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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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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3
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Sakai Y, Wilkens GD, Wolski K, Zapotoczny S, Heddle JG. Topogami: Topologically Linked DNA Origami. ACS NANOSCIENCE AU 2022; 2:57-63. [PMID: 35211697 PMCID: PMC8861903 DOI: 10.1021/acsnanoscienceau.1c00027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 12/19/2022]
Abstract
DNA origami is a widely used DNA nanotechnology that allows construction of two-dimensional and three-dimensional nanometric shapes. The designability and rigidity of DNA origami make it an ideal material for construction of topologically linked molecules such as catenanes, which are attractive for their potential as motors and molecular machines. However, a general method for production of topologically linked DNA origami has been lacking. Here, we show that catenated single-stranded DNA circles can be produced and used as a universal scaffold for the production of topologically linked (catenated) DNA origami structures where the individual linked structures can be of any arbitrary design. Assembly of these topologically linked DNA origami structures is achieved via a simple one-pot annealing protocol.
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Affiliation(s)
- Yusuke Sakai
- Bionanoscience and Biochemistry Laboratory, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland
| | - Gerrit D Wilkens
- Bionanoscience and Biochemistry Laboratory, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland.,Postgraduate School of Molecular Medicine, Żwirki I Wigury 61, 02-091 Warsaw, Poland
| | - Karol Wolski
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Szczepan Zapotoczny
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Jonathan G Heddle
- Bionanoscience and Biochemistry Laboratory, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland
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4
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De Fazio AF, Misatziou D, Baker YR, Muskens OL, Brown T, Kanaras AG. Chemically modified nucleic acids and DNA intercalators as tools for nanoparticle assembly. Chem Soc Rev 2021; 50:13410-13440. [PMID: 34792047 PMCID: PMC8628606 DOI: 10.1039/d1cs00632k] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Indexed: 12/26/2022]
Abstract
The self-assembly of inorganic nanoparticles to larger structures is of great research interest as it allows the fabrication of novel materials with collective properties correlated to the nanoparticles' individual characteristics. Recently developed methods for controlling nanoparticle organisation have enabled the fabrication of a range of new materials. Amongst these, the assembly of nanoparticles using DNA has attracted significant attention due to the highly selective recognition between complementary DNA strands, DNA nanostructure versatility, and ease of DNA chemical modification. In this review we discuss the application of various chemical DNA modifications and molecular intercalators as tools for the manipulation of DNA-nanoparticle structures. In detail, we discuss how DNA modifications and small molecule intercalators have been employed in the chemical and photochemical DNA ligation in nanostructures; DNA rotaxanes and catenanes associated with reconfigurable nanoparticle assemblies; and DNA backbone modifications including locked nucleic acids, peptide nucleic acids and borane nucleic acids, which affect the stability of nanostructures in complex environments. We conclude by highlighting the importance of maximising the synergy between the communities of DNA chemistry and nanoparticle self-assembly with the aim to enrich the library of tools available for the manipulation of nanostructures.
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Affiliation(s)
- Angela F De Fazio
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
- Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Doxi Misatziou
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
| | - Ysobel R Baker
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Otto L Muskens
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Antonios G Kanaras
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
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5
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Abstract
DNA walkers are molecular machines that can move with high precision onthe nanoscale due to their structural and functional programmability. Despite recent advances in the field that allow exploring different energy sources, stimuli, and mechanisms of action for these nanomachines, the continuous operation and reusability of DNA walkers remains challenging because in most cases the steps, once taken by the walker, cannot be taken again. Herein we report the path regeneration of a burnt-bridges DNA catenane walker using RNase A. This walker uses a T7RNA polymerase that produces long RNA transcripts to hybridize to the path and move forward while the RNA remains hybridized to the path and blocks it for an additional walking cycle. We show that RNA degradation triggered by RNase A restores the path and returns the walker to the initial position. RNase inhibition restarts the function of the walker.
