1
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Li Q, Centola M, Keppner D, Valero J, Famulok M. Reconfigurable Nanopolygons Made of DNA Catenanes. Bioconjug Chem 2023; 34:105-110. [PMID: 36595299 DOI: 10.1021/acs.bioconjchem.2c00464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The development of new types of bonds and linkages that can reversibly tune the geometry and structural features of molecules is an elusive goal in chemistry. Herein, we report the use of catenated DNA structures as nanolinkages that can reversibly switch their angle and form different kinds of polygonal nanostructures. We designed a reconfigurable catenane that can self-assemble into a triangular or hexagonal structure upon addition of programmable DNA strands that function via toehold strand-displacement. The nanomechanical and structural features of these catenated nanojoints can be applied for the construction of dynamic systems such as molecular motors with switchable functionalities.
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Affiliation(s)
- Qi Li
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Xianlie Middle Road 100, 510070 Guangzhou, China.,LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Mathias Centola
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany.,Chemical Biology Max-Planck-Fellow Group, Max-Planck Institute for Neurobiology of Behavior - Caesar, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Daniel Keppner
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Julián Valero
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Michael Famulok
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany.,Chemical Biology Max-Planck-Fellow Group, Max-Planck Institute for Neurobiology of Behavior - Caesar, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
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2
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Lee JY, Yang Q, Chang X, Wisniewski H, Olivera TR, Saji M, Kim S, Perumal D, Zhang F. Nucleic acid paranemic structures: a promising building block for functional nanomaterials in biomedical and bionanotechnological applications. J Mater Chem B 2022; 10:7460-7472. [PMID: 35912570 DOI: 10.1039/d2tb00605g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Over the past few decades, DNA has been recognized as a powerful self-assembling material capable of crafting supramolecular nanoarchitectures with quasi-angstrom precision, which promises various applications in the fields of materials science, nanoengineering, and biomedical science. Notable structural features include biocompatibility, biodegradability, high digital encodability by Watson-Crick base pairing, nanoscale dimension, and surface addressability. Bottom-up fabrication of complex DNA nanostructures relies on the design of fundamental DNA motifs, including parallel (PX) and antiparallel (AX) crossovers. However, paranemic or PX motifs have not been thoroughly explored for the construction of DNA-based nanostructures compared to AX motifs. In this review, we summarize the developments of PX-based DNA nanostructures, highlight the advantages as well as challenges of PX-based assemblies, and give an overview of the structural and chemical features that lend their utilization in a variety of applications. The works presented cover PX-based DNA nanostructures in biological systems, dynamic systems, and biomedical contexts. The possible future advances of PX structures and applications are also summarized, discussed, and postulated.
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Affiliation(s)
- Jung Yeon Lee
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.
| | - Qi Yang
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.
| | - Xu Chang
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.
| | - Henry Wisniewski
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.
| | | | - Minu Saji
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.
| | - Suchan Kim
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.
| | | | - Fei Zhang
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.
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3
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Yao S, Chang Y, Zhai Z, Sugiyama H, Endo M, Zhu W, Xu Y, Yang Y, Qian X. DNA-Based Daisy Chain Rotaxane Nanocomposite Hydrogels as Dual-Programmable Dynamic Scaffolds for Stem Cell Adhesion. ACS APPLIED MATERIALS & INTERFACES 2022; 14:20739-20748. [PMID: 35485950 DOI: 10.1021/acsami.2c03265] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Interlocked DNA nanostructures perform programmable movements in nanoscales such as sliding, contraction, and expansion. However, utilizing nanoscaled interlocked movements to regulate the functions of larger length scaled matrix and developing their applications has not yet been reported. Herein we describe the assembly of DNA-based daisy chain rotaxane nanostructure (DNA-DCR) composed of two hollow DNA nanostructures as macrocycles, two interlocked axles and two triangular prism-shaped DNA structures as stoppers, in which three mechanical states─fixed extended state (FES), sliding state (SS), and fixed contracted state (FCS)─are characterized by using toehold-mediated strand displacement reaction (SDR). The DNA-DCRs are further used as nanocomposites and introduced into hydrogel matrix to produce interlocked hydrogels, which shows modulable stiffness by elongating the interlocked axles to regulate the hydrogel swelling with hybridization chain reaction (HCR) treatment. Then the DCR-hydrogels are employed as dynamic biointerfaces for human mesenchymal stem cells (hMSCs) adhesion studies. First, hMSCs showed lower cell density on bare DCR-hydrogel treated with HCR-initiated swelling for stiffness decreasing. Second, the cell adhesion ligand (RGD) modified DNA-DCRs are constructed for hydrogel functionalization. DCR(RGD) hydrogel endows the mobility of RGDs by switching the mechanical states of DNA-DCR. HMSCs showed increased cell density on DCRSS(RGD) hydrogel than on DCRFCS(RGD) hydrogel. Therefore, our DNA-DCR nanocomposite hydrogel exhibit dual-programmable performances including swelling adjustment and offering sliding for incorporated ligands, which can be both utilized as dynamic scaffolds for regulating the stem cell adhesion. The dual-programmable cross-scale regulation from interlocked DNA nanostructures to hydrogel matrix was achieved, demonstrating a new pathway of DNA-based materials.
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Affiliation(s)
- Shengtao Yao
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai200237, China
| | - Yongyun Chang
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai200011, China
| | - Zanjing Zhai
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai200011, China
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto606-8502, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto606-8502, Japan
| | - Weiping Zhu
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai200237, China
| | - Yufang Xu
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai200237, China
| | - Yangyang Yang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai200237, China
| | - Xuhong Qian
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai200237, China
- State Key Laboratory of Bioreactor, East China University of Science and Technology, Shanghai200237, China
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4
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Guo F, Li K, Wu J, Wang Y, Zhang L. Sliding dynamics of ring chain on a knotted polymer in rotaxane. POLYMER 2021. [DOI: 10.1016/j.polymer.2021.124226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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5
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Yu Z, Centola M, Valero J, Matthies M, Šulc P, Famulok M. A Self-Regulating DNA Rotaxane Linear Actuator Driven by Chemical Energy. J Am Chem Soc 2021; 143:13292-13298. [PMID: 34398597 DOI: 10.1021/jacs.1c06226] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Nature-inspired molecular machines can exert mechanical forces by controlling and varying the distance between two molecular subunits in response to different inputs. Here, we present an automated molecular linear actuator composed of T7 RNA polymerase (T7RNAP) and a DNA [2]rotaxane. A T7 promoter region and terminator sequences are introduced into the rotaxane axle to achieve automated and iterative binding and detachment of T7RNAP in a self-controlled fashion. Transcription by T7RNAP is exploited to control the release of the macrocycle from a single-stranded (ss) region in the T7 promoter to switch back and forth from a static state (hybridized macrocycle) to a dynamic state (movable macrocycle). During transcription, the T7RNAP keeps restricting the movement range on the axle available for the interlocked macrocycle and prevents its return to the promotor region. Since this range is continuously depleted as T7RNAP moves along, a directional and active movement of the macrocycle occurs. When it reaches the transcription terminator, the polymerase detaches, and the system can reset as the macrocycle moves back to hybridize again to the ss-promoter docking site. The hybridization is required for the initiation of a new transcription cycle. The rotaxane actuator runs autonomously and repeats these self-controlled cycles of transcription and movement as long as NTP-fuel is available.
