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Ye R, Wang Y, Liu Y, Cai P, Song J. Self-assembled methodologies for the construction of DNA nanostructures and biological applications. Biomater Sci 2024; 12:3712-3724. [PMID: 38912847 DOI: 10.1039/d4bm00584h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Over the past decades, deoxyribonucleic acid (DNA), as a versatile building block, has been widely employed to construct functionalized nanostructures. Among the diverse types of materials, DNA related nanostructures have gained growing attention due to their intrinsic programmability, favorable biocompatibility, and strong molecular recognition capability. The conventional construction strategy for building DNA structures is based on Watson-Crick base-pairing rules, which are mainly driven by the hydrogen bonding of bases. However, hydrogen bonding-based DNA nanostructures cannot meet the requirements of specific morphology and multifunctionality. Currently, various functional elements have been introduced to expand the synthetic methodologies for constructing the DNA hybrid nanostructures, including small molecules, peptide polymers, organic ligands and transition metal ions. Besides, the potential applications for these DNA hybrid nanostructures have also been explored. It has been demonstrated that DNA hybrid structures with various properties can be extensively applied in the fields of magnetic resonance, luminescence imaging, biomedical detection, and drug delivery systems. In this review, we highlight the pioneering contributions to the methodologies of DNA-based nanostructure assembly. Furthermore, the recent advances in drug delivery systems and biomedical diagnosis based on DNA hybrid nanostructures are briefly summarized.
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Affiliation(s)
- Rui Ye
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Yuqi Wang
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
- Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Liu
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Ping Cai
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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2
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Abendstein L, Noteborn WEM, Veenman LS, Dijkstra DJ, van de Bovenkamp FS, Trouw LA, Sharp TH. DNA Nanostructure-Templated Antibody Complexes Provide Insights into the Geometric Requirements of Human Complement Cascade Activation. J Am Chem Soc 2024; 146:13455-13466. [PMID: 38703132 PMCID: PMC11099972 DOI: 10.1021/jacs.4c02772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2024]
Abstract
The classical complement pathway is activated by antigen-bound IgG antibodies. Monomeric IgG must oligomerize to activate complement via the hexameric C1q complex, and hexamerizing mutants of IgG appear as promising therapeutic candidates. However, structural data have shown that it is not necessary to bind all six C1q arms to initiate complement, revealing a symmetry mismatch between C1 and the hexameric IgG complex that has not been adequately explained. Here, we use DNA nanotechnology to produce specific nanostructures to template antigens and thereby spatially control IgG valency. These DNA-nanotemplated IgG complexes can activate complement on cell-mimetic lipid membranes, which enabled us to determine the effect of IgG valency on complement activation without the requirement to mutate antibodies. We investigated this using biophysical assays together with 3D cryo-electron tomography. Our data revealed the importance of interantigen distance on antibody-mediated complement activation, and that the cleavage of complement component C4 by the C1 complex is proportional to the number of ideally spaced antigens. Increased IgG valency also translated to better terminal pathway activation and membrane attack complex formation. Together, these data provide insights into how nanopatterning antigen-antibody complexes influence the activation of the C1 complex and suggest routes to modulate complement activation by antibody engineering. Furthermore, to our knowledge, this is the first time DNA nanotechnology has been used to study the activation of the complement system.
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Affiliation(s)
- Leoni Abendstein
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2300 RC, The Netherlands
| | - Willem E M Noteborn
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2300 RC, The Netherlands
| | - Luc S Veenman
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2300 RC, The Netherlands
| | - Douwe J Dijkstra
- Department of Immunology, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | | | - Leendert A Trouw
- Department of Immunology, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Thomas H Sharp
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden 2300 RC, The Netherlands
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K
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3
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Kosara S, Singh R, Bhatia D. Structural DNA nanotechnology at the nexus of next-generation bio-applications: challenges and perspectives. NANOSCALE ADVANCES 2024; 6:386-401. [PMID: 38235105 PMCID: PMC10790967 DOI: 10.1039/d3na00692a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 12/15/2023] [Indexed: 01/19/2024]
Abstract
DNA nanotechnology has significantly progressed in the last four decades, creating nucleic acid structures widely used in various biological applications. The structural flexibility, programmability, and multiform customization of DNA-based nanostructures make them ideal for creating structures of all sizes and shapes and multivalent drug delivery systems. Since then, DNA nanotechnology has advanced significantly, and numerous DNA nanostructures have been used in biology and other scientific disciplines. Despite the progress made in DNA nanotechnology, challenges still need to be addressed before DNA nanostructures can be widely used in biological interfaces. We can open the door for upcoming uses of DNA nanoparticles by tackling these issues and looking into new avenues. The historical development of various DNA nanomaterials has been thoroughly examined in this review, along with the underlying theoretical underpinnings, a summary of their applications in various fields, and an examination of the current roadblocks and potential future directions.
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Affiliation(s)
- Sanjay Kosara
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar Palaj Gujarat 382355 India
| | - Ramesh Singh
- Department of Mechanical Engineering, Colorado State University Fort Collins CO USA
| | - Dhiraj Bhatia
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar Palaj Gujarat 382355 India
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4
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Yuwen L, Zhang S, Chao J. Recent Advances in DNA Nanotechnology-Enabled Biosensors for Virus Detection. BIOSENSORS 2023; 13:822. [PMID: 37622908 PMCID: PMC10452139 DOI: 10.3390/bios13080822] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/05/2023] [Accepted: 08/12/2023] [Indexed: 08/26/2023]
Abstract
Virus-related infectious diseases are serious threats to humans, which makes virus detection of great importance. Traditional virus-detection methods usually suffer from low sensitivity and specificity, are time-consuming, have a high cost, etc. Recently, DNA biosensors based on DNA nanotechnology have shown great potential in virus detection. DNA nanotechnology, specifically DNA tiles and DNA aptamers, has achieved atomic precision in nanostructure construction. Exploiting the programmable nature of DNA nanostructures, researchers have developed DNA nanobiosensors that outperform traditional virus-detection methods. This paper reviews the history of DNA tiles and DNA aptamers, and it briefly describes the Baltimore classification of virology. Moreover, the advance of virus detection by using DNA nanobiosensors is discussed in detail and compared with traditional virus-detection methods. Finally, challenges faced by DNA nanobiosensors in virus detection are summarized, and a perspective on the future development of DNA nanobiosensors in virus detection is also provided.
