiliation(s)
- Yuezhou Zhang
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
| | - Jing Tu
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
| | - Dongqing Wang
- Department of Radiology, Affiliated Hospital of Jiangsu University Jiangsu University, 212001, Zhenjiang, P. R. China
| | - Haitao Zhu
- Department of Radiology, Affiliated Hospital of Jiangsu University Jiangsu University, 212001, Zhenjiang, P. R. China
| | | | - Xiangmeng Qu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 200241, Shanghai, P. R. China
| | - Bram Bogaert
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 200241, Shanghai, P. R. China
| | - Hongbo Zhang
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
- Department of Radiology, Affiliated Hospital of Jiangsu University Jiangsu University, 212001, Zhenjiang, P. R. China
- Turku Center for Biotechnology, Åbo Akademi University, 20520, Turku, Finland
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Nummelin S, Kommeri J, Kostiainen MA, Linko V. Evolution of Structural DNA Nanotechnology. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1703721. [PMID: 29363798 DOI: 10.1002/adma.201703721] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 09/17/2017] [Indexed: 05/24/2023]
Abstract
The research field entitled structural DNA nanotechnology emerged in the beginning of the 1980s as the first immobile synthetic nucleic acid junctions were postulated and demonstrated. Since then, the field has taken huge leaps toward advanced applications, especially during the past decade. This Progress Report summarizes how the controllable, custom, and accurate nanostructures have recently evolved together with powerful design and simulation software. Simultaneously they have provided a significant expansion of the shape space of the nanostructures. Today, researchers can select the most suitable fabrication methods, and design paradigms and software from a variety of options when creating unique DNA nanoobjects and shapes for a plethora of implementations in materials science, optics, plasmonics, molecular patterning, and nanomedicine.
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Affiliation(s)
- Sami Nummelin
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076, Aalto, Finland
| | - Juhana Kommeri
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076, Aalto, Finland
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076, Aalto, Finland
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076, Aalto, Finland
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Julin S, Nummelin S, Kostiainen MA, Linko V. DNA nanostructure-directed assembly of metal nanoparticle superlattices. JOURNAL OF NANOPARTICLE RESEARCH : AN INTERDISCIPLINARY FORUM FOR NANOSCALE SCIENCE AND TECHNOLOGY 2018; 20:119. [PMID: 29950921 PMCID: PMC5997120 DOI: 10.1007/s11051-018-4225-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/13/2018] [Indexed: 05/19/2023]
Abstract
Structural DNA nanotechnology provides unique, well-controlled, versatile, and highly addressable motifs and templates for assembling materials at the nanoscale. These methods to build from the bottom-up using DNA as a construction material are based on programmable and fully predictable Watson-Crick base pairing. Researchers have adopted these techniques to an increasing extent for creating numerous DNA nanostructures for a variety of uses ranging from nanoelectronics to drug-delivery applications. Recently, an increasing effort has been put into attaching nanoparticles (the size range of 1-20 nm) to the accurate DNA motifs and into creating metallic nanostructures (typically 20-100 nm) using designer DNA nanoshapes as molds or stencils. By combining nanoparticles with the superior addressability of DNA-based scaffolds, it is possible to form well-ordered materials with intriguing and completely new optical, plasmonic, electronic, and magnetic properties. This focused review discusses the DNA structure-directed nanoparticle assemblies covering the wide range of different one-, two-, and three-dimensional systems.
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Affiliation(s)
- Sofia Julin
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland
| | - Sami Nummelin
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland
| | - Mauri A. Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland
- HYBER Center of Excellence, Department of Applied Physics, Aalto University, Espoo, Finland
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland
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Ahmadi Y, De Llano E, Barišić I. (Poly)cation-induced protection of conventional and wireframe DNA origami nanostructures. NANOSCALE 2018; 10:7494-7504. [PMID: 29637957 DOI: 10.1039/c7nr09461b] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
DNA nanostructures hold immense potential to be used for biological and medical applications. However, they are extremely vulnerable towards salt depletion and nucleases, which are common under physiological conditions. In this contribution, we used chitosan and linear polyethyleneimine for coating and long-term stabilization of several three-dimensional DNA origami nanostructures. The impact of the degree of polymerization and the charge density of the polymer together with the N/P charge ratio (ratio of the amines in polycations to the phosphates in DNA) on the stability of encapsulated DNA origami nanostructures in the presence of nucleases and in low-salt media was examined. The polycation shells were compatible with enzyme- and aptamer-based functionalization of the DNA nanostructures. Additionally, we showed that despite being highly vulnerable to salt depletion and nucleolytic digestion, self-assembled DNA nanostructures are stable in cell culture media up to a week. This was contrary to unassembled DNA scaffolds that degraded in one hour, showing that placing DNA strands into a spatially designed configuration crucially affect the structural integrity. The stability of naked DNA nanostructures in cell culture was shown to be mediated by growth media. DNA origami nanostructures kept in growth media were significantly more resistant towards low-salt denaturation, DNase I and serum-mediated digestion than when in a conventional buffer. Moreover, we confirmed that DNA origami nanostructures remain not only structurally intact but also fully functional after exposure to cell media. Agarose gel electrophoresis and negative stain transmission electron microscopy analysis revealed the hybridization of DNA origami nanostructures to their targets in the presence of serum proteins and nucleases. The structural integrity and functionality of DNA nanostructures in physiological fluids validate their use particularly for short-time biological applications in which the shape and structural details of DNA nanodevices are functionally critical.
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Affiliation(s)
- Yasaman Ahmadi
- Molecular Diagnostics, Centre for Health and Bioresources, AIT Austrian Institute of Technology GmbH, 1190 Vienna, Austria.
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Abstract
A synthetic topology for everted viruses is reported. The topology is a single-stranded virion DNA assembled into a hollow cube with exterior decorated with HIV-Tat transduction domains. The cube incorporates a pH-responsive lid allowing for the controlled encapsulation of functional proteins and their transfer and release into live cells. Unlike viruses, which are protein shells with a [3,5]-fold rotational symmetry that encase nucleic acids, these cubes are [3, 4]-fold DNA boxes encapsulating proteins. Like viruses, such everted DNA-built viruses are monodisperse nanoscale assemblies that infect human cells with a specialist cargo. The design offers a bespoke bottom-up platform for engineering nonpolyhedral, nonprotein synthetic viruses.
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Affiliation(s)
- Jonathan R. Burns
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, U.K
- Department of Chemistry, University College London, London, WC1E 6BT, U.K
| | - Baptiste Lamarre
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, U.K
| | - Alice L. B. Pyne
- London Centre for Nanotechnology, University College London, London, WC1E 6BT, U.K
| | - James E. Noble
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, U.K
| | - Maxim G. Ryadnov
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, U.K
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