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Affiliation(s)
- Ze Yu
- LIMES Chemical Biology Unit, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | - Mathias Centola
- LIMES Chemical Biology Unit, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.,Center of Advanced European Studies and Research, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Julián Valero
- LIMES Chemical Biology Unit, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.,Interdisciplinary Nanoscience Center - INANO-MBG, iNANO-huset, Gustav Wieds Vej 14, building 1592, 328, 8000 Århus C, Denmark
| | - Michael Matthies
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Michael Famulok
- LIMES Chemical Biology Unit, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.,Center of Advanced European Studies and Research, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
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6
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Vázquez-González M, Willner I. Aptamer-Functionalized Hybrid Nanostructures for Sensing, Drug Delivery, Catalysis and Mechanical Applications. Int J Mol Sci 2021; 22:1803. [PMID: 33670386 PMCID: PMC7918352 DOI: 10.3390/ijms22041803] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 01/05/2023] Open
Abstract
Sequence-specific nucleic acids exhibiting selective recognition properties towards low-molecular-weight substrates and macromolecules (aptamers) find growing interest as functional biopolymers for analysis, medical applications such as imaging, drug delivery and even therapeutic agents, nanotechnology, material science and more. The present perspective article introduces a glossary of examples for diverse applications of aptamers mainly originated from our laboratory. These include the introduction of aptamer-functionalized nanomaterials such as graphene oxide, Ag nanoclusters and semiconductor quantum dots as functional hybrid nanomaterials for optical sensing of target analytes. The use of aptamer-functionalized DNA tetrahedra nanostructures for multiplex analysis and aptamer-loaded metal-organic framework nanoparticles acting as sense-and-treat are introduced. Aptamer-functionalized nano and microcarriers are presented as stimuli-responsive hybrid drug carriers for controlled and targeted drug release, including aptamer-functionalized SiO2 nanoparticles, carbon dots, metal-organic frameworks and microcapsules. A further application of aptamers involves the conjugation of aptamers to catalytic units as a means to mimic enzyme functions "nucleoapzymes". In addition, the formation and dissociation of aptamer-ligand complexes are applied to develop mechanical molecular devices and to switch nanostructures such as origami scaffolds. Finally, the article discusses future challenges in applying aptamers in material science, nanotechnology and catalysis.
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Affiliation(s)
- Margarita Vázquez-González
- Center for Nanoscience and Nanotechnology, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- Center for Nanoscience and Nanotechnology, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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7
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Wu JT, Liu R, Chen YR, Zheng XQ, Wu ZS. The hierarchical assembly of a multi-level DNA ring-based nanostructure in a precise order and its application for screening tumor cells. Biomater Sci 2021; 9:2262-2270. [PMID: 33533777 DOI: 10.1039/d0bm00085j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA nanotechnology can be used to precisely construct nanostructures of different shapes, sizes and surface chemistry, which is appreciated in a variety of areas such as biomaterials, nanodevices, disease diagnosis, imaging, and drug delivery. Enzymatic degradation resistance and cell-targeting capability are indispensable for the applications of DNA nanostructures in biological and biomedical fields, and is challenging to rationally design the desirable nanoscale DNA materials suitable for the clinical translation by the existing assembly methodologies. Herein, we present a simple and efficient method for the hierarchical assembly of a three-level DNA ring-based nanostructure (DNA h-Nanoring) in a precise order, where DNA compositions at the primary level, the second level and the third level are a single DNA ring, two-ring-hybridized duplex and uniform complex macro-cycle, respectively. Most as-assembled DNA h-Nanorings exhibit the regular two-dimensional cycle-shaped structure characterized by atomic force microscopy (AFM). The Nanoring exhibits a significantly enhanced resistance to enzymatic attack, such that it can remain intact in 10% fetal bovine serum (FBS) for 24 h, and even stably exist in the presence of nuclease at a high concentration. More importantly, it is very easy to modify the DNA h-Nanoring with functional moieties (e.g., targeting ligand aptamer) because there are many single-stranded fragments available for further hybridization. By combining with receptor-targeted Sgc8, the nanoring can be used to accomplish the cell imaging and criminate target CEM cells from control cells, demonstrating a potential platform for in vivo tumor imaging and targeted chemotherapeutics delivery.
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Affiliation(s)
- Jing-Ting Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China.
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8
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Xue C, Zhang S, Yu X, Hu S, Lu Y, Wu Z. Periodically Ordered, Nuclease‐Resistant DNA Nanowires Decorated with Cell‐Specific Aptamers as Selective Theranostic Agents. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004805] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Chang Xue
- Cancer Metastasis Alert and Prevention Center Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy National and Local Joint Biomedical Engineering Research Center on Photodynamic Technologies Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350002 China
| | - Songbai Zhang
- Cancer Metastasis Alert and Prevention Center Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy National and Local Joint Biomedical Engineering Research Center on Photodynamic Technologies Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350002 China
- College of Chemistry and Materials Engineering Hunan University of Arts and Science Changde 415000 China
| | - Xin Yu
- Cancer Metastasis Alert and Prevention Center Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy National and Local Joint Biomedical Engineering Research Center on Photodynamic Technologies Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350002 China
| | - Shuyao Hu
- Cancer Metastasis Alert and Prevention Center Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy National and Local Joint Biomedical Engineering Research Center on Photodynamic Technologies Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350002 China
| | - Yi Lu
- Department of Chemistry Cancer Center at Illinois University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Zai‐Sheng Wu
- Cancer Metastasis Alert and Prevention Center Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy National and Local Joint Biomedical Engineering Research Center on Photodynamic Technologies Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment College of Chemistry Fuzhou University Fuzhou 350002 China
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9
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Xue C, Zhang S, Yu X, Hu S, Lu Y, Wu ZS. Periodically Ordered, Nuclease-Resistant DNA Nanowires Decorated with Cell-Specific Aptamers as Selective Theranostic Agents. Angew Chem Int Ed Engl 2020; 59:17540-17547. [PMID: 32613705 DOI: 10.1002/anie.202004805] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Indexed: 12/21/2022]
Abstract
DNA nanostructures have shown potential in cancer therapy. However, their clinical application is hampered by the difficulty to deliver them into cancer cells and susceptibility to nuclease degradation. To overcome these limitations, we report herein a periodically ordered nick-hidden DNA nanowire (NW) with high serum stability and active targeting functionality. The inner core is made of multiple connected DNA double helices, and the outer shell is composed of regularly arranged standing-up hairpin aptamers. All termini of the components are hidden from nuclease attack, whereas the target-binding sites are exposed to allow delivery to the cancer target. The DNA NW remained intact during incubation for 24 h in serum solution. Animal imaging and cell apoptosis showed that NWs loaded with an anticancer drug displayed long blood-circulation time and high specificity in inducing cancer-cell apoptosis, thus validating this approach for the targeted imaging and therapy of cancers.