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Affiliation(s)
- Lihui Yuwen
- State Key Laboratory of Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (L.Y.); (S.Z.)
| | - Shifeng Zhang
- State Key Laboratory of Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (L.Y.); (S.Z.)
| | - Jie Chao
- School of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
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5
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Zhang Y, Yang D, Wang P, Ke Y. Building Large DNA Bundles via Controlled Hierarchical Assembly of DNA Tubes. ACS NANO 2023. [PMID: 37207344 DOI: 10.1021/acsnano.3c01342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Structural DNA nanotechnology is capable of fabricating designer nanoscale artificial architectures. Developing simple and yet versatile assembly methods to construct large DNA structures of defined spatial features and dynamic capabilities has remained challenging. Herein, we designed a molecular assembly system where DNA tiles can assemble into tubes and then into large one-dimensional DNA bundles following a hierarchical pathway. A cohesive link was incorporated into the tile to induce intertube binding for the formation of DNA bundles. DNA bundles with length of dozens of micrometers and width of hundreds of nanometers were produced, whose assembly was revealed to be collectively determined by cationic strength and linker designs (binding strength, spacer length, linker position, etc.). Furthermore, multicomponent DNA bundles with programmable spatial features and compositions were realized by using various distinct tile designs. Lastly, we implemented dynamic capability into large DNA bundles to realize reversible reconfigurations among tile, tube, and bundles following specific molecular stimulations. We envision this assembly strategy can enrich the toolbox of DNA nanotechnology for rational design of large-size DNA materials of defined features and properties that may be applied to a variety of fields in materials science, synthetic biology, biomedical science, and beyond.
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Affiliation(s)
- Yunlong Zhang
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Donglei Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yonggang Ke
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
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Abstract
Enzymes fold into three-dimensional structures to distribute amino acid residues for catalysis, which inspired the supramolecular approach to construct enzyme-mimicking catalysts. A key concern in the development of supramolecular strategies is the ability to confine and orient functional groups to form enzyme-like active sites in artificial materials. This review introduces the design principles and construction of supramolecular nanomaterials exhibiting catalytic functions of heme-dependent enzymes, a large class of metalloproteins, which rely on a heme cofactor and spatially configured residues to catalyze diverse reactions via a complex multistep mechanism. We focus on the structure-activity relationship of the supramolecular catalysts and their applications in materials synthesis/degradation, biosensing, and therapeutics. The heme-free catalysts that catalyze reactions achieved by hemeproteins are also briefly discussed. Towards the end of the review, we discuss the outlook on the challenges related to catalyst design and future prospective, including the development of structure-resolving techniques and design concepts, with the aim of creating enzyme-mimicking materials that possess catalytic power rivaling that of natural enzymes..
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Affiliation(s)
- Yuanxi Liu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Zhen-Gang Wang
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
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7
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Huang J, Gambietz S, Saccà B. Self-Assembled Artificial DNA Nanocompartments and Their Bioapplications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2202253. [PMID: 35775957 DOI: 10.1002/smll.202202253] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Compartmentalization is the strategy evolved by nature to control reactions in space and time. The ability to emulate this strategy through synthetic compartmentalization systems has rapidly evolved in the past years, accompanied by an increasing understanding of the effects of spatial confinement on the thermodynamic and kinetic properties of the guest molecules. DNA nanotechnology has played a pivotal role in this scientific endeavor and is still one of the most promising approaches for the construction of nanocompartments with programmable structural features and nanometer-scaled addressability. In this review, the design approaches, bioapplications, and theoretical frameworks of self-assembled DNA nanocompartments are surveyed. From DNA polyhedral cages to virus-like capsules, the construction principles of such intriguing architectures are illustrated. Various applications of DNA nanocompartments, including their use for programmable enzyme scaffolding, single-molecule studies, biosensing, and as artificial nanofactories, ending with an ample description of DNA nanocages for biomedical purposes, are then reported. Finally, the theoretical hypotheses that make DNA nanocompartments, and nanosystems in general, a topic of great interest in modern science, are described and the progresses that have been done until now in the comprehension of the peculiar phenomena that occur within nanosized environments are summarized.
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Affiliation(s)
- Jing Huang
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
| | - Sabrina Gambietz
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
| | - Barbara Saccà
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
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Zhou C, Yang D, Sensale S, Sharma P, Wang D, Yu L, Arya G, Ke Y, Wang P. A bistable and reconfigurable molecular system with encodable bonds. SCIENCE ADVANCES 2022; 8:eade3003. [PMID: 36399380 PMCID: PMC9674029 DOI: 10.1126/sciadv.ade3003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Molecular systems with ability to controllably transform between different conformations play pivotal roles in regulating biochemical functions. Here, we report the design of a bistable DNA origami four-way junction (DOJ) molecular system that adopts two distinct stable conformations with controllable reconfigurability by using conformation-controlled base stacking. Exquisite control over DOJ's conformation and transformation is realized by programming the stacking bonds (quasi-blunt-ends) within the junction to induce prescribed coaxial stacking of neighboring junction arms. A specific DOJ conformation may be achieved by encoding the stacking bonds with binary stacking sequences based on thermodynamic calculations. Dynamic transformations of DOJ between various conformations are achieved by using specific environmental and molecular stimulations to reprogram the stacking codes. This work provides a useful platform for constructing self-assembled DNA nanostructures and nanomachines and insights for future design of artificial molecular systems with increasing complexity and reconfigurability.
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Affiliation(s)
- Chunyang Zhou
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322, USA
- College of Life Sciences and Technology, Changchun University of Science and Technology, Changchun 130013, Jilin, China
| | - Donglei Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Sebastian Sensale
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Pranav Sharma
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Dongfang Wang
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322, USA
| | - Lei Yu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322, USA
| | - Gaurav Arya
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322, USA
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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9
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Yang D, Wang P. A DNA-Based Molecular System That Can Autonomously Add and Extract Components. ACS APPLIED MATERIALS & INTERFACES 2021; 13:41004-41011. [PMID: 34412465 DOI: 10.1021/acsami.1c14105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Many molecular systems in nature undergo autonomous addition and extraction of components in order to execute diverse functions, which rely on molecular components that can sense, process, and transmit information from the environment. Building artificial molecular systems using a similar strategy may lead to the construction of life-like synthetic materials. Herein, we report the design of a dynamic multicomponent molecular system from DNA self-assembly, which is capable of autonomously adding and extracting molecular components initiated by molecular triggers. Orthogonality was integrated into molecular components by harnessing the design capacity of DNA sequences. As a proof of concept, we built a three-component DNA tubular system, which can selectively add or extract one, two, or three components in an orthogonal and programmable manner. We further demonstrated that molecular extraction may be designed in response to environmental cues such as protons. Moreover, the tubes can be disassembled on demand to facilitate their uptake by cells. This work may prime the design of artificial multicomponent molecular systems with increasing complexity, diversity, and functionality that may guide the development of new synthetic materials beyond DNA self-assembly.
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Affiliation(s)
- Donglei Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Pengfei Wang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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10
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Lv H, Li Q, Shi J, Fan C, Wang F. Biocomputing Based on DNA Strand Displacement Reactions. Chemphyschem 2021; 22:1151-1166. [PMID: 33871136 DOI: 10.1002/cphc.202100140] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 04/10/2021] [Indexed: 11/12/2022]
Abstract
The high sequence specificity and precise base complementary pairing principle of DNA provides a rich orthogonal molecular library for molecular programming, making it one of the most promising materials for developing bio-compatible intelligence. In recent years, DNA has been extensively studied and applied in the field of biological computing. Among them, the toehold-mediated strand displacement reaction (SDR) with properties including enzyme free, flexible design and precise control, have been extensively used to construct biological computing circuits. This review provides a systemic overview of SDR design principles and the applications. Strategies for designing DNA-only, enzymes-assisted, other molecules-involved and external stimuli-controlled SDRs are described. The recently realized computing functions and the application of DNA computing in other fields are introduced. Finally, the advantages and challenges of SDR-based computing are discussed.