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Affiliation(s)
- Julián Valero
- LIMES Chemical Biology UnitUniversität BonnGerhard-Domagk-Straße 153121BonnGermany
- Center of Advanced European Studies and ResearchLudwig-Erhard-Allee 253175BonnGermany
- Present address: Interdisciplinary Nanoscience Center—INANO-MBG, iNANO-husetGustav Wieds Vej 14, building 1592, 3288000Aarhus CDenmark
| | - Michael Famulok
- LIMES Chemical Biology UnitUniversität BonnGerhard-Domagk-Straße 153121BonnGermany
- Center of Advanced European Studies and ResearchLudwig-Erhard-Allee 253175BonnGermany
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6
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Ma Y, Centola M, Keppner D, Famulok M. Interlocked DNA Nanojoints for Reversible Thermal Sensing. Angew Chem Int Ed Engl 2020; 59:12455-12459. [PMID: 32567796 PMCID: PMC7384075 DOI: 10.1002/anie.202003991] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/12/2020] [Indexed: 01/12/2023]
Abstract
The ability to precisely measure and monitor temperature at high resolution at the nanoscale is an important task for better understanding the thermodynamic properties of functional entities at the nanoscale in complex systems, or at the level of a single cell. However, the development of high-resolution and robust thermal nanosensors is challenging. The design, assembly, and characterization of a group of thermal-responsive deoxyribonucleic acid (DNA) joints, consisting of two interlocked double-stranded DNA (dsDNA) rings, is described. The DNA nanojoints reversibly switch between the static and mobile state at different temperatures without a special annealing process. The temperature response range of the DNA nanojoint can be easily tuned by changing the length or the sequence of the hybridized region in its structure, and because of its interlocked structure the temperature response range of the DNA nanojoint is largely unaffected by its own concentration; this contrasts with systems that consist of separated components.
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Affiliation(s)
- Yinzhou Ma
- LIMES Chemical Biology UnitUniversität BonnGerhard-Domagk-Straße 153121BonnGermany
| | - Mathias Centola
- LIMES Chemical Biology UnitUniversität BonnGerhard-Domagk-Straße 153121BonnGermany
- Center of Advanced European Studies and ResearchLudwig-Erhard-Allee 253175BonnGermany
| | - Daniel Keppner
- LIMES Chemical Biology UnitUniversität BonnGerhard-Domagk-Straße 153121BonnGermany
| | - Michael Famulok
- LIMES Chemical Biology UnitUniversität BonnGerhard-Domagk-Straße 153121BonnGermany
- Center of Advanced European Studies and ResearchLudwig-Erhard-Allee 253175BonnGermany
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7
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Valero J, Famulok M. Regeneration of Burnt Bridges on a DNA Catenane Walker. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Julián Valero
- LIMES Chemical Biology UnitUniversität Bonn Gerhard-Domagk-Straße 1 53121 Bonn Germany
- Center of Advanced European Studies and Research Ludwig-Erhard-Allee 2 53175 Bonn Germany
- Present address: Interdisciplinary Nanoscience Center—INANO-MBG, iNANO-huset Gustav Wieds Vej 14, building 1592, 328 8000 Aarhus C Denmark
| | - Michael Famulok
- LIMES Chemical Biology UnitUniversität 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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8
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Ma Y, Centola M, Keppner D, Famulok M. Interlocked DNA Nanojoints for Reversible Thermal Sensing. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Yinzhou Ma
- 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
| | - Daniel Keppner
- LIMES Chemical Biology Unit 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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9
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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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10
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Li J, Mohammed-Elsabagh M, Paczkowski F, Li Y. Circular Nucleic Acids: Discovery, Functions and Applications. Chembiochem 2020; 21:1547-1566. [PMID: 32176816 DOI: 10.1002/cbic.202000003] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/13/2020] [Indexed: 12/14/2022]
Abstract
Circular nucleic acids (CNAs) are nucleic acid molecules with a closed-loop structure. This feature comes with a number of advantages including complete resistance to exonuclease degradation, much better thermodynamic stability, and the capability of being replicated by a DNA polymerase in a rolling circle manner. Circular functional nucleic acids, CNAs containing at least a ribozyme/DNAzyme or a DNA/RNA aptamer, not only inherit the advantages of CNAs but also offer some unique application opportunities, such as the design of topology-controlled or enabled molecular devices. This article will begin by summarizing the discovery, biogenesis, and applications of naturally occurring CNAs, followed by discussing the methods for constructing artificial CNAs. The exploitation of circular functional nucleic acids for applications in nanodevice engineering, biosensing, and drug delivery will be reviewed next. Finally, the efforts to couple functional nucleic acids with rolling circle amplification for ultra-sensitive biosensing and for synthesizing multivalent molecular scaffolds for unique applications in biosensing and drug delivery will be recapitulated.