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Affiliation(s)
- Chang Xue
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National and Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Songbai Zhang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National and Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China.,College of Chemistry and Materials Engineering, Hunan University of Arts and Science, Changde, 415000, China
| | - Xin Yu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National and Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Shuyao Hu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National and Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Yi Lu
- Department of Chemistry, Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National and Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, Pharmaceutical Photocatalysis of State Key Laboratory of, Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
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10
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Liang X, Li L, Tang J, Komiyama M, Ariga K. Dynamism of Supramolecular DNA/RNA Nanoarchitectonics: From Interlocked Structures to Molecular Machines. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20200012] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Lin Li
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Jiaxuan Tang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Katsuhiko Ariga
- WPI-MANA, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
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11
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Abstract
Nucleic acids hold great promise for bottom-up construction of nanostructures via programmable self-assembly. Especially, the emerging of advanced sequence design principles and the maturation of chemical synthesis of nucleic acids together have led to the rapid development of structural DNA/RNA nanotechnology. Diverse nucleic acids-based nano objects and patterns have been constructed with near-atomic resolutions and with controllable sizes and geometries. The monodispersed distribution of objects, the up-to-submillimeter scalability of patterns, and the excellent feasibility of carrying other materials with spatial and temporal resolutions have made DNA/RNA assemblies extremely unique in molecular engineering. In this review, we summarize recent advances in nucleic acids-based (mainly DNA-based) near-atomic fabrication by focusing on state-of-the-art design techniques, toolkits for DNA/RNA nanoengineering, and related applications in a range of areas.
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Affiliation(s)
- Kai Xia
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences , Fudan University , Shanghai 200032 , China
| | - Jianlei Shen
- School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Qian Li
- School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Hongzhou Gu
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences , Fudan University , Shanghai 200032 , China
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12
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Peil A, Zhan P, Liu N. DNA Origami Catenanes Templated by Gold Nanoparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1905987. [PMID: 31917513 DOI: 10.1002/smll.201905987] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/13/2019] [Indexed: 06/10/2023]
Abstract
Mechanically interlocked molecules have marked a breakthrough in the field of topological chemistry and boosted the vigorous development of molecular machinery. As an archetypal example of the interlocked molecules, catenanes comprise macrocycles that are threaded through one another like links in a chain. Inspired by the transition metal-templated approach of catenanes synthesis, the hierarchical assembly of DNA origami catenanes templated by gold nanoparticles is demonstrated in this work. DNA origami catenanes, which contain two, three or four interlocked rings are successfully created. In particular, the origami rings within the individual catenanes can be set free with respect to one another by releasing the interconnecting gold nanoparticles. This work will set the basis for rich progress toward DNA-based molecular architectures with unique structural programmability and well-defined topology.
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Affiliation(s)
- Andreas Peil
- Max-Planck-Institute for Intelligent Systems, Heisenbergstr. 3, 70569, Stuttgart, Germany
- Kirchhoff-Institute for Physics, Im Neuenheimer Feld 227, 69120, Heidelberg, Germany
| | - Pengfei Zhan
- Max-Planck-Institute for Intelligent Systems, Heisenbergstr. 3, 70569, Stuttgart, Germany
| | - Na Liu
- Max-Planck-Institute for Intelligent Systems, Heisenbergstr. 3, 70569, Stuttgart, Germany
- Kirchhoff-Institute for Physics, Im Neuenheimer Feld 227, 69120, Heidelberg, Germany
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13
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Design, assembly, characterization, and operation of double-stranded interlocked DNA nanostructures. Nat Protoc 2019; 14:2818-2855. [DOI: 10.1038/s41596-019-0198-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/16/2019] [Indexed: 01/03/2023]
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14
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Shen W, Liu Q, Ding B, Shen Z, Zhu C, Mao C. The study of the paranemic crossover (PX) motif in the context of self-assembly of DNA 2D crystals. Org Biomol Chem 2018; 14:7187-90. [PMID: 27404049 DOI: 10.1039/c6ob01146b] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
This manuscript systematically studies the self-assembly behavior of the paranemic crossover (PX) motif in the context of DNA 2D crystallization. The PX structure is a class of DNA nanomotifs that has been suggested as a model for DNA homologous recognition in cells and, more importantly, used as a cohesion mechanism/building block (tile) for DNA nanoconstruction. However, there is no vigorous examination on the relationship between structural variation and assembly behavior. The lack of this essential information prevents us from applying the PX motif to complex nanoconstruction. In this study, we have devised a system that allows us to systematically examine this relationship and found the best PX motif that best suits the assembly of 2D crystals.
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Affiliation(s)
- Weili Shen
- College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, China.
| | - Qing Liu
- National Center for NanoScience and Technology, ZhongGuanCun, Beijing 100190, China
| | - Baoquan Ding
- National Center for NanoScience and Technology, ZhongGuanCun, Beijing 100190, China
| | - Zhiyong Shen
- College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, China.
| | - Changqing Zhu
- College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, China.
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
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15
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Haydell MW, Centola M, Adam V, Valero J, Famulok M. Temporal and Reversible Control of a DNAzyme by Orthogonal Photoswitching. J Am Chem Soc 2018; 140:16868-16872. [DOI: 10.1021/jacs.8b08738] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Michael W. Haydell
- LIMES Chemical
Biology Unit, Universität Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Mathias Centola
- LIMES Chemical
Biology Unit, Universität Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Volker Adam
- LIMES Chemical
Biology Unit, Universität Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Julián Valero
- LIMES Chemical
Biology Unit, Universität Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
- Center of Advanced European Studies and Research, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Michael Famulok
- LIMES Chemical
Biology Unit, Universität Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
- Center of Advanced European Studies and Research, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
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16
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Wang X, Chandrasekaran AR, Shen Z, Ohayon YP, Wang T, Kizer ME, Sha R, Mao C, Yan H, Zhang X, Liao S, Ding B, Chakraborty B, Jonoska N, Niu D, Gu H, Chao J, Gao X, Li Y, Ciengshin T, Seeman NC. Paranemic Crossover DNA: There and Back Again. Chem Rev 2018; 119:6273-6289. [PMID: 29911864 DOI: 10.1021/acs.chemrev.8b00207] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Over the past 35 years, DNA has been used to produce various nanometer-scale constructs, nanomechanical devices, and walkers. Construction of complex DNA nanostructures relies on the creation of rigid DNA motifs. Paranemic crossover (PX) DNA is one such motif that has played many roles in DNA nanotechnology. Specifically, PX cohesion has been used to connect topologically closed molecules, to assemble a three-dimensional object, and to create two-dimensional DNA crystals. Additionally, a sequence-dependent nanodevice based on conformational change between PX and its topoisomer, JX2, has been used in robust nanoscale assembly lines, as a key component in a DNA transducer, and to dictate polymer assembly. Furthermore, the PX motif has recently found a new role directly in basic biology, by possibly serving as the molecular structure for double-stranded DNA homology recognition, a prominent feature of molecular biology and essential for many crucial biological processes. This review discusses the many attributes and usages of PX-DNA-its design, characteristics, applications, and potential biological relevance-and aims to accelerate the understanding of PX-DNA motif in its many roles and manifestations.