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Affiliation(s)
- Hui Lv
- University of Chinese Academy of Sciences, Beijing, 100049, China.,Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 201240, China
| | - Jiye Shi
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 201240, China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 201240, China
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11
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Advances in the Integration of Nucleic Acid Nanotechnology into CRISPR-Cas System. JOURNAL OF ANALYSIS AND TESTING 2021. [DOI: 10.1007/s41664-021-00180-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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12
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Athanasiadou D, Carneiro KMM. DNA nanostructures as templates for biomineralization. Nat Rev Chem 2021; 5:93-108. [PMID: 37117611 DOI: 10.1038/s41570-020-00242-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2020] [Indexed: 12/22/2022]
Abstract
Nature uses extracellular matrix scaffolds to organize biominerals into hierarchical structures over various length scales. This has inspired the design of biomimetic mineralization scaffolds, with DNA nanostructures being among the most promising. DNA nanotechnology makes use of molecular recognition to controllably give 1D, 2D and 3D nanostructures. The control we have over these structures makes them attractive templates for the synthesis of mineralized tissues, such as bones and teeth. In this Review, we first summarize recent work on the crystallization processes and structural features of biominerals on the nanoscale. We then describe self-assembled DNA nanostructures and come to the intersection of these two themes: recent applications of DNA templates in nanoscale biomineralization, a crucial process to regenerate mineralized tissues.
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13
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Liu S, Du P, Sun H, Yu HY, Wang ZG. Bioinspired Supramolecular Catalysts from Designed Self-Assembly of DNA or Peptides. ACS Catal 2020. [DOI: 10.1021/acscatal.0c03753] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Siyuan Liu
- State Key Laboratory of Organic−Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing University of Chemical Technology, Beijing 100029, China
- College of Chemistry and Materials Science, Anhui Normal University, 189 Jiuhua Nanlu, Wuhu, Anhui 241002, China
| | - Peidong Du
- State Key Laboratory of Organic−Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing University of Chemical Technology, Beijing 100029, China
| | - Hao Sun
- State Key Laboratory of Organic−Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing University of Chemical Technology, Beijing 100029, China
| | - Hai-Yin Yu
- College of Chemistry and Materials Science, Anhui Normal University, 189 Jiuhua Nanlu, Wuhu, Anhui 241002, China
| | - Zhen-Gang Wang
- State Key Laboratory of Organic−Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing University of Chemical Technology, Beijing 100029, China
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14
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Insights into the Structure and Energy of DNA Nanoassemblies. Molecules 2020; 25:molecules25235466. [PMID: 33255286 PMCID: PMC7727707 DOI: 10.3390/molecules25235466] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/14/2020] [Accepted: 11/16/2020] [Indexed: 11/16/2022] Open
Abstract
Since the pioneering work of Ned Seeman in the early 1980s, the use of the DNA molecule as a construction material experienced a rapid growth and led to the establishment of a new field of science, nowadays called structural DNA nanotechnology. Here, the self-recognition properties of DNA are employed to build micrometer-large molecular objects with nanometer-sized features, thus bridging the nano- to the microscopic world in a programmable fashion. Distinct design strategies and experimental procedures have been developed over the years, enabling the realization of extremely sophisticated structures with a level of control that approaches that of natural macromolecular assemblies. Nevertheless, our understanding of the building process, i.e., what defines the route that goes from the initial mixture of DNA strands to the final intertwined superstructure, is, in some cases, still limited. In this review, we describe the main structural and energetic features of DNA nanoconstructs, from the simple Holliday junction to more complicated DNA architectures, and present the theoretical frameworks that have been formulated until now to explain their self-assembly. Deeper insights into the underlying principles of DNA self-assembly may certainly help us to overcome current experimental challenges and foster the development of original strategies inspired to dissipative and evolutive assembly processes occurring in nature.
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15
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Wang D, Yu L, Ji B, Chang S, Song J, Ke Y. Programming the Curvatures in Reconfigurable DNA Domino Origami by Using Asymmetric Units. NANO LETTERS 2020; 20:8236-8241. [PMID: 33095024 DOI: 10.1021/acs.nanolett.0c03348] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The DNA origami technique is a robust method for the design of DNA nanostructures with prescribed shapes, including complex curved geometries. In addition to static structures, dynamic DNA origami has been used to construct sophisticated nanomachines that can reconfigure their shapes in response to external stimuli. Here, we report a new method to design DNA origami structures that can transform between a noncurved conformation and curved conformation. The reconfigurable structures are developed on the basis of dynamic DNA domino origami, which can transform in a cascading process initiated by trigger DNA strands. The degree of curvature could be programmed by tuning the sizes of DNA units within the origami.
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Affiliation(s)
- Dongfang Wang
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lei Yu
- The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China
| | - Bin Ji
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shuai Chang
- The State Key Laboratory of Refractories and Metallurgy, the Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
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16
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Bottom-Up Self-Assembly Based on DNA Nanotechnology. NANOMATERIALS 2020; 10:nano10102047. [PMID: 33081252 PMCID: PMC7603033 DOI: 10.3390/nano10102047] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 11/23/2022]
Abstract
Manipulating materials at the atomic scale is one of the goals of the development of chemistry and materials science, as it provides the possibility to customize material properties; however, it still remains a huge challenge. Using DNA self-assembly, materials can be controlled at the nano scale to achieve atomic- or nano-scaled fabrication. The programmability and addressability of DNA molecules can be applied to realize the self-assembly of materials from the bottom-up, which is called DNA nanotechnology. DNA nanotechnology does not focus on the biological functions of DNA molecules, but combines them into motifs, and then assembles these motifs to form ordered two-dimensional (2D) or three-dimensional (3D) lattices. These lattices can serve as general templates to regulate the assembly of guest materials. In this review, we introduce three typical DNA self-assembly strategies in this field and highlight the significant progress of each. We also review the application of DNA self-assembly and propose perspectives in this field.
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17
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Wang Y, Ge W, Lu B, Zhu JJ, Xiao SJ. Two-layer stacked multi-arm junction tiles and nanostructures assembled with small circular DNA molecules serving as scaffolds. NANOSCALE 2020; 12:19597-19603. [PMID: 32996986 DOI: 10.1039/d0nr05860b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
One-layer multi-arm junction (mAJ) motifs have been investigated extensively for many kinds of planar 2D (two-dimension) lattices, surface-curved 3D (three-dimension) polyhedra, and complex 3D wireframe and tensegrity structures. Herein, we report the weaving strategy to achieve two-layer stacked multi-arm junction tiles (abbreviated as mAJ2) of 3AJ2 and 4AJ2, and several primary tessellation nanostructures of nanocages and 2D rhombus lattices carrying beautifully embossed 4-point stars. Challenges for perfect tessellation are also raised regarding the increase of motif complexity from 2D to 3D.
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Affiliation(s)
- Yu Wang
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, Jiangsu, China.