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Affiliation(s)
- Jiuxing Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Mostafa Mohammed-Elsabagh
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Freeman Paczkowski
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Yingfu Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
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11
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Li L, An R, Tang J, Sui Z, Wang G, Komiyama M, Liang X. Facile Characterization of Topology of DNA Catenanes. Biophys J 2020; 118:1702-1708. [PMID: 32101717 DOI: 10.1016/j.bpj.2020.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/27/2020] [Accepted: 02/06/2020] [Indexed: 11/19/2022] Open
Abstract
During the preparation of single-stranded DNA catenanes, topological isomers of different linking numbers (Lk) are intrinsically produced, and they must be separated from each other to construct sophisticated nanostructures accurately. In many previous studies, however, mixtures of these isomers were directly employed to construct nanostructures without sufficient characterization. Here, we present a method that easily and clearly characterizes the isomers by polyacrylamide gel electrophoresis. To the mixtures of topological isomers of [2]catenanes, two-strut oligonucleotides, which are complementary with a part of both rings, were added to connect the rings and fix the whole conformations of isomers. As a result, the order of migration rate was always Lk3 > Lk2 > Lk1, irrespective of gel concentration. Thus, all the topological isomers were unanimously characterized by only one polyacrylamide gel electrophoresis experiment. Well-characterized DNA catenanes are obtainable by this two-strut strategy, opening the way to more advanced nanotechnology.
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Affiliation(s)
- Lin Li
- College of Food Science and Engineering, Ocean University of China, Nucleic acids Chemistry and Biotechnology Laboratory, Shinan-qu, Qingdao, China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Nucleic acids Chemistry and Biotechnology Laboratory, Shinan-qu, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jiaxuan Tang
- College of Food Science and Engineering, Ocean University of China, Nucleic acids Chemistry and Biotechnology Laboratory, Shinan-qu, Qingdao, China
| | - Zhe Sui
- College of Food Science and Engineering, Ocean University of China, Nucleic acids Chemistry and Biotechnology Laboratory, Shinan-qu, Qingdao, China
| | - Guoqing Wang
- College of Food Science and Engineering, Ocean University of China, Nucleic acids Chemistry and Biotechnology Laboratory, Shinan-qu, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Nucleic acids Chemistry and Biotechnology Laboratory, Shinan-qu, Qingdao, China.
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Nucleic acids Chemistry and Biotechnology Laboratory, Shinan-qu, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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12
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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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13
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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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14
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Two-Holder Strategy for Efficient and Selective Synthesis of Lk 1 ssDNA Catenane. Molecules 2018; 23:molecules23092270. [PMID: 30189687 PMCID: PMC6225352 DOI: 10.3390/molecules23092270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 08/31/2018] [Accepted: 09/05/2018] [Indexed: 11/23/2022] Open
Abstract
DNA catenanes are characterized by their flexible and dynamic motions and have been regarded as one of the key players in sophisticated DNA-based molecular machines. There, the linking number (Lk) between adjacent interlocked rings is one of the most critical factors, since it governs the feasibility of dynamic motions. However, there has been no established way to synthesize catenanes in which Lk is controlled to a predetermined value. This paper reports a new methodology to selectively synthesize Lk 1 catenanes composed of single-stranded DNA rings, in which these rings can most freely rotate each other due to minimal inter-ring interactions. To the mixture for the synthesis, two holder strands (oligonucleotides of 18–46 nt) were added, and the structure of the quasi-catenane intermediate was interlocked through Watson–Crick base pairings into a favorable conformation for Lk 1 catenation. The length of the complementary part between the two quasi-rings was kept at 10 bp or shorter. Under these steric constraints, two quasi-rings were cyclized with the use of T4 DNA ligase. By this simple procedure, the formation of undesired topoisomers (Lk ≥ 2) was almost completely inhibited, and Lk 1 catenane was selectively prepared in high yield up to 70 mole%. These Lk 1 catenanes have high potentials as dynamic parts for versatile DNA architectures.