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Affiliation(s)
- Xing Wang
- Department of Chemistry and Chemical Biology and The Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | | | - Zhiyong Shen
- College of Chemistry and Materials Science , Anhui Normal University , Wuhu , Anhui 241000 , China
| | - Yoel P Ohayon
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Tong Wang
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Megan E Kizer
- Department of Chemistry and Chemical Biology and The Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Ruojie Sha
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Chengde Mao
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Hao Yan
- Department of Chemistry and Biochemistry and The Biodesign Institute , Arizona State University , Tempe , Arizona 85287 , United States
| | - Xiaoping Zhang
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Shiping Liao
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Baoquan Ding
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Banani Chakraborty
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Natasha Jonoska
- Department of Mathematics and Statistics , University of South Florida , Tampa , Florida 33620 , United States
| | - Dong Niu
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Hongzhou Gu
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Jie Chao
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Xiang Gao
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Yuhang Li
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Tanashaya Ciengshin
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Nadrian C Seeman
- Department of Chemistry , New York University , New York , New York 10012 , United States
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17
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Valero J, Pal N, Dhakal S, Walter NG, Famulok M. A bio-hybrid DNA rotor-stator nanoengine that moves along predefined tracks. NATURE NANOTECHNOLOGY 2018; 13:496-503. [PMID: 29632399 PMCID: PMC5994166 DOI: 10.1038/s41565-018-0109-z] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 03/01/2018] [Indexed: 05/25/2023]
Abstract
Biological motors are highly complex protein assemblies that generate linear or rotary motion, powered by chemical energy. Synthetic motors based on DNA nanostructures, bio-hybrid designs or synthetic organic chemistry have been assembled. However, unidirectionally rotating biomimetic wheel motors with rotor-stator units that consume chemical energy are elusive. Here, we report a bio-hybrid nanoengine consisting of a catalytic stator that unidirectionally rotates an interlocked DNA wheel, powered by NTP hydrolysis. The engine consists of an engineered T7 RNA polymerase (T7RNAP-ZIF) attached to a dsDNA nanoring that is catenated to a rigid rotating dsDNA wheel. The wheel motor produces long, repetitive RNA transcripts that remain attached to the engine and are used to guide its movement along predefined ssDNA tracks arranged on a DNA nanotube. The simplicity of the design renders this walking nanoengine adaptable to other biological nanoarchitectures, facilitating the construction of complex bio-hybrid structures that achieve NTP-driven locomotion.
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Affiliation(s)
- Julián Valero
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, University of Bonn, Bonn, Germany
- Center of Advanced European Studies and Research (CAESAR), Bonn, Germany
| | - Nibedita Pal
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Soma Dhakal
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Michael Famulok
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, University of Bonn, Bonn, Germany.
- Center of Advanced European Studies and Research (CAESAR), Bonn, Germany.
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18
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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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19
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Centola M, Valero J, Famulok M. Allosteric Control of Oxidative Catalysis by a DNA Rotaxane Nanostructure. J Am Chem Soc 2017; 139:16044-16047. [DOI: 10.1021/jacs.7b08839] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Mathias Centola
- LIMES
Chemical Biology Unit, Universität Bonn, Gerhard-Domagk-Straße
1, 53121 Bonn, Germany
| | - Julián Valero
- LIMES
Chemical Biology Unit, Universität Bonn, Gerhard-Domagk-Straße
1, 53121 Bonn, Germany
- Center of Advanced European Studies and Research, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Michael Famulok
- LIMES
Chemical Biology Unit, Universität Bonn, Gerhard-Domagk-Straße
1, 53121 Bonn, Germany
- Center of Advanced European Studies and Research, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
- Center
of Aptamer Research and Development, University of Bonn, Gerhard-Domagk-Straße
1, 53121 Bonn, Germany
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20
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Valero J, Lohmann F, Famulok M. Interlocked DNA topologies for nanotechnology. Curr Opin Biotechnol 2017; 48:159-167. [PMID: 28505598 DOI: 10.1016/j.copbio.2017.04.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 04/07/2017] [Accepted: 04/17/2017] [Indexed: 11/19/2022]
Abstract
Interlocked molecular architectures are well known in supramolecular chemistry and are widely used for various applications like sensors, molecular machines and logic gates. The use of DNA for constructing these interlocked structures has increased significantly within the current decade. Because of Watson-Crick base pairing rules, DNA is an excellent material for the self-assembly of well-defined interlocked nanoarchitectures. These DNA nanostructures exhibit sufficient stability, good solubility in aqueous media, biocompatibility, and can be easily combined with other biomolecules in bio-hybrid nano-assemblies. Therefore, the study of novel DNA-based interlocked systems is of interest for nanotechnology, synthetic biology, supramolecular chemistry, biotechnology, and for sensing purposes. Here we summarize recent developments and applications of interlocked supramolecular architectures made of DNA. Examples illustrating that these systems can be precisely controlled by switching on and off the molecular motion of its mechanically trapped components are discussed. Introducing different triggers into such systems creates molecular assemblies capable of performing logic gate operations and/or catalytic activity control. Interlocked DNA-based nanostructures thus represent promising frameworks for building increasingly complex and dynamic nanomachines with highly controllable functionality.
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Affiliation(s)
- Julián Valero
- Life and Medical Sciences (LIMES) Institute, Chemical Biology and Medicinal Chemistry Unit, c/o Kekulé Institut für Organische Chemie und Biochemie, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany; Center of Advanced European Studies and Research (CASEAR), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Finn Lohmann
- Life and Medical Sciences (LIMES) Institute, Chemical Biology and Medicinal Chemistry Unit, c/o Kekulé Institut für Organische Chemie und Biochemie, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | - Michael Famulok
- Life and Medical Sciences (LIMES) Institute, Chemical Biology and Medicinal Chemistry Unit, c/o Kekulé Institut für Organische Chemie und Biochemie, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany; Center of Advanced European Studies and Research (CASEAR), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany.