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18
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Li Q, Zhao J, Liu L, Jonchhe S, Rizzuto FJ, Mandal S, He H, Wei S, Sleiman HF, Mao H, Mao C. A poly(thymine)-melamine duplex for the assembly of DNA nanomaterials. NATURE MATERIALS 2020; 19:1012-1018. [PMID: 32661383 PMCID: PMC7732259 DOI: 10.1038/s41563-020-0728-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 06/09/2020] [Indexed: 06/11/2023]
Abstract
The diversity of DNA duplex structures is limited by a binary pair of hydrogen-bonded motifs. Here we show that poly(thymine) self-associates into antiparallel, right-handed duplexes in the presence of melamine, a small molecule that presents a triplicate set of the hydrogen-bonding face of adenine. X-ray crystallography shows that in the complex two poly(thymine) strands wrap around a helical column of melamine, which hydrogen bonds to thymine residues on two of its three faces. The mechanical strength of the thymine-melamine-thymine triplet surpasses that of adenine-thymine base pairs, which enables a sensitive detection of melamine at 3 pM. The poly(thymine)-melamine duplex is orthogonal to native DNA base pairing and can undergo strand displacement without the need for overhangs. Its incorporation into two-dimensional grids and hybrid DNA-small-molecule polymers highlights the poly(thymine)-melamine duplex as an additional tool for DNA nanotechnology.
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Affiliation(s)
- Qian Li
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Jiemin Zhao
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Longfei Liu
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Sagun Jonchhe
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, USA
| | - Felix J Rizzuto
- Department of Chemistry, McGill University, Montréal, Québec, Canada
| | - Shankar Mandal
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, USA
| | - Huawei He
- Biological Science Research Center, Southwest University, Chongqing, China
| | - Sansen Wei
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, Montréal, Québec, Canada.
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, USA.
- Advanced Materials and Liquid Crystal Institute, Kent State University, Kent, OH, USA.
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, USA.
- College of Pharmaceutical Sciences, Southwest University, Chongqing, China.
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19
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Dong Y, Yao C, Zhu Y, Yang L, Luo D, Yang D. DNA Functional Materials Assembled from Branched DNA: Design, Synthesis, and Applications. Chem Rev 2020; 120:9420-9481. [DOI: 10.1021/acs.chemrev.0c00294] [Citation(s) in RCA: 168] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Yuhang Dong
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Chi Yao
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Yi Zhu
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Lu Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Dan Luo
- Department of Biological & Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
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20
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Stoev ID, Cao T, Caciagli A, Yu J, Ness C, Liu R, Ghosh R, O'Neill T, Liu D, Eiser E. On the role of flexibility in linker-mediated DNA hydrogels. SOFT MATTER 2020; 16:990-1001. [PMID: 31853526 DOI: 10.1039/c9sm01398a] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Three-dimensional DNA networks, composed of tri- or higher valent nanostars with sticky, single-stranded DNA overhangs, have been previously studied in the context of designing thermally responsive, viscoelastic hydrogels. In this work, we use linker-mediated gels, where the sticky ends of two trivalent nanostars are connected through the complementary sticky ends of a linear DNA duplex. We can design this connection to be either rigid or flexible by introducing flexible, non-binding bases. The additional flexibility provided by these non-binding bases influences the effective elasticity of the percolating gel formed at low temperatures. Here we show that by choosing the right length of the linear duplex and non-binding flexible joints, we obtain a completely different phase behaviour to that observed for rigid linkers. In particular, we use dynamic light scattering as a microrheological tool to monitor the self-assembly of DNA nanostars with linear linkers as a function of temperature. While we observe classical gelation when using rigid linkers, the presence of flexible joints leads to a cluster fluid with a much-reduced viscosity. Using both the oxDNA model and a coarse-grained simulation to investigate the nanostar-linker topology, we hypothesise on the possible structure formed by the DNA clusters. Moreover, we present a systematic study of the strong viscosity increase of aqueous solutions in the presence of these DNA building blocks.
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Affiliation(s)
- Iliya D Stoev
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, CB3 0HE, UK.
| | - Tianyang Cao
- Department of Chemistry, Tsinghua University, Beijing, 100084, P. R. China.
| | - Alessio Caciagli
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, CB3 0HE, UK.
| | - Jiaming Yu
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, CB3 0HE, UK.
| | - Christopher Ness
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
| | - Ren Liu
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, CB3 0HE, UK.
| | - Rini Ghosh
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, CB3 0HE, UK.
| | - Thomas O'Neill
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, CB3 0HE, UK.
| | - Dongsheng Liu
- Department of Chemistry, Tsinghua University, Beijing, 100084, P. R. China.
| | - Erika Eiser
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, CB3 0HE, UK.
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21
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Ghosh D, Datta LP, Govindaraju T. Molecular architectonics of DNA for functional nanoarchitectures. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2020; 11:124-140. [PMID: 31976202 PMCID: PMC6964666 DOI: 10.3762/bjnano.11.11] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 12/09/2019] [Indexed: 05/08/2023]
Abstract
DNA is the key biomolecule central to almost all processes in living organisms. The eccentric idea of utilizing DNA as a material building block in molecular and structural engineering led to the creation of numerous molecular-assembly systems and materials at the nanoscale. The molecular structure of DNA is believed to have evolved over billions of years, with structure and stability optimizations that allow life forms to sustain through the storage and transmission of genetic information with fidelity. The nanoscale structural characteristics of DNA (2 nm thickness and ca. 40-50 nm persistence length) have inspired the creation of numerous functional patterns and architectures through noncovalent conventional and unconventional base pairings as well as through mutual templating-interactions with small organic molecules and metal ions. The recent advancements in structural DNA nanotechnology allowed researchers to design new DNA-based functional materials with chemical and biological properties distinct from their parent components. The modulation of structural and functional properties of hybrid DNA ensembles of small functional molecules (SFMs) and short oligonucleotides by adapting the principles of molecular architectonics enabled the creation of novel DNA nanoarchitectures with potential applications, which has been termed as templated DNA nanotechnology or functional DNA nanoarchitectonics. This review highlights the molecular architectonics-guided design principles and applications of the derived DNA nanoarchitectures. The advantages and ability of functional DNA nanoarchitectonics to overcome the trivial drawbacks of classical DNA nanotechnology to fulfill realistic and practical applications are highlighted, and an outlook on future developments is presented.
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Affiliation(s)
- Debasis Ghosh
- Bioorganic Chemistry Laboratory, New Chemistry Unit and The School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P. O., Bengaluru 560064, Karnataka, India
| | - Lakshmi P Datta
- Bioorganic Chemistry Laboratory, New Chemistry Unit and The School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P. O., Bengaluru 560064, Karnataka, India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit and The School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P. O., Bengaluru 560064, Karnataka, India
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22
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Shen Q, Grome MW, Yang Y, Lin C. Engineering Lipid Membranes with Programmable DNA Nanostructures. ADVANCED BIOSYSTEMS 2020; 4:1900215. [PMID: 31934608 PMCID: PMC6957268 DOI: 10.1002/adbi.201900215] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Indexed: 12/18/2022]
Abstract
Lipid and DNA are abundant biomolecules with critical functions in cells. The water-insoluble, amphipathic lipid molecules are best known for their roles in energy storage (e.g. as triglyceride), signaling (e.g. as sphingolipid), and compartmentalization (e.g. by forming membrane-enclosed bodies). The soluble, highly negatively charged DNA, which stores cells' genetic information, has proven to be an excellent material for constructing programmable nanostructures in vitro thanks to its self-assembling capabilities. These two seemingly distant molecules make contact within cell nuclei, often via lipidated proteins, with proposed functions of modulating chromatin structures. Carefully formulated lipid/DNA complexes are promising reagents for gene therapy. The past few years saw an emerging research field of interfacing DNA nanostructures with lipid membranes, with an overarching goal of generating DNA/lipid hybrid materials that possess novel and controllable structure, dynamics, and function. An arsenal of DNA-based tools has been created to coat, mold, deform, and penetrate lipid bilayers, affording us the ability to manipulate membranes with nanoscopic precision. These membrane engineering methods not only enable quantitative biophysical studies, but also open new opportunities in synthetic biology (e.g. artificial cells) and therapeutics (e.g. drug delivery).