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15
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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: 90] [Impact Index Per Article: 15.0] [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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16
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Hu Y, Cecconello A, Idili A, Ricci F, Willner I. Triplex DNA Nanostructures: From Basic Properties to Applications. Angew Chem Int Ed Engl 2017; 56:15210-15233. [PMID: 28444822 DOI: 10.1002/anie.201701868] [Citation(s) in RCA: 230] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Indexed: 12/16/2022]
Abstract
Triplex nucleic acids have recently attracted interest as part of the rich "toolbox" of structures used to develop DNA-based nanostructures and materials. This Review addresses the use of DNA triplexes to assemble sensing platforms and molecular switches. Furthermore, the pH-induced, switchable assembly and dissociation of triplex-DNA-bridged nanostructures are presented. Specifically, the aggregation/deaggregation of nanoparticles, the reversible oligomerization of origami tiles and DNA circles, and the use of triplex DNA structures as functional units for the assembly of pH-responsive systems and materials are described. Examples include semiconductor-loaded DNA-stabilized microcapsules, DNA-functionalized dye-loaded metal-organic frameworks (MOFs), and the pH-induced release of the loads. Furthermore, the design of stimuli-responsive DNA-based hydrogels undergoing reversible pH-induced hydrogel-to-solution transitions using triplex nucleic acids is introduced, and the use of triplex DNA to assemble shape-memory hydrogels is discussed. An outlook for possible future applications of triplex nucleic acids is also provided.
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Affiliation(s)
- Yuwei Hu
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Alessandro Cecconello
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Andrea Idili
- Department of Chemistry, University of Rome, Tor Vergata, via della Ricerca Scientifica, 00133, Rome, Italy
| | - Francesco Ricci
- Department of Chemistry, University of Rome, Tor Vergata, via della Ricerca Scientifica, 00133, Rome, Italy
| | - Itamar Willner
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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17
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Hu Y, Cecconello A, Idili A, Ricci F, Willner I. Triplex-DNA-Nanostrukturen: von grundlegenden Eigenschaften zu Anwendungen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701868] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Yuwei Hu
- Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | | | - Andrea Idili
- Department of Chemistry; Universität Rom; Tor Vergata, via della Ricerca Scientifica 00133 Rom Italien
| | - Francesco Ricci
- Department of Chemistry; Universität Rom; Tor Vergata, via della Ricerca Scientifica 00133 Rom Italien
| | - Itamar Willner
- Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
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18
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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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19
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Hu Y, Ren J, Lu CH, Willner I. Programmed pH-Driven Reversible Association and Dissociation of Interconnected Circular DNA Dimer Nanostructures. NANO LETTERS 2016; 16:4590-4594. [PMID: 27225955 DOI: 10.1021/acs.nanolett.6b01891] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The switchable pH-driven reversible assembly and dissociation of interlocked circular DNA dimers is presented. The circular DNA dimers are interconnected by pH-responsive nucleic acid bridges. In one configuration, the two-ring nanostructure is separated at pH = 5.0 to individual rings by reconfiguring the interlocking bridges into C-G·C(+) triplex units, and the two-ring assembly is reformed at pH = 7.0. In the second configuration, the dimer of circular DNAs is bridged at pH = 7.0 by the T-A·T triplex bridging units that are separated at pH = 10.0, leading to the dissociation of the dimer to single circular DNA nanostructures. The two circular DNA units are also interconnected by two pH-responsive locks. The pH-programmed opening of the locks at pH = 5.0 or pH = 10.0 yields two isomeric dimer structures composed of two circular DNAs. The switchable reconfigured states of the circular DNA nanostructures are followed by time-dependent fluorescence changes of fluorophore/quencher labeled systems and by complementary gel electrophoresis experiments. The dimer circular DNA structures are further implemented as scaffolds for the assembly of Au nanoparticle dimers exhibiting controlled spatial separation.
