1
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Kuwahara K, Yajima S, Yamano Y, Nagatsugi F, Onizuka K. Formation of Direction-Controllable Pseudorotaxane and Catenane Using Chemically Cyclized Oligodeoxynucleotides and Their Noncovalent RNA Labeling. Bioconjug Chem 2023. [PMID: 36930464 DOI: 10.1021/acs.bioconjchem.3c00031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
The formation of interlocked structures, such as rotaxane and catenane, enables noncovalent conjugations. We previously confirmed that the chemically cyclized pseudorotaxane-forming oligodeoxynucleotides (prfODNs) with double-tailed parts formed a pseudorotaxane structure with the target DNA and RNA via the slipping process. Here, we report the one-step synthesis of cyclized prfODNs from alkyne-modified ODNs, after which we investigated the properties and mechanism of the slipping process and performed noncovalent RNA labeling with prfODNs. Additionally, the catenane structure was formed by the combination of pseudorotaxane formation with a 5'-end-phosphorylated RNA and enzymatic ligation. The newly synthesized prfODN represents a new tool for achieving the noncovalent conjugation of various functional moieties to RNAs.
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Affiliation(s)
- Kazuki Kuwahara
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Sayaka Yajima
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Yuuhei Yamano
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8578, Japan.,Division for the Establishment of Frontier Sciences of Organization for Advanced Studies, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8577, Japan
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2
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Onizuka K, Yamano Y, Abdelhady AM, Nagatsugi F. Hybridization-specific chemical reactions to create interstrand crosslinking and threaded structures of nucleic acids. Org Biomol Chem 2022; 20:4699-4708. [PMID: 35622064 DOI: 10.1039/d2ob00551d] [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
The interstrand crosslinking and threaded structures of nucleic acids have high potential in oligonucleotide therapeutics, chemical biology, and nanotechnology. For example, properly designed crosslinking structures provide high activity and nuclease resistance for anti-miRNAs. The noncovalent labeling and modification by the threaded structures are useful as new chemical biology tools. Photoreversible crosslinking creates smart materials, such as reversible photoresponsive gels and DNA origami objects. This review introduces the creation of interstrand crosslinking and threaded structures, such as catenanes and rotaxanes, based on hybridization-specific chemical reactions and their functions and perspectives.
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Affiliation(s)
- Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan. .,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan.,Division for the Establishment of Frontier Sciences of Organization for Advanced Studies, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Yuuhei Yamano
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.
| | - Ahmed Mostafa Abdelhady
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan. .,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan.,Department of Chemistry, Faculty of Science, Al-Azhar University, Nasr City, 11884, Cairo, Egypt
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan. .,Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
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3
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Chen YR, Sun S, Yin H, Wang W, Liu R, Xu H, Yang Y, Wu ZS. Tumor-targeting [2]catenane-based grid-patterned periodic DNA monolayer array for in vivo theranostic application. J Mater Chem B 2022; 10:1969-1979. [PMID: 35014661 DOI: 10.1039/d1tb01978c] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
DNA nanotechnology is often used to build various nano-structures for signaling and/or drug delivery, but it essentially suffers from several major limitations, such as a large number of DNA strands and limited targeting ligands. Moreover, there is no report on in vivo two-dimensional DNA arrays because of various technical challenges. By cross-catenating two palindromic DNA rings, herein, we demonstrate a catenane-based grid-patterned periodic DNA monolayer array ([2]GDA) capable of preferentially accumulating in tumor tissues without any targeting ligands, with a thickness equal to the double-helical DNA monolayer (nearly 2 nm). The structural flexibility of [2]GDA enabled it to fold into a spherical object in solution, favoring cellular uptake. Thus, its cellular internalization activity was comparable with that of the commercial lipofectamine 3000. Moreover, [2]GDA retained the structural integrity over 24 h incubation in biological solutions, achieving a 360-fold improvement in in vivo stability. Significantly, anticancer drug-loaded [2]GDA exhibits desirable therapeutic efficacy in tumor-bearing animals without detectable side effects.