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21
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22
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Powell JT, Akhuetie-Oni BO, Zhang Z, Lin C. DNA Origami Rotaxanes: Tailored Synthesis and Controlled Structure Switching. Angew Chem Int Ed Engl 2016; 55:11412-6. [PMID: 27527591 PMCID: PMC5019031 DOI: 10.1002/anie.201604621] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 07/08/2016] [Indexed: 11/09/2022]
Abstract
Mechanically interlocked supramolecular assemblies are appealing building blocks for creating functional nanodevices. Herein, we describe the multistep assembly of large DNA origami rotaxanes that are capable of programmable structural switching. We validated the topology and structural integrity of these rotaxanes by analyzing the intermediate and final products of various assembly routes by electrophoresis and electron microscopy. We further analyzed two structure-switching behaviors of our rotaxanes, which are both mediated by DNA hybridization. In the first mechanism, the translational motion of the macrocycle can be triggered or halted at either terminus. In the second mechanism, the macrocycle can be elongated after completion of the rotaxane assembly, giving rise to a unique structure that is otherwise difficult to access.
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Affiliation(s)
- John T Powell
- Department of Cell Biology & Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, CT, 06516, USA
| | - Benjamin O Akhuetie-Oni
- Department of Molecular, Cellular, and Developmental Biology & Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, CT, 06516, USA
| | - Zhao Zhang
- Department of Cell Biology & Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, CT, 06516, USA
| | - Chenxiang Lin
- Department of Cell Biology & Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, CT, 06516, USA.
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23
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Powell JT, Akhuetie-Oni BO, Zhang Z, Lin C. DNA Origami Rotaxanes: Tailored Synthesis and Controlled Structure Switching. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201604621] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- John T. Powell
- Department of Cell Biology & Nanobiology Institute; Yale University; 850 West Campus Drive West Haven CT 06516 USA
| | - Benjamin O. Akhuetie-Oni
- Department of Molecular, Cellular, and Developmental Biology & Nanobiology Institute; Yale University; 850 West Campus Drive West Haven CT 06516 USA
| | - Zhao Zhang
- Department of Cell Biology & Nanobiology Institute; Yale University; 850 West Campus Drive West Haven CT 06516 USA
| | - Chenxiang Lin
- Department of Cell Biology & Nanobiology Institute; Yale University; 850 West Campus Drive West Haven CT 06516 USA
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24
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Long-range movement of large mechanically interlocked DNA nanostructures. Nat Commun 2016; 7:12414. [PMID: 27492061 PMCID: PMC4980458 DOI: 10.1038/ncomms12414] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 06/30/2016] [Indexed: 02/07/2023] Open
Abstract
Interlocked molecules such as catenanes and rotaxanes, connected only via mechanical bonds have the ability to perform large-scale sliding and rotational movements, making them attractive components for the construction of artificial molecular machines and motors. We here demonstrate the realization of large, rigid rotaxane structures composed of DNA origami subunits. The structures can be easily modified to carry a molecular cargo or nanoparticles. By using multiple axle modules, rotaxane constructs are realized with axle lengths of up to 355 nm and a fuel/anti-fuel mechanism is employed to switch the rotaxanes between a mobile and a fixed state. We also create extended pseudo-rotaxanes, in which origami rings can slide along supramolecular DNA filaments over several hundreds of nanometres. The rings can be actively moved and tracked using atomic force microscopy. Rotaxanes are interlocked molecules that can undergo sliding and rotational movements and can be used in artificial molecular machines and motors. Here, Simmel and co-workers show a rigid rotaxane structures consisting of DNA origami subunits that can slide over several hundreds of nanometres.
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25
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Lu CH, Cecconello A, Willner I. Recent Advances in the Synthesis and Functions of Reconfigurable Interlocked DNA Nanostructures. J Am Chem Soc 2016; 138:5172-85. [DOI: 10.1021/jacs.6b00694] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Chun-Hua Lu
- The Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Alessandro Cecconello
- The Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- The Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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26
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Zhang C, Shen L, Liang C, Dong Y, Yang J, Xu J. DNA Sequential Logic Gate Using Two-Ring DNA. ACS APPLIED MATERIALS & INTERFACES 2016; 8:9370-9376. [PMID: 26990044 DOI: 10.1021/acsami.6b00847] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Sequential DNA detection is a fundamental issue for elucidating the interactive relationships among complex gene systems. Here, a sequential logic DNA gate was achieved by utilizing the two-ring DNA structure, with the ability to recognize "before" and "after" triggering sequences of DNA signals. By taking advantage of a "loop-open" mechanism, separations of two-ring DNAs were controlled. Three triggering pathways with different sequential DNA treatments were distinguished by comparing fluorescent outputs. Programmed nanoparticle arrangement guided by "interlocked" two-ring DNA was also constructed to demonstrate the achievement of designed nanostrucutres. Such sequential logic DNA operation may guide future molecular sensors to monitor more complex gene network in biological systems.
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Affiliation(s)
- Cheng Zhang
- Institute of Software, School of Electronics Engineering and Computer Science, Key Laboratory of High Confidence Software Technologies, Ministry of Education, Peking University , Beijing 100871, China
| | - Linjing Shen
- College of Life Science, Shannxi Normal University , Xi'an 710062, China
| | - Chao Liang
- School of Control and Computer Engineering, North China Electric Power University , Beijing 102206, China
| | - Yafei Dong
- College of Life Science, Shannxi Normal University , Xi'an 710062, China
| | - Jing Yang
- School of Control and Computer Engineering, North China Electric Power University , Beijing 102206, China
| | - Jin Xu
- Institute of Software, School of Electronics Engineering and Computer Science, Key Laboratory of High Confidence Software Technologies, Ministry of Education, Peking University , Beijing 100871, China
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27
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Valero J, Lohmann F, Keppner D, Famulok M. Single-Stranded Tile Stoppers for Interlocked DNA Architectures. Chembiochem 2016; 17:1146-9. [DOI: 10.1002/cbic.201500685] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Julián Valero
- Life and Medical Science (LIMES) Institute; Chemical Biology & Medicinal Chemistry Unit; University of Bonn; Gerhard-Domagk Strasse 1 53121 Bonn Germany
| | - Finn Lohmann
- Life and Medical Science (LIMES) Institute; Chemical Biology & Medicinal Chemistry Unit; University of Bonn; Gerhard-Domagk Strasse 1 53121 Bonn Germany
| | - Daniel Keppner
- Life and Medical Science (LIMES) Institute; Chemical Biology & Medicinal Chemistry Unit; University of Bonn; Gerhard-Domagk Strasse 1 53121 Bonn Germany
| | - Michael Famulok
- Life and Medical Science (LIMES) Institute; Chemical Biology & Medicinal Chemistry Unit; University of Bonn; Gerhard-Domagk Strasse 1 53121 Bonn Germany
- Center of Advanced European Studies and Research (CAESAR); Ludwig-Erhard-Allee 2 53175 Bonn Germany
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28
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Weigandt J, Chung CL, Jester SS, Famulok M. Daisy Chain Rotaxanes Made from Interlocked DNA Nanostructures. Angew Chem Int Ed Engl 2016; 55:5512-6. [PMID: 27010370 PMCID: PMC4850751 DOI: 10.1002/anie.201601042] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 03/03/2016] [Indexed: 11/08/2022]
Abstract
We report the stepwise assembly of supramolecular daisy chain rotaxanes (DCR) made of double-stranded DNA: Small dsDNA macrocycles bearing an axle assemble into a pseudo-DCR precursor that was connected to rigid DNA stoppers to form DCR with the macrocycles hybridized to the axles. In presence of release oligodeoxynucleotides (rODNs), the macrocycles are released from their respective hybridization sites on the axles, leading to stable mechanically interlocked DCRs. Besides the expected threaded DCRs, certain amounts of externally hybridized structures were observed, which dissociate into dumbbell structures in presence of rODNs. We show that the genuine DCRs have significantly higher degrees of freedom in their movement along the thread axle than the hybridized DCR precursors. Interlocking of DNA in DCRs might serve as a versatile principle for constructing functional DNA nanostructures where the movement of the subunits is restricted within precisely confined tolerance ranges.