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Affiliation(s)
- Qi Shen
- Department of Cell Biology and Nanobiology Institute, Yale University
| | - Michael W Grome
- Department of Cell Biology and Nanobiology Institute, Yale University
| | - Yang Yang
- Department of Cell Biology and Nanobiology Institute, Yale University
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine
| | - Chenxiang Lin
- Department of Cell Biology and Nanobiology Institute, Yale University
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23
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Carloni LE, Bezzu CG, Bonifazi D. Patterning Porous Networks through Self-Assembly of Programmed Biomacromolecules. Chemistry 2019; 25:16179-16200. [PMID: 31491049 DOI: 10.1002/chem.201902576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/11/2019] [Indexed: 11/08/2022]
Abstract
Two-dimensional (2D) porous networks are of great interest for the fabrication of complex organized functional materials for potential applications in nanotechnologies and nanoelectronics. This review aims at providing an overview of bottom-up approaches towards the engineering of 2D porous networks by using biomacromolecules, with a particular focus on nucleic acids and proteins. The first part illustrates how the advancements in DNA nanotechnology allowed for the attainment of complex ordered porous two-dimensional DNA nanostructures, thanks to a biomimetic approach based on DNA molecules self-assembly through specific hydrogen-bond base pairing. The second part focuses the attention on how polypeptides and proteins structural properties could be used to engineer organized networks templating the formation of multifunctional materials. The structural organization of all examples is discussed as revealed by scanning probe microscopy or transmission electron microscopy imaging techniques.
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Affiliation(s)
- Laure-Elie Carloni
- Department of Chemistry and Namur Research College (NARC), University of Namur, Rue de Bruxelles 61, Namur, 5000, Belgium
| | - C Grazia Bezzu
- Cardiff University, School of Chemistry, Park Place, Main Building, CF10 3AT, Cardiff, Wales, UK
| | - Davide Bonifazi
- Cardiff University, School of Chemistry, Park Place, Main Building, CF10 3AT, Cardiff, Wales, UK
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24
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Xiao M, Lai W, Man T, Chang B, Li L, Chandrasekaran AR, Pei H. Rationally Engineered Nucleic Acid Architectures for Biosensing Applications. Chem Rev 2019; 119:11631-11717. [DOI: 10.1021/acs.chemrev.9b00121] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Tiantian Man
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Binbin Chang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
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25
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Fan J, Wang HH, Xie S, Wang M, Nie Z. Engineering Cell-Surface Receptors with DNA Nanotechnology for Cell Manipulation. Chembiochem 2019; 21:282-293. [PMID: 31364788 DOI: 10.1002/cbic.201900315] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 06/19/2019] [Indexed: 12/11/2022]
Abstract
Cell-surface receptors play pivotal roles in the regulation of cell fate. Molecular engineering of cell-surface receptors enables control of cell signaling and manipulation of cell behavior in a user-defined way. Currently, the development of chemical-biological approaches for non-genetic engineering and regulation of membrane receptors is attracting significant interest. Recent research advances in functional nucleic acids and DNA nanotechnology have made it possible to use DNA as a new and promising molecular toolkit for controlling receptor-mediated signaling and cell fates. In this minireview we summarize the advances in the use of DNA nanotechnology for the spatiotemporal regulation of cell receptors and highlight practical applications in manipulating cell functions including cell adhesion, cell-cell contact, cell migration, and cellular immunity. We also provide a perspective on the potential of and challenges facing DNA-based receptor engineering in future applications of cell manipulation and cell-based therapy.
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Affiliation(s)
- Jiahui Fan
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, China
| | - Hong-Hui Wang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, China
| | - Shiyi Xie
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, China
| | - Miao Wang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, China
| | - Zhou Nie
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, China
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26
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Huang K, Yang D, Tan Z, Chen S, Xiang Y, Mi Y, Mao C, Wei B. Self-Assembly of Wireframe DNA Nanostructures from Junction Motifs. Angew Chem Int Ed Engl 2019; 58:12123-12127. [PMID: 31190457 DOI: 10.1002/anie.201906408] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Indexed: 01/15/2023]
Abstract
Wireframe frameworks have been investigated for the construction of complex nanostructures from a scaffolded DNA origami approach; however, a similar framework is yet to be fully explored in a scaffold-free "LEGO" approach. Herein, we describe a general design scheme to construct wireframe DNA nanostructures entirely from short synthetic strands. A typical edge of the resulting structures in this study is composed of two parallel duplexes with crossovers on both ends, and three, four, or five edges radiate out from a certain vertex. By using such a self-assembly scheme, we produced planar lattices and polyhedral objects.
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Affiliation(s)
- Kai Huang
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Donglei Yang
- School of Chemical Science and Engineering, Tongji University, Shanghai, 200092, China.,Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200127, China
| | - Zhenyu Tan
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China.,Present address: Biophysics Program, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Silian Chen
- Center for Infectious Disease Research, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing Advanced Innvation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China.,School of Life Sciences, Peking University, Beijing, 100084, China
| | - Ye Xiang
- Center for Infectious Disease Research, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing Advanced Innvation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Yongli Mi
- School of Chemical Science and Engineering, Tongji University, Shanghai, 200092, China.,Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Bryan Wei
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
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27
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Huang K, Yang D, Tan Z, Chen S, Xiang Y, Mi Y, Mao C, Wei B. Self‐Assembly of Wireframe DNA Nanostructures from Junction Motifs. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906408] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kai Huang
- School of Life Sciences Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology Tsinghua University Beijing 100084 China
| | - Donglei Yang
- School of Chemical Science and Engineering Tongji University Shanghai 200092 China
- Institute of Molecular Medicine (IMM) Renji Hospital Shanghai Jiao Tong University School of Medicine Shanghai 200127 China
| | - Zhenyu Tan
- School of Life Sciences Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology Tsinghua University Beijing 100084 China
- Present address: Biophysics Program University of Michigan Ann Arbor MI 48109 USA
| | - Silian Chen
- Center for Infectious Disease Research Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases Beijing Advanced Innvation Center for Structural Biology Department of Basic Medical Sciences School of Medicine Tsinghua University Beijing 100084 China
- School of Life Sciences Peking University Beijing 100084 China
| | - Ye Xiang
- Center for Infectious Disease Research Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases Beijing Advanced Innvation Center for Structural Biology Department of Basic Medical Sciences School of Medicine Tsinghua University Beijing 100084 China
| | - Yongli Mi
- School of Chemical Science and Engineering Tongji University Shanghai 200092 China
- Department of Chemical and Biological Engineering Hong Kong University of Science and Technology Kowloon Hong Kong SAR China
| | - Chengde Mao
- Department of Chemistry Purdue University West Lafayette IN 47907 USA
| | - Bryan Wei
- School of Life Sciences Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology Tsinghua University Beijing 100084 China
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28
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A minimalist's approach for DNA nanoconstructions. Adv Drug Deliv Rev 2019; 147:22-28. [PMID: 30769045 DOI: 10.1016/j.addr.2019.02.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 01/03/2019] [Accepted: 02/08/2019] [Indexed: 12/21/2022]
Abstract
Structural DNA nanotechnology takes DNA, a biopolymer, far beyond being the molecule that stores and transmits genetic information in biological systems. DNA has been employed as building blocks for the assembly of designed, nanoscaled, supramolecular DNA architectures for applications in biophysics, structure determination, synthetic biology, diagnostics, and drug delivery. Herein, we review a symmetric approach of tile-based DNA self-assembly. This approach allows the construction of DNA nanostructures from minimal numbers of different types of DNA strands based on sequence and structural symmetries. Some examples of the applications of this approach in siRNA delivery are discussed as well.