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Affiliation(s)
- Yan-Ru Chen
- 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, 305108, China
| | - Shujuan Sun
- 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, 305108, China
| | - Hongwei Yin
- 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, 305108, China
| | - Weijun Wang
- 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, 305108, China
| | - Ran Liu
- 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, 305108, China
| | - Huo Xu
- 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, 305108, China
| | - Ya Yang
- 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, 305108, China
| | - Zai-Sheng 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, 305108, China
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4
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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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5
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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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6
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Nicolaou KC, Shelke YG, Dherange BD, Kempema A, Lin B, Gu C, Sandoval J, Hammond M, Aujay M, Gavrilyuk J. Design, Synthesis, and Biological Investigation of Epothilone B Analogues Featuring Lactone, Lactam, and Carbocyclic Macrocycles, Epoxide, Aziridine, and 1,1-Difluorocyclopropane and Other Fluorine Residues. J Org Chem 2020; 85:2865-2917. [DOI: 10.1021/acs.joc.0c00123] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- K. C. Nicolaou
- Department of Chemistry, BioScience Research Collaborative, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Yogesh G. Shelke
- Department of Chemistry, BioScience Research Collaborative, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Balu D. Dherange
- Department of Chemistry, BioScience Research Collaborative, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Aaron Kempema
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
| | - Baiwei Lin
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
| | - Christine Gu
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
| | - Joseph Sandoval
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
| | - Mikhail Hammond
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
| | - Monette Aujay
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
| | - Julia Gavrilyuk
- AbbVie, Inc., 400 East Jamie Court, South San Francisco, California 94080, United States
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7
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Rajasekaran VV, Paul I, Schmittel M. Reversible switching from a three- to a nine-fold degenerate dynamic slider-on-deck through catenation. Chem Commun (Camb) 2020; 56:12821-12824. [DOI: 10.1039/d0cc05578f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Two dynamic slider-on-deck assemblies, i.e. a two-component threefold degenerate (k298 = 34.9 kHz) and a catenated three-component ninefold degenerate (k298 = 27.9 kHz) system with allosteric effects on the sliding rates, were quantitatively interconverted.
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Affiliation(s)
| | - Indrajit Paul
- Center of Micro and Nanochemistry and Engineering
- Organische Chemie I
- Universität Siegen
- Germany
| | - Michael Schmittel
- Center of Micro and Nanochemistry and Engineering
- Organische Chemie I
- Universität Siegen
- Germany
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8
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Onizuka K, Miyashita T, Chikuni T, Ozawa M, Abe H, Nagatsugi F. Structural optimization of pseudorotaxane-forming oligonucleotides for efficient and stable complex formation. Nucleic Acids Res 2019; 46:8710-8719. [PMID: 30260454 PMCID: PMC6158610 DOI: 10.1093/nar/gky744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 08/06/2018] [Indexed: 01/15/2023] Open
Abstract
Interlocked structures, such as rotaxane and catenane, combine both static and dynamic properties. To expand their unique properties into the chemical biology field, a spontaneous formation method of the interlocked structures with the target would be ideal. We have previously developed a pseudorotaxane-forming oligo DNA (prfODN) to spontaneously form topological DNA/RNA architectures. In this study, we report the structural optimization of prfODNs for the efficient and stable complex formation. The optimized prfODNs efficiently formed pseudorotaxane structures with a DNA or RNA target, and the yield for the RNA target reached 85% in 5 min. In addition, the optimized prfODNs could form the pseudorotaxane structure with a smaller ring size and the structure significantly increased the kinetic stability. Furthermore, the catenane structure was successfully formed with the optimized prfODNs to provide the conclusive evidence for the formation of the threaded structure. This information will be valuable for developing new chemical methods using functional nucleic acids for antisense oligo nucleotides and DNA/RNA nanotechnology.