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Affiliation(s)
- Johannes Weigandt
- LIMES Chemical Biology Unit, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Chia-Ling Chung
- LIMES Chemical Biology Unit, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Stefan-S Jester
- Kekulé-Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Michael Famulok
- LIMES Chemical Biology Unit, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany. .,Center of Advanced European Studies and Research, Ludwig-Erhard-Allee 2, 53175, Bonn, Germany.
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29
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Weigandt J, Chung C, Jester S, Famulok M. Daisy Chain Rotaxanes Made from Interlocked DNA Nanostructures. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Johannes Weigandt
- LIMES Chemical Biology Unit Universität Bonn Gerhard-Domagk-Strasse 1 53121 Bonn Germany
| | - Chia‐Ling Chung
- LIMES Chemical Biology Unit Universität Bonn Gerhard-Domagk-Strasse 1 53121 Bonn Germany
| | - Stefan‐S. Jester
- Kekulé-Institut für Organische Chemie und Biochemie Universität Bonn Gerhard-Domagk-Strasse 1 53121 Bonn Germany
| | - Michael Famulok
- LIMES Chemical Biology Unit Universität Bonn Gerhard-Domagk-Strasse 1 53121 Bonn Germany
- Center of Advanced European Studies and Research Ludwig-Erhard-Allee 2 53175 Bonn Germany
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30
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Affiliation(s)
- Sundus Erbas-Cakmak
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - David A. Leigh
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Charlie T. McTernan
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Alina
L. Nussbaumer
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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31
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Abstract
The base sequence in nucleic acids encodes substantial structural and functional information into the biopolymer. This encoded information provides the basis for the tailoring and assembly of DNA machines. A DNA machine is defined as a molecular device that exhibits the following fundamental features. (1) It performs a fuel-driven mechanical process that mimics macroscopic machines. (2) The mechanical process requires an energy input, "fuel." (3) The mechanical operation is accompanied by an energy consumption process that leads to "waste products." (4) The cyclic operation of the DNA devices, involves the use of "fuel" and "anti-fuel" ingredients. A variety of DNA-based machines are described, including the construction of "tweezers," "walkers," "robots," "cranes," "transporters," "springs," "gears," and interlocked cyclic DNA structures acting as reconfigurable catenanes, rotaxanes, and rotors. Different "fuels", such as nucleic acid strands, pH (H⁺/OH⁻), metal ions, and light, are used to trigger the mechanical functions of the DNA devices. The operation of the devices in solution and on surfaces is described, and a variety of optical, electrical, and photoelectrochemical methods to follow the operations of the DNA machines are presented. We further address the possible applications of DNA machines and the future perspectives of molecular DNA devices. These include the application of DNA machines as functional structures for the construction of logic gates and computing, for the programmed organization of metallic nanoparticle structures and the control of plasmonic properties, and for controlling chemical transformations by DNA machines. We further discuss the future applications of DNA machines for intracellular sensing, controlling intracellular metabolic pathways, and the use of the functional nanostructures for drug delivery and medical applications.
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32
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Li T, Lohmann F, Famulok M. Interlocked DNA nanostructures controlled by a reversible logic circuit. Nat Commun 2014; 5:4940. [PMID: 25229207 PMCID: PMC4199106 DOI: 10.1038/ncomms5940] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 08/07/2014] [Indexed: 12/04/2022] Open
Abstract
DNA nanostructures constitute attractive devices for logic computing and nanomechanics. An emerging interest is to integrate these two fields and devise intelligent DNA nanorobots. Here we report a reversible logic circuit built on the programmable assembly of a double-stranded (ds) DNA [3]pseudocatenane that serves as a rigid scaffold to position two separate branched-out head-motifs, a bimolecular i-motif and a G-quadruplex. The G-quadruplex only forms when preceded by the assembly of the i-motif. The formation of the latter, in turn, requires acidic pH and unhindered mobility of the head-motif containing dsDNA nanorings with respect to the central ring to which they are interlocked, triggered by release oligodeoxynucleotides. We employ these features to convert the structural changes into Boolean operations with fluorescence labelling. The nanostructure behaves as a reversible logic circuit consisting of tandem YES and AND gates. Such reversible logic circuits integrated into functional nanodevices may guide future intelligent DNA nanorobots to manipulate cascade reactions in biological systems.
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Affiliation(s)
- Tao Li
- Chemical Biology and Medicinal Chemistry Unit, Life and Medical Science (LIMES) Institute, University of Bonn, 53121 Bonn, Germany
| | - Finn Lohmann
- Chemical Biology and Medicinal Chemistry Unit, Life and Medical Science (LIMES) Institute, University of Bonn, 53121 Bonn, Germany
| | - Michael Famulok
- Chemical Biology and Medicinal Chemistry Unit, Life and Medical Science (LIMES) Institute, University of Bonn, 53121 Bonn, Germany
- Center of Advanced European Studies and Research (CAESAR), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
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33
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Lohmann F, Weigandt J, Valero J, Famulok M. Logic Gating by Macrocycle Displacement Using a Double-Stranded DNA [3]Rotaxane Shuttle. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405447] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Lohmann F, Weigandt J, Valero J, Famulok M. Logic gating by macrocycle displacement using a double-stranded DNA [3]rotaxane shuttle. Angew Chem Int Ed Engl 2014; 53:10372-6. [PMID: 25078433 DOI: 10.1002/anie.201405447] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Indexed: 12/31/2022]
Abstract
Molecular interlocked systems with mechanically trapped components can serve as versatile building blocks for dynamic nanostructures. Here we report the synthesis of unprecedented double-stranded (ds) DNA [2]- and [3]rotaxanes with two distinct stations for the hybridization of the macrocycles on the axle. In the [3]rotaxane, the release and migration of the "shuttle ring" mobilizes a second macrocycle in a highly controlled fashion. Different oligodeoxynucleotides (ODNs) employed as inputs induce structural changes in the system that can be detected as diverse logically gated output signals. We also designed nonsymmetrical [2]rotaxanes which allow unambiguous localization of the position of the macrocycle by use of atomic force microscopy (AFM). Either light irradiation or the use of fuel ODNs can drive the threaded macrocycle to the desired station in these shuttle systems. The DNA nanostructures introduced here constitute promising prototypes for logically gated cargo delivery and release shuttles.