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29
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Zeng J, Fu W, Qi Z, Zhu Q, He H, Huang C, Zuo H, Mao C. Self-Assembly of Microparticles by Supramolecular Homopolymerization of One Component DNA Molecule. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1805552. [PMID: 30734479 DOI: 10.1002/smll.201805552] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 01/18/2019] [Indexed: 06/09/2023]
Abstract
DNA is a superb molecule for self-assembly of nanostructures. Often many DNA strands are required for the assembly of one DNA nanostructure. For lowering the cost of synthesizing DNA strands and facilitating the assembly process, it is highly desirable to use a minimal number of unique strands for potential technological applications. Herein, a strategy is reported to assemble a series of DNA microparticles (DNAµPs) from one component DNA strand. As a demonstration of the application of the resulting DNAµPs, the design and assembled DNAµPs are modified to carry additional single-stranded tails on their surfaces. The modified DNAµPs can either capture other nucleic acids or display CpG motifs to stimulate immune responses.
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Affiliation(s)
- Jie Zeng
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, China
| | - Wenhao Fu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, China
| | - Zhenping Qi
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, China
| | - Qiushuang Zhu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, China
| | - Huawei He
- Biological Science Research Center, Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, 400716, China
| | - Chengzhi Huang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, China
| | - Hua Zuo
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, China
| | - Chengde Mao
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, China
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
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30
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Ali M, Afshan N, Jiang C, Xiao SJ. DNA dumbbell tiles with uneven widths for 2D arrays. Org Biomol Chem 2019; 17:1277-1283. [DOI: 10.1039/c8ob02709a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA dumbbell tiles of AO(E) and BO(E), with stem spans of 11 and 16 bp twisting two head loop motifs of each tile into parallel and antiparallel conformations respectively, were constructed to grow planar nanoribbon arrays and nanotubes as well.
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Affiliation(s)
- Mashooq Ali
- State Key Laboratory of Coordination Chemistry
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210093
- China
| | - Noshin Afshan
- Institute of Molecular Medicine
- Renji Hospital Affiliated To Shanghai Jiao Tong University
- School of Medicine
- Shanghai 200001
- China
| | - Chuan Jiang
- State Key Laboratory of Coordination Chemistry
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210093
- China
| | - Shou-Jun Xiao
- State Key Laboratory of Coordination Chemistry
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210093
- China
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31
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Wang ZG, Li N, Wang T, Ding B. Surface-Guided Chemical Processes on Self-Assembled DNA Nanostructures. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14954-14962. [PMID: 29884022 DOI: 10.1021/acs.langmuir.8b01060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Solid-liquid interfaces have been of great significance in the activation of chemical reactions via restricting the conformation or orientation of the reactants. Self-assembled DNA nanostructures encoded with tremendous chemical and physical information provide an efficient platform to unravel and regulate mechanisms of surface chemical processes. In this review, we discuss the surface addressability, morphological features, and charged properties of DNA nanostructures as well as the recognition, catalytic, and dynamic properties of DNA molecules. We highlight the synergies between the surface properties of DNA nanostructures and the molecular features of DNA strands, which is a key to the synthesis of conductive polymer nanomaterials with well-defined shapes or electronic/optical properties. We also focus on the control over the substrate channeling pathways of enzyme networks or metal nucleation on DNA nanostructures toward the production of specifically emissive metal nanoclusters. In the end, we provide an outlook of future possible directions based on the rational design of DNA-based self-assembly, including dynamic energy transfer, stimuli-responsive synthesis, and programmable activation of the mechanophores on the surfaces of DNA nanostructures.
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Affiliation(s)
- Zhen-Gang Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , P. R. China
| | - Na Li
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , P. R. China
| | - Ting Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , P. R. China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , P. R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
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32
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Taylor LLK, Riddell IA, Smulders MMJ. Selbstorganisation von funktionellen diskreten dreidimensionalen Architekturen in Wasser. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806297] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Lauren L. K. Taylor
- School of Chemistry; University of Manchester; Oxford Road M13 9PL Großbritannien
| | - Imogen A. Riddell
- School of Chemistry; University of Manchester; Oxford Road M13 9PL Großbritannien
| | - Maarten M. J. Smulders
- Laboratory of Organic Chemistry; Wageningen University, P.O. Box 8026; 6700EG Wageningen Niederlande
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33
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Taylor LLK, Riddell IA, Smulders MMJ. Self-Assembly of Functional Discrete Three-Dimensional Architectures in Water. Angew Chem Int Ed Engl 2018; 58:1280-1307. [DOI: 10.1002/anie.201806297] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Indexed: 01/01/2023]
Affiliation(s)
| | - Imogen A. Riddell
- School of Chemistry; University of Manchester; Oxford Road M13 9PL UK
| | - Maarten M. J. Smulders
- Laboratory of Organic Chemistry; Wageningen University, P.O. Box 8026; 6700EG Wageningen The Netherlands
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34
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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: 121] [Impact Index Per Article: 20.2] [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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35
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Guo X, Wang XM, Wei S, Xiao SJ. Construction of a Holliday Junction in Small Circular DNA Molecules for Stable Motifs and Two-Dimensional Lattices. Chembiochem 2018; 19:1379-1385. [PMID: 29644789 DOI: 10.1002/cbic.201800122] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Indexed: 11/10/2022]
Abstract
Design rules for DNA nanotechnology have been mostly learnt from using linear single-stranded (ss) DNA as the source material. For example, the core structure of a typical DAO (double crossover, antiparallel, odd half-turns) tile for assembling 2D lattices is constructed from only two linear ss-oligonucleotide scaffold strands, similar to two ropes making a square knot. Herein, a new type of coupled DAO (cDAO) tile and 2D lattices of small circular ss-oligonucleotides as scaffold strands and linear ss-oligonucleotides as staple strands are reported. A cDAO tile of cDAO-c64nt (c64nt: circular 64 nucleotides), shaped as a solid parallelogram, is constructed with a Holliday junction (HJ) at the center and two HJs at both poles of a c64nt; similarly, cDAO-c84nt, shaped as a crossed quadrilateral composed of two congruent triangles, is formed with a HJ at the center and four three-way junctions at the corners of a c84nt. Perfect 2D lattices were assembled from cDAO tiles: infinite nanostructures of nanoribbons, nanotubes, and nanorings, and finite nanostructures. The structural relationship between the visible lattices imaged by AFM and the corresponding invisible secondary and tertiary molecular structures of HJs, inclination angle of hydrogen bonds against the double-helix axis, and the chirality of the tile can be interpreted very well. This work could shed new light on DNA nanotechnology with unique circular tiles.