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Affiliation(s)
- Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Takuya Miyashita
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Tomoko Chikuni
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Mamiko Ozawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Hiroshi Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
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9
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Cui Y, Han X, An R, Zhang Y, Cheng K, Liang X, Komiyama M. Terminal hairpin in oligonucleotide dominantly prioritizes intramolecular cyclization by T4 ligase over intermolecular polymerization: an exclusive methodology for producing ssDNA rings. Nucleic Acids Res 2018; 46:e132. [PMID: 30169701 PMCID: PMC6294566 DOI: 10.1093/nar/gky769] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/02/2018] [Accepted: 08/22/2018] [Indexed: 12/22/2022] Open
Abstract
When oligonucleotide bearing a hairpin near either its 3'- or 5'-end was treated with T4 DNA ligase, the intramolecular cyclization dominantly proceeded and its monomeric cyclic ring was obtained in extremely high selectivity. The selectivity was hardly dependent on the concentration of the oligonucleotide, and thus it could be added in one portion to the mixture at the beginning of the reaction. Without the hairpin, however, the formation of polymeric byproducts was dominant under the same conditions. Hairpin-bearing oligonucleotides primarily take the folded form, and the enzymatically reactive species (its open form) is minimal. As the result, the intermolecular reactions are efficiently suppressed due to both thermodynamic and kinetic factors. The 'terminal hairpin strategy' was applicable to large-scale preparation of a variety of DNA rings. The combination of this methodology with 'diluted buffer strategy', developed previously, is still more effective for the purpose. When large amount of l-DNA bearing a terminal hairpin (e.g. 40 μM) was treated in a diluted ligase buffer (0.1× buffer) with T4 DNA ligase, the DNA ring was prepared in 100% selectivity. Even at [l-DNA]0 = 100 μM in 0.1× buffer, the DNA ring was also obtained in pure form, simply by removing tiny quantity of linear byproducts by Exonuclease I.
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Affiliation(s)
- Yixiao Cui
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Xutiange Han
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Yaping Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Kai Cheng
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
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10
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Garoni E, Boixel J, Dorcet V, Roisnel T, Roberto D, Jacquemin D, Guerchais V. Controlling the emission in flexibly-linked (N^C^N)platinum dyads. Dalton Trans 2018; 47:224-232. [DOI: 10.1039/c7dt03695g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Comparative luminescence studies of the mononuclear complex Pt-1 and the differently linked dinuclear complexes Pt-2 and Pt-3 reveal distinctive luminescent properties. The emission of Pt-2 can be readily modulated over a wide range of the visible part of the spectrum.
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Affiliation(s)
- Eleonora Garoni
- Institut des Sciences Chimiques de Rennes
- UMR CNRS 6226
- 35042 Rennes Cedex
- France
- Dipartimento di Chimica
| | - Julien Boixel
- Institut des Sciences Chimiques de Rennes
- UMR CNRS 6226
- 35042 Rennes Cedex
- France
| | - Vincent Dorcet
- Institut des Sciences Chimiques de Rennes
- UMR CNRS 6226
- 35042 Rennes Cedex
- France
| | - Thierry Roisnel
- Institut des Sciences Chimiques de Rennes
- UMR CNRS 6226
- 35042 Rennes Cedex
- France
| | - Dominique Roberto
- Dipartimento di Chimica
- Università degli Studi di Milano
- 20133 Milano
- Italy
| | - Denis Jacquemin
- CEISAM laboratory
- UMR 6230
- University of Nantes
- 44322 Nantes
- France
| | - Véronique Guerchais
- Institut des Sciences Chimiques de Rennes
- UMR CNRS 6226
- 35042 Rennes Cedex
- France
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11
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Cui Y, Han X, An R, Zhou G, Komiyama M, Liang X. Cyclization of secondarily structured oligonucleotides to single-stranded rings by using Taq DNA ligase at high temperatures. RSC Adv 2018; 8:18972-18979. [PMID: 35539641 PMCID: PMC9080623 DOI: 10.1039/c8ra02804d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 05/10/2018] [Indexed: 11/21/2022] Open
Abstract