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Affiliation(s)
- Finn Lohmann
- Life and Medical Science (LIMES) Institute, Chemical Biology & Medicinal Chemistry Unit, University of Bonn, Gerhard-Domagk Strasse 1, 53121 Bonn (Germany) http://www.famuloklab.de
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35
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Jester SS, Famulok M. Mechanically interlocked DNA nanostructures for functional devices. Acc Chem Res 2014; 47:1700-9. [PMID: 24627986 DOI: 10.1021/ar400321h] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
CONSPECTUS: Self-assembled functional DNA oligonucleotide based architectures represent highly promising candidates for the creation of nanoscale devices. The field of DNA nanotechnology has emerged to a high level of maturity and currently constitutes one of the most dynamic, creative, and exciting modern research areas. The transformation from structural DNA nanotechnology to functional DNA architectures is already taking place with tremendous pace. Particularly the advent of DNA origami technology has propelled DNA nanotechnology forward. DNA origami provided a versatile method for precisely aligning structural and functional DNA modules in two and three dimensions, thereby serving as a means for constructing scaffolds and chassis required for the precise orchestration of multiple functional DNA architectures. Key modules of these will contain interlocked nanomechanical components made of DNA. The mechanical interlocking allows for performing highly specific and controlled motion, by reducing the dimensionality of diffusion-controlled processes without restrictions in motional flexibility. Examples for nanoscale interlocked DNA architectures illustrate how elementary functional units of future nanomachines can be designed and realized, and show what role interlocked DNA architectures may play in this endeavor. Functional supramolecular systems, in general, and nanomachinery, in particular, self-organize into architectures that reflect different levels of complexity with respect to their function, their arrangement in the second and third dimension, their suitability for different purposes, and their functional interplay. Toward this goal, DNA nanotechnology and especially the DNA origami technology provide opportunities for nanomechanics, nanorobotics, and nanomachines. In this Account, we address approaches that apply to the construction of interlocked DNA nanostructures, drawing largely form our own contributions to interlocked architectures based on double-stranded (ds) circular geometries, and describe progress, opportunities, and challenges in rotaxanes and pseudorotaxanes made of dsDNA. Operating nanomechanical devices in a reliable and repetitive fashion requires methods for switching movable parts in DNA nanostructures from one state to another. An important issue is the orthogonality of switches that allow for operating different parts in parallel under spatiotemporal control. A variety of switching methods have been applied to switch individual components in interlocked DNA nanostructures like rotaxanes and catenanes. They are based on toehold, light, pseudocomplementary peptide nucleic acids (pcPNAs), and others. The key issues discussed here illustrate our perspective on the future prospects of interlocked DNA-based devices and the challenges that lay ahead.
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Affiliation(s)
- Stefan-S. Jester
- Kekulé-Institut für Organische Chemie und Biochemie and ‡LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und BiochemieUniversität Bonn, Gerhard-Domagk-Straße. 1, 53121 Bonn, Germany
| | - Michael Famulok
- Kekulé-Institut für Organische Chemie und Biochemie and ‡LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und BiochemieUniversität Bonn, Gerhard-Domagk-Straße. 1, 53121 Bonn, Germany
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36
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Lohmann F, Valero J, Famulok M. A novel family of structurally stable double stranded DNA catenanes. Chem Commun (Camb) 2014; 50:6091-3. [DOI: 10.1039/c4cc02030h] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The design, assembly and characterisation by gel electrophoresis and AFM of a new family of double-stranded DNA catenanes are reported in this study.
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Affiliation(s)
- Finn Lohmann
- Universität Bonn
- LIMES-Life and Medical Science Institut
- Program Unit Chemical Biology & Medicinal Chemistry
- 53121 Bonn, Germany
| | - Julián Valero
- Universität Bonn
- LIMES-Life and Medical Science Institut
- Program Unit Chemical Biology & Medicinal Chemistry
- 53121 Bonn, Germany
| | - Michael Famulok
- Universität Bonn
- LIMES-Life and Medical Science Institut
- Program Unit Chemical Biology & Medicinal Chemistry
- 53121 Bonn, Germany
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37
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Choudhary U, Northrop BH. Allyl-Functionalized Dioxynaphthalene[38]Crown-10 Macrocycles: Synthesis, Self-Assembly, and Thiol-ene Functionalization. Chemistry 2013; 20:999-1009. [DOI: 10.1002/chem.201303864] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Indexed: 12/26/2022]
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38
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Escárcega-Bobadilla MV, Zelada-Guillén GA, Pyrlin SV, Wegrzyn M, Ramos MM, Giménez E, Stewart A, Maier G, Kleij AW. Nanorings and rods interconnected by self-assembly mimicking an artificial network of neurons. Nat Commun 2013; 4:2648. [DOI: 10.1038/ncomms3648] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 09/19/2013] [Indexed: 11/09/2022] Open
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39
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Ackermann D, Famulok M. Pseudo-complementary PNA actuators as reversible switches in dynamic DNA nanotechnology. Nucleic Acids Res 2013; 41:4729-39. [PMID: 23444144 PMCID: PMC3632119 DOI: 10.1093/nar/gkt121] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The structural reorganization of nanoscale DNA architectures is a fundamental aspect in dynamic DNA nanotechnology. Commonly, DNA nanoarchitectures are reorganized by means of toehold-expanded DNA sequences in a strand exchange process. Here we describe an unprecedented, toehold-free switching process that relies on pseudo-complementary peptide nucleic acid (pcPNA) by using a mechanism that involves double-strand invasion. The usefulness of this approach is demonstrated by application of these peptide nucleic acids (PNAs) as switches in a DNA rotaxane architecture. The monomers required for generating the pcPNA were obtained by an improved synthesis strategy and were incorporated into a PNA actuator sequence as well as into a short DNA strand that subsequently was integrated into the rotaxane architecture. Alternate addition of a DNA and PNA actuator sequence allowed the multiple reversible switching between a mobile rotaxane macrocycle and a stationary pseudorotaxane state. The switching occurs in an isothermal process at room temperature and is nearly quantitative in each switching step. pcPNAs can potentially be combined with light- and toehold-based switches, thus broadening the toolbox of orthogonal switching approaches for DNA architectures that open up new avenues in dynamic DNA nanotechnology.