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Affiliation(s)
- Xin Guo
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, P.R. China
| | - Xue-Mei Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, P.R. China
| | - Shuai Wei
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Shou-Jun Xiao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, P.R. China.,State Key Laboratory of Bioelectronics, Southeast University, Nanjing, 210096, P.R. China
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36
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Ke Y, Castro C, Choi JH. Structural DNA Nanotechnology: Artificial Nanostructures for Biomedical Research. Annu Rev Biomed Eng 2018; 20:375-401. [PMID: 29618223 DOI: 10.1146/annurev-bioeng-062117-120904] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Structural DNA nanotechnology utilizes synthetic or biologic DNA as designer molecules for the self-assembly of artificial nanostructures. The field is founded upon the specific interactions between DNA molecules, known as Watson-Crick base pairing. After decades of active pursuit, DNA has demonstrated unprecedented versatility in constructing artificial nanostructures with significant complexity and programmability. The nanostructures could be either static, with well-controlled physicochemical properties, or dynamic, with the ability to reconfigure upon external stimuli. Researchers have devoted considerable effort to exploring the usability of DNA nanostructures in biomedical research. We review the basic design methods for fabricating both static and dynamic DNA nanostructures, along with their biomedical applications in fields such as biosensing, bioimaging, and drug delivery.
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Affiliation(s)
- Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Emory University School of Medicine, Atlanta, Georgia 30322, USA;
| | - Carlos Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio 43214, USA
| | - Jong Hyun Choi
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana 47907, USA
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37
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Xavier PL, Chandrasekaran AR. DNA-based construction at the nanoscale: emerging trends and applications. NANOTECHNOLOGY 2018; 29:062001. [PMID: 29232197 DOI: 10.1088/1361-6528/aaa120] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The field of structural DNA nanotechnology has evolved remarkably-from the creation of artificial immobile junctions to the recent DNA-protein hybrid nanoscale shapes-in a span of about 35 years. It is now possible to create complex DNA-based nanoscale shapes and large hierarchical assemblies with greater stability and predictability, thanks to the development of computational tools and advances in experimental techniques. Although it started with the original goal of DNA-assisted structure determination of difficult-to-crystallize molecules, DNA nanotechnology has found its applications in a myriad of fields. In this review, we cover some of the basic and emerging assembly principles: hybridization, base stacking/shape complementarity, and protein-mediated formation of nanoscale structures. We also review various applications of DNA nanostructures, with special emphasis on some of the biophysical applications that have been reported in recent years. In the outlook, we discuss further improvements in the assembly of such structures, and explore possible future applications involving super-resolved fluorescence, single-particle cryo-electron (cryo-EM) and x-ray free electron laser (XFEL) nanoscopic imaging techniques, and in creating new synergistic designer materials.
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Affiliation(s)
- P Lourdu Xavier
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY) and Department of Physics, University of Hamburg, D-22607 Hamburg, Germany. Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany
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38
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Avakyan N, Conway JW, Sleiman HF. Long-Range Ordering of Blunt-Ended DNA Tiles on Supported Lipid Bilayers. J Am Chem Soc 2017; 139:12027-12034. [PMID: 28783358 DOI: 10.1021/jacs.7b06572] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Nicole Avakyan
- Department of Chemistry, McGill University, 801
Sherbrooke Street West, Montreal QC H3A 0B8, Canada
| | - Justin W. Conway
- Department of Chemistry, McGill University, 801
Sherbrooke Street West, Montreal QC H3A 0B8, Canada
| | - Hanadi F. Sleiman
- Department of Chemistry, McGill University, 801
Sherbrooke Street West, Montreal QC H3A 0B8, Canada
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39
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Li M, Zuo H, Yu J, Zhao X, Mao C. One DNA strand homo-polymerizes into defined nanostructures. NANOSCALE 2017; 9:10601-10605. [PMID: 28726950 DOI: 10.1039/c7nr03640j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We report a strategy for programmed DNA self-assembly that is favorable in terms of both thermodynamics and kinetics. In a previous study, it has been demonstrated that DNA self-assembly is primarily driven by thermodynamics and the assembly kinetics is not considered. To reach such stable states at equilibria, prolonged annealing duration is needed. In addition, there are cases where the desired structures could not compete with alternative structures. For example, a single-stranded DNA with a palindromic sequence quickly folds into a one-stranded hairpin instead of forming a two-stranded DNA duplex. Given that most of the DNA tiles are multi-stranded complexes, the kinetic trap represents a challenge to DNA self-assembly. To overcome this problem, we have developed a one-stranded motif that can intramolecularly and quickly fold from a single DNA strand and can be programmed to assemble into a range of nanostructures, including a one-dimensional (1D) ladder, a 1D chain, a two-dimensional (2D) array, and a three-dimensional (3D) triangular prism. All structures have been characterized by polyacrylamide gel electrophoresis (PAGE) and atomic force microscopy (AFM) imaging.
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Affiliation(s)
- Mo Li
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
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40
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Wang P, Wu S, Tian C, Yu G, Jiang W, Wang G, Mao C. Retrosynthetic Analysis-Guided Breaking Tile Symmetry for the Assembly of Complex DNA Nanostructures. J Am Chem Soc 2016; 138:13579-13585. [PMID: 27726355 DOI: 10.1021/jacs.6b06074] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
| | | | | | | | | | - Guansong Wang
- Institute
of Respiratory Diseases, Xinqiao Hospital, Chongqing 400037, China
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41
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Aslan H, Krissanaprasit A, Besenbacher F, Gothelf KV, Dong M. Protein patterning by a DNA origami framework. NANOSCALE 2016; 8:15233-15240. [PMID: 27487933 DOI: 10.1039/c6nr03199d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A spatial arrangement of proteins provides structural and functional advantages in vast technological applications as well as fundamental research. Most protein patterning procedures employ complicated, time consuming and very costly nanofabrication techniques. As an alternative route, we developed a fully biomolecular self-assembly method using DNA Origami Frames (DOF) as a template for both small and large scale protein patterning. We employed a triangular DOF (tDOF) to arrange the Bovine Serum Albumin (BSA) protein. Our in situ protein patterning strategy provides a novel, fully organic platform using a fast and low-cost surface approach with possible utilization in fundamental science and technological applications.