Single-stranded DNA rings play important roles in nanoarchitectures, molecular machines, DNA detection, etc. Although T4 DNA ligase has been widely employed to cyclize single-stranded oligonucleotides into rings, the cyclization efficiency is very low when the oligonucleotides (l-DNAs) take complicated secondary structures at ambient temperatures. In the present study, this problem has been solved by using Thermus aquaticus DNA ligase (Taq DNA ligase) at higher temperatures (65 and 70 °C) where the secondary structures are less stable or completely destroyed. This method is based on our new finding that this ligase successfully functions even when the splint strand is short and forms no stable duplex with l-DNA (at least in the absence of the enzyme). In order to increase the efficiency of cyclization, various operation factors (lengths and sequences of splint, as well as the size of the DNA ring) have been investigated. Based on these results, DNA rings have been successfully synthesized from secondarily structured oligonucleotides in high yields and high selectivity. The present methodology is applicable to the preparation of versatile DNA rings involving complicated secondary structures, which should show novel properties and greatly widen the scope of DNA-based nanotechnology. We have achieved the efficient preparation of single-stranded DNA rings from secondarily structured oligonucleotides.![]()
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Affiliation(s)
- Yixiao Cui
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
| | - Xutiange Han
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
| | - Ran An
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
- Laboratory for Marine Drugs and Bioproducts
| | - Guangqing Zhou
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
| | - Makoto Komiyama
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
- National Institute for Materials Science (NIMS)
| | - Xingguo Liang
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
- Laboratory for Marine Drugs and Bioproducts
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12
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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: 223] [Impact Index Per Article: 31.9] [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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13
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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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14
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Khanal A, Fang S. Solid Phase Stepwise Synthesis of Polyethylene Glycols. Chemistry 2017; 23:15133-15142. [PMID: 28834652 PMCID: PMC5658237 DOI: 10.1002/chem.201703004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Indexed: 01/20/2023]
Abstract
Polyethylene glycol (PEG) and derivatives with eight and twelve ethylene glycol units were synthesized by stepwise addition of tetraethylene glycol monomers on a polystyrene solid support. The monomer contains a tosyl group at one end and a dimethoxytrityl group at the other. The Wang resin, which contains the 4-benzyloxy benzyl alcohol function, was used as the support. The synthetic cycle consists of deprotonation, Williamson ether formation (coupling), and detritylation. Cleavage of PEGs from solid support was achieved with trifluoroacetic acid. The synthesis including monomer synthesis was entirely chromatography-free. PEG products including those with different functionalities at the two termini were obtained in high yields. The products were analyzed with ESI and MALDI-TOF MS and were found close to monodispersity.
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Affiliation(s)
- Ashok Khanal
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Shiyue Fang
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
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15
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An R, Li Q, Fan Y, Li J, Pan X, Komiyama M, Liang X. Highly efficient preparation of single-stranded DNA rings by T4 ligase at abnormally low Mg(II) concentration. Nucleic Acids Res 2017; 45:e139. [PMID: 28655200 PMCID: PMC5587803 DOI: 10.1093/nar/gkx553] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 05/27/2017] [Accepted: 06/15/2017] [Indexed: 12/04/2022] Open
Abstract
Preparation of large amount of single-stranded circular DNA in high selectivity is crucial for further developments of nanotechnology and other DNA sciences. Herein, a simple but practically useful methodology to prepare DNA rings has been presented. One of the essential factors is to use highly diluted T4 ligase buffer for ligase reactions. This strategy is based on our unexpected finding that, in diluted T4 buffers, intermolecular polymerization of DNA fragments is greatly suppressed with respect to their intramolecular cyclization. This promotion of cyclization is attributable to abnormally low concentration of Mg2+ ion (0.5-1.0 mM) but not ATP in the media for T4 ligase reactions. The second essential factor is to add DNA substrate intermittently to the mixture and maintain its temporal concentration low. By combining these two factors, single-stranded DNA rings of various sizes (31-74 nt) were obtained in high selectivity (89 mol% for 66-nt DNA) and in satisfactorily high productivity (∼0.2 mg/ml). A linear 72-nt DNA was converted to the corresponding DNA ring in nearly 100% selectivity. The superiority of this new method was further substantiated by the fact that small-sized DNA rings (31-42 nt), which were otherwise hardly obtainable, were successfully prepared in reasonable yields.