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Affiliation(s)
- Yuwei Hu
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Jiangtao Ren
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Chun-Hua Lu
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Itamar Willner
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
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20
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Zhou W, Li D, Chai Y, Yuan R, Xiang Y. RNA responsive and catalytic self-assembly of DNA nanostructures for highly sensitive fluorescence detection of microRNA from cancer cells. Chem Commun (Camb) 2016; 51:16494-7. [PMID: 26411332 DOI: 10.1039/c5cc06429e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Catalytic self-assembly of DNA nanostructures triggered by microRNA 21 (miR-21) is achieved through isothermal toe-hold strand displacement reactions. The miR-21 is autonomously recycled during the self-assembly process, which makes the generation of the DNA nanostructures proceed in a catalytic fashion. The miR-21-triggered self-assembly of DNA nanostructures can also serve as a remarkable signal amplification platform to achieve ultrasensitive detection of miR-21 from as low as 10 MCF-7 human breast cancer cells.
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Affiliation(s)
- Wenjiao Zhou
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
| | - Daxiu Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
| | - Yaqin Chai
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
| | - Yun Xiang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
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21
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Wu ZS, Shen Z, Tram K, Salena BJ, Li Y. Topological DNA Assemblies Containing Identical or Fraternal Twins. Chembiochem 2016; 17:1142-5. [PMID: 26994736 DOI: 10.1002/cbic.201600036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Indexed: 01/10/2023]
Affiliation(s)
- Zai-Sheng Wu
- Departments of Biochemistry and Biomedical Sciences; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
- Cancer Metastasis Alert and Prevention Center; Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment; Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy; College of Chemistry; Fuzhou University; Fuzhou 350002 China
| | - Zhifa Shen
- Departments of Biochemistry and Biomedical Sciences; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
- School of Laboratory Medicine and Life Sciences; Wenzhou Medical University; Wenzhou Chashan University Town Wenzhou Zhejiang 325035 China
| | - Kha Tram
- Departments of Biochemistry and Biomedical Sciences; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Bruno J. Salena
- Department of Medicine; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Yingfu Li
- Departments of Biochemistry and Biomedical Sciences; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
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22
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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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23
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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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24
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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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25
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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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26
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Li T, Zhang H, Hu L, Shao F. Topoisomerase-Based Preparation and AFM Imaging of Multi-Interlocked Circular DNA. Bioconjug Chem 2016; 27:616-20. [PMID: 26745453 DOI: 10.1021/acs.bioconjchem.5b00606] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Multi-interlocked circular DNA structures have been in high demand for fabricating complicated functional DNA architectures and nanodevices such as molecular switches, shuttles, and motors. Even though various innovative methods have been developed in the past, creation of multi-interlocked circular DNA structures with defined numbers of DNA molecules and linking patterns is still a challenging task nowadays. Here, we propose a top-down decatenation of kinetoplast DNA as a new approach for creating multi-interlocked circular DNA structures. Through optimizing the amount and reaction time of topoisomerase II, we synthesized completely mutually interlocked tricircular, tetra-circular, and oligo-circular DNA structures, which have not yet been acquirable through any other existing synthetic means. The catenation structures of multiple circular DNA were further verified through atomic force microscopic analysis of the backbone overlapping patterns and the circumference. It accordingly is our expectation that the top-down enzymatic approaches could offer a highly interlocked network with defined numbers of circular DNA with simple protocols, and could consequently be beneficial to the design and fabrication of sophisticated functional molecules and nanodevices in the areas of supramolecular chemistry, DNA nanotechnology, and material science.