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Affiliation(s)
- Damian Ackermann
- Chemical Biology and Medicinal Chemistry Unit, LIMES Institute, c/o Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
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40
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Abstract
The folding of various intra- and intermolecular i-motif DNAs is systematically studied to expand the toolbox for the control of mechanical operations in DNA nanoarchitectures. We analyzed i-motif DNAs with two C-tracts under acidic conditions by gel electrophoresis, circular dichroism, and thermal denaturation and show that their intra- versus intermolecular folding primarily depends on the length of the C-tracts. Two stretches of six or fewer C-residues favor the intermolecular folding of i-motifs, whereas longer C-tracts promote the formation of intramolecular i-motif structures with unusually high thermal stability. We then introduced intra- and intermolecular i-motifs formed by DNAs containing two C-tracts into single-stranded regions within otherwise double-stranded DNA nanocircles. By adjusting the length of C-tracts we can control the intra- and intermolecular folding of i-motif DNAs and achieve programmable functionalization of dsDNA nanocircles. Single-stranded gaps in the nanocircle that are functionalized with an intramolecular i-motif enable the reversible contraction and extension of the DNA circle, as monitored by fluorescence quenching. Thereby, the nanocircle behaves as a proton-fueled DNA prototype machine. In contrast, nanorings containing intermolecular i-motifs induce the assembly of defined multicomponent DNA architectures in response to proton-triggered predicted structural changes, such as dimerization, "kiss", and cyclization. The resulting DNA nanostructures are verified by gel electrophoresis and visualized by atomic force microscopy, including different folding topologies of an intermolecular i-motif. The i-motif-functionalized DNA nanocircles may serve as a versatile tool for the formation of larger interlocked dsDNA nanostructures, like rotaxanes and catenanes, to achieve diverse mechanical operations.
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Affiliation(s)
- Tao Li
- Life and Medical Science (LIMES) Institute, Program Unit Chemical Biology and Medicinal Chemistry, University of Bonn, 53121 Bonn, Germany
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41
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Raja M, Iyer RG, Gwengo C, Reger DL, Pellechia PJ, Smith MD, Pascui AE. Design, Synthesis, and Structural Characterization of a New Class of Ferrocene-Containing Heterometallic Triple-Stranded Helicates. Organometallics 2012. [DOI: 10.1021/om300843r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Muthukrishna Raja
- Department of Chemistry, Claflin University, Orangeburg, South Carolina 29115,
United States
| | - Ratnasabapathy G. Iyer
- Department of Chemistry, Claflin University, Orangeburg, South Carolina 29115,
United States
| | - Chengeto Gwengo
- Department of Chemistry, Claflin University, Orangeburg, South Carolina 29115,
United States
| | - Daniel L. Reger
- Department
of Chemistry, University of South Carolina, Columbia, South Carolina
29208, United States
| | - Perry J. Pellechia
- Department
of Chemistry, University of South Carolina, Columbia, South Carolina
29208, United States
| | - Mark D. Smith
- Department
of Chemistry, University of South Carolina, Columbia, South Carolina
29208, United States
| | - Andrea E. Pascui
- Department
of Chemistry, University of South Carolina, Columbia, South Carolina
29208, United States
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42
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Xiao T, Feng X, Ye S, Guan Y, Li SL, Wang Q, Ji Y, Zhu D, Hu X, Lin C, Pan Y, Wang L. Highly Controllable Ring–Chain Equilibrium in Quadruply Hydrogen Bonded Supramolecular Polymers. Macromolecules 2012. [DOI: 10.1021/ma302459n] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Tangxin Xiao
- Key Laboratory of Mesoscopic
Chemistry of MOE, Center for Multimolecular Chemistry, School of Chemistry
and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Xiaoqing Feng
- Key Laboratory of Mesoscopic
Chemistry of MOE, Center for Multimolecular Chemistry, School of Chemistry
and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Shuyang Ye
- Key Laboratory of Mesoscopic
Chemistry of MOE, Center for Multimolecular Chemistry, School of Chemistry
and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Yangfan Guan
- Key Laboratory of Mesoscopic
Chemistry of MOE, Center for Multimolecular Chemistry, School of Chemistry
and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Shao-Lu Li
- Key Laboratory of Mesoscopic
Chemistry of MOE, Center for Multimolecular Chemistry, School of Chemistry
and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Qi Wang
- Key Laboratory of Mesoscopic
Chemistry of MOE, Center for Multimolecular Chemistry, School of Chemistry
and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Ya Ji
- Key Laboratory of Mesoscopic
Chemistry of MOE, Center for Multimolecular Chemistry, School of Chemistry
and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Dunru Zhu
- State Key Laboratory of Material-Oriented
Chemical Engineering, College of Chemistry and Chemical Engineering, Nanjing University of Technology, Nanjing 210093, China
| | - Xiaoyu Hu
- Key Laboratory of Mesoscopic
Chemistry of MOE, Center for Multimolecular Chemistry, School of Chemistry
and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Chen Lin
- Key Laboratory of Mesoscopic
Chemistry of MOE, Center for Multimolecular Chemistry, School of Chemistry
and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Yi Pan
- Key Laboratory of Mesoscopic
Chemistry of MOE, Center for Multimolecular Chemistry, School of Chemistry
and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Leyong Wang
- Key Laboratory of Mesoscopic
Chemistry of MOE, Center for Multimolecular Chemistry, School of Chemistry
and Chemical Engineering, Nanjing University, Nanjing 210093, China
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43
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Lohmann F, Ackermann D, Famulok M. Reversible light switch for macrocycle mobility in a DNA rotaxane. J Am Chem Soc 2012; 134:11884-7. [PMID: 22780815 PMCID: PMC3404550 DOI: 10.1021/ja3042096] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Indexed: 01/21/2023]
Abstract
A recent trend in DNA nanotechnology consists of the assembly of architectures with dynamic properties that can be regulated by employing external stimuli. Reversible processes are important for implementing molecular motion into DNA architectures as they allow for the regeneration of the original state. Here we describe two different approaches for the reversible switching of a double-stranded DNA rotaxane architecture from a stationary pseudorotaxane mode into a state with movable components. Both states only marginally differ in their respective topologies but their mechanical properties are fundamentally different. In the two approaches, the switching operation is based on strand-displacement reactions. One of them employs toehold-extended oligodeoxynucleotides whereas in the other one the switching is achieved by light-irradiation. In both cases, multiple back and forth switching between the stationary and the mobile states was achieved in nearly quantitative fashion. The ability to reversibly operate mechanical motion in an interlocked DNA nanostructure opens exciting new avenues in DNA nanotechnology.
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Affiliation(s)
| | | | - Michael Famulok
- LIMES Institute,
Chemical Biology & Medicinal Chemistry
Unit, c/o Kekulé Institute of Organic Chemistry
and Biochemistry, Gerhard-Domagk-Strasse 1, 53121 Bonn,
Germany
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44
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Nakamura M, Fukuda M, Takada T, Yamana K. Highly ordered pyrene π-stacks on an RNA duplex display static excimer fluorescence. Org Biomol Chem 2012; 10:9620-6. [DOI: 10.1039/c2ob26773j] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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