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Affiliation(s)
- Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Qi Li
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Yiqiao Fan
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Jing Li
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Xiaoming Pan
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
- National Institute for Materials Science (NIMS), Namiki, Tsukuba 305-0044, Japan
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
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16
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Onizuka K, Chikuni T, Amemiya T, Miyashita T, Onizuka K, Abe H, Nagatsugi F. Pseudorotaxane formation via the slippage process with chemically cyclized oligonucleotides. Nucleic Acids Res 2017; 45:5036-5047. [PMID: 28407122 PMCID: PMC5435984 DOI: 10.1093/nar/gkx265] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 04/05/2017] [Indexed: 01/19/2023] Open
Abstract
Circular nucleic acids have been utilized for versatile applications by taking advantage of the unique characteristic of their circular structure. In our previous study, we found that the chemically-cyclized ODN (cyODN) with double-tailed parts formed a pseudorotaxane structure with the target via the slippage process. We now report the investigation of the slippage properties and the mechanism of the slippage process using six different cyODNs. Our results indicate that the formation efficiency significantly depend on the temperature, the ring size, the target length and the mismatched position of the target. The kinetic studies also showed that this pseudorotaxane formation would proceed via a non-threaded structure which hybridizes with the target at the double-tailed parts. In addition, the resulting pseudorotaxanes showed interesting characteristics unlike the canonical duplex such as the hysteresis loop in the Tm measurements and the kinetic stabilization by lengthening the target. This information will be fundamentally important for finding new functions of circular nucleic acids and elucidating the threading mechanism regarding other synthetic small molecules and biopolymers.
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Affiliation(s)
- Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Tomoko Chikuni
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Takuya Amemiya
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Takuya Miyashita
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Kyoko Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Hiroshi Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
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17
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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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18
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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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19
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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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20
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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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21
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Lu CH, Cecconello A, Qi XJ, Wu N, Jester SS, Famulok M, Matthies M, Schmidt TL, Willner I. Switchable Reconfiguration of a Seven-Ring Interlocked DNA Catenane Nanostructure. NANO LETTERS 2015; 15:7133-7137. [PMID: 26360345 DOI: 10.1021/acs.nanolett.5b03280] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The synthesis, purification, and structure characterization of a seven-ring interlocked DNA catenane is described. The design of the seven-ring catenane allows the dynamic reconfiguration of any of the four rings (R1, R3, R4, and R6) on the catenane scaffold, or the simultaneous switching of any combination of two, three, or all four rings to yield 16 different isomeric states of the catenane. The dynamic reconfiguration across the states is achieved by implementing the strand-displacement process in the presence of appropriate fuel/antifuel strands and is probed by fluorescence spectroscopy. Each of the 16 isomers of the catenane can be transformed into any of the other isomers, thus allowing for 240 dynamic transitions within the system.
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Affiliation(s)
- Chun-Hua Lu
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Alessandro Cecconello
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Xiu-Juan Qi
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
- The Key Laboratory of Analysis and Detection Technology for Food Safety of the MOE, College of Chemistry, Fuzhou University , Fuzhou 350002, China
| | - Na Wu
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Stefan-Sven Jester
- 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
- Center of Advanced European Studies and Research (CAESAR) , Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Michael Matthies
- Cluster of Excellence Centre for Advancing Electronics Dresden (cfaed), Technische Universität Dresden , 01062 Dresden, Germany
| | - Thorsten-Lars Schmidt
- Cluster of Excellence Centre for Advancing Electronics Dresden (cfaed), Technische Universität Dresden , 01062 Dresden, Germany
| | - Itamar Willner
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
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22
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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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23
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Tashiro R, Iwamoto M, Morinaga H, Emura T, Hidaka K, Endo M, Sugiyama H. Linking two DNA duplexes with a rigid linker for DNA nanotechnology. Nucleic Acids Res 2015; 43:6692-700. [PMID: 26130712 PMCID: PMC4538841 DOI: 10.1093/nar/gkv662] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 06/11/2015] [Accepted: 06/17/2015] [Indexed: 