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Affiliation(s)
- Hüsnü Aslan
- Center for DNA Nanotechnology (CDNA) and Interdisciplinary Nanoscience (iNANO) Center, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
| | - Abhichart Krissanaprasit
- Center for DNA Nanotechnology (CDNA) and Interdisciplinary Nanoscience (iNANO) Center, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
| | - Flemming Besenbacher
- Center for DNA Nanotechnology (CDNA) and Interdisciplinary Nanoscience (iNANO) Center, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
| | - Kurt V Gothelf
- Center for DNA Nanotechnology (CDNA) and Interdisciplinary Nanoscience (iNANO) Center, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
| | - Mingdong Dong
- Center for DNA Nanotechnology (CDNA) and Interdisciplinary Nanoscience (iNANO) Center, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
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42
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Wang W, Lin T, Zhang S, Bai T, Mi Y, Wei B. Self-assembly of fully addressable DNA nanostructures from double crossover tiles. Nucleic Acids Res 2016; 44:7989-96. [PMID: 27484479 PMCID: PMC5027514 DOI: 10.1093/nar/gkw670] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/20/2016] [Indexed: 11/23/2022] Open
Abstract
DNA origami and single-stranded tile (SST) are two proven approaches to self-assemble finite-size complex DNA nanostructures. The construction elements appeared in structures from these two methods can also be found in multi-stranded DNA tiles such as double crossover tiles. Here we report the design and observation of four types of finite-size lattices with four different double crossover tiles, respectively, which, we believe, in terms of both complexity and robustness, will be rival to DNA origami and SST structures.
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Affiliation(s)
- Wen Wang
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China Bioengineering Graduate Program, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Depatment of Chemistry, Tongji University, Shanghai 200092, China
| | - Tong Lin
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Suoyu Zhang
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Tanxi Bai
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Yongli Mi
- Bioengineering Graduate Program, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Depatment of Chemistry, Tongji University, Shanghai 200092, China Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Bryan Wei
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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43
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Wang P, Gaitanaros S, Lee S, Bathe M, Shih WM, Ke Y. Programming Self-Assembly of DNA Origami Honeycomb Two-Dimensional Lattices and Plasmonic Metamaterials. J Am Chem Soc 2016; 138:7733-40. [DOI: 10.1021/jacs.6b03966] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Pengfei Wang
- Wallance
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Stavros Gaitanaros
- Department
of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Seungwoo Lee
- SKKU
Advanced Institute of Nanotechnology & School of Chemical Engineering, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
| | - Mark Bathe
- Department
of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - William M. Shih
- Wyss
Institute for Biologically Inspired Engineering and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical
School, Harvard University, Boston, Massachusetts 02115, United States
| | - Yonggang Ke
- Wallance
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
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44
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Pfeifer W, Saccà B. From Nano to Macro through Hierarchical Self-Assembly: The DNA Paradigm. Chembiochem 2016; 17:1063-80. [DOI: 10.1002/cbic.201600034] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Wolfgang Pfeifer
- Centre for Medical Biotechnology (ZMB); University of Duisburg-Essen; Universitätstrasse 2 45117 Essen Germany
| | - Barbara Saccà
- Centre for Medical Biotechnology (ZMB); University of Duisburg-Essen; Universitätstrasse 2 45117 Essen Germany
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45
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Chandrasekaran AR, Wady H, Subramanian HKK. Nucleic Acid Nanostructures for Chemical and Biological Sensing. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:2689-2700. [PMID: 27040036 DOI: 10.1002/smll.201503854] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 01/23/2016] [Indexed: 06/05/2023]
Abstract
The nanoscale features of DNA have made it a useful molecule for bottom-up construction of nanomaterials, for example, two- and three-dimensional lattices, nanomachines, and nanodevices. One of the emerging applications of such DNA-based nanostructures is in chemical and biological sensing, where they have proven to be cost-effective, sensitive and have shown promise as point-of-care diagnostic tools. DNA is an ideal molecule for sensing not only because of its specificity but also because it is robust and can function under a broad range of biologically relevant temperatures and conditions. DNA nanostructure-based sensors provide biocompatibility and highly specific detection based on the molecular recognition properties of DNA. They can be used for the detection of single nucleotide polymorphism and to sense pH both in solution and in cells. They have also been used to detect clinically relevant tumor biomarkers. In this review, recent advances in DNA-based biosensors for pH, nucleic acids, tumor biomarkers and cancer cell detection are introduced. Some challenges that lie ahead for such biosensors to effectively compete with established technologies are also discussed.
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Affiliation(s)
| | - Heitham Wady
- Upstate Medical University, State University of New York, Syracuse, NY, 13210, USA
| | - Hari K K Subramanian
- Department of Mechanical Engineering, University of California, Riverside, CA, 92521, USA
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46
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Chandrasekaran AR, Zavala J, Halvorsen K. Programmable DNA Nanoswitches for Detection of Nucleic Acid Sequences. ACS Sens 2015. [DOI: 10.1021/acssensors.5b00178] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Arun Richard Chandrasekaran
- The RNA
Institute, University
at Albany, State University of New York, Albany, New York 12222, United States
| | - Johnny Zavala
- The RNA
Institute, University
at Albany, State University of New York, Albany, New York 12222, United States
| | - Ken Halvorsen
- The RNA
Institute, University
at Albany, State University of New York, Albany, New York 12222, United States
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47
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Kumari R, Banerjee SS, Bhowmick AK, Das P. DNA-melamine hybrid molecules: from self-assembly to nanostructures. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2015. [PMID: 26199847 PMCID: PMC4505151 DOI: 10.3762/bjnano.6.148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Single-stranded DNA-melamine hybrid molecular building blocks were synthesized using a phosphoramidation cross-coupling reaction with a zero linker approach. The self-assembly of the DNA-organic hybrid molecules was achieved by DNA hybridization. Following self-assembly, two distinct types of nanostructures in the form of linear chains and network arrays were observed. The morphology of the self-assembled nanostructures was found to depend on the number of DNA strands that were attached to a single melamine molecule.
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Affiliation(s)
- Rina Kumari
- Department of Chemistry, Indian Institute of Technology Patna, Patna 800013, India
| | - Shib Shankar Banerjee
- Department of Materials Science and Engineering, Indian Institute of Technology Patna, Patna 800013, India
| | - Anil K Bhowmick
- Rubber Technology Centre, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Prolay Das
- Department of Chemistry, Indian Institute of Technology Patna, Patna 800013, India
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48
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Miller EJ, Garcia KJ, Holahan EC, Ciccarelli RM, Bergin RA, Casino SL, Bogaczyk TL, Krout MR, Findeis PM, Stockland RA. Resolved P-metalated nucleoside phosphoramidites. Inorg Chem 2014; 53:12680-2. [PMID: 25437274 DOI: 10.1021/ic5024357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthesis of resolved P-metalated nucleoside phosphoramidites is described. These rare compounds were initially prepared with gold as the metal center; however, the gold can be removed using basic phosphines or solid-supported triphenylphosphine. Treatment of the free nucleoside phosphoramidite with a platinum source generated a unique platinated dinucleoside species with a diastereomeric ratio of >99:1.
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Affiliation(s)
- Erica J Miller
- Department of Chemistry, Bucknell University , Lewisburg, Pennsylvania 17837, United States
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