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Affiliation(s)
- Tevin Li
- Lexington High School , 251 Waltham Street, Lexington, Massachusetts 02421, United States
| | - Hao Zhang
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University , 21 Nanyang Link, Singapore, 637371
| | - Lianzhe Hu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University , 21 Nanyang Link, Singapore, 637371
| | - Fangwei Shao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University , 21 Nanyang Link, Singapore, 637371
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27
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Hayashi R, Slavík P, Mutoh Y, Kasama T, Saito S. Sequence-Selective Synthesis of Rotacatenane Isomers. J Org Chem 2016; 81:1175-84. [DOI: 10.1021/acs.joc.5b02697] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Ryuto Hayashi
- Department
of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku, Tokyo, 162-8601, Japan
| | - Petr Slavík
- Department
of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku, Tokyo, 162-8601, Japan
| | - Yuichiro Mutoh
- Department
of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku, Tokyo, 162-8601, Japan
| | - Takeshi Kasama
- Research
Center for Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo, Tokyo, 113-8510, Japan
| | - Shinichi Saito
- Department
of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku, Tokyo, 162-8601, Japan
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28
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Cassinelli V, Oberleitner B, Sobotta J, Nickels P, Grossi G, Kempter S, Frischmuth T, Liedl T, Manetto A. One-Step Formation of "Chain-Armor"-Stabilized DNA Nanostructures. Angew Chem Int Ed Engl 2015; 54:7795-8. [PMID: 25980669 DOI: 10.1002/anie.201500561] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Indexed: 12/12/2022]
Abstract
DNA-based self-assembled nanostructures are widely used to position organic and inorganic objects with nanoscale precision. A particular promising application of DNA structures is their usage as programmable carrier systems for targeted drug delivery. To provide DNA-based templates that are robust against degradation at elevated temperatures, low ion concentrations, adverse pH conditions, and DNases, we built 6-helix DNA tile tubes consisting of 24 oligonucleotides carrying alkyne groups on their 3'-ends and azides on their 5'-ends. By a mild click reaction, the two ends of selected oligonucleotides were covalently connected to form rings and interlocked DNA single strands, so-called DNA catenanes. Strikingly, the structures stayed topologically intact in pure water and even after precipitation from EtOH. The structures even withstood a temperature of 95 °C when all of the 24 strands were chemically interlocked.
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Affiliation(s)
- Valentina Cassinelli
- baseclick GmbH, Bahnhofstrasse 9-15, 82327 Tutzing (Germany).,Department Chemistry and Biochemistry, Ludwig-Maximilians-Universität (LMU), Butenandtstrasse 5-13, 81377 Munich (Germany)
| | | | - Jessica Sobotta
- baseclick GmbH, Bahnhofstrasse 9-15, 82327 Tutzing (Germany).,Department Applied Chemistry, Technische Hochschule Nürnberg G. S. Ohm, Kesslerplatz 12, 90489 Nürnberg (Germany)
| | - Philipp Nickels
- Physics Department and CeNS, Ludwig-Maximilians-Universität (LMU), Geschwister-Scholl-Platz 1, 80539 Munich (Germany)
| | - Guido Grossi
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus (Denmark)
| | - Susanne Kempter
- Physics Department and CeNS, Ludwig-Maximilians-Universität (LMU), Geschwister-Scholl-Platz 1, 80539 Munich (Germany)
| | | | - Tim Liedl
- Physics Department and CeNS, Ludwig-Maximilians-Universität (LMU), Geschwister-Scholl-Platz 1, 80539 Munich (Germany)
| | - Antonio Manetto
- baseclick GmbH, Bahnhofstrasse 9-15, 82327 Tutzing (Germany).
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29
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Cassinelli V, Oberleitner B, Sobotta J, Nickels P, Grossi G, Kempter S, Frischmuth T, Liedl T, Manetto A. Eintopfsynthese von “Kettenhemd”-stabilisierten DNA-Nanostrukturen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201500561] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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30
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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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31
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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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32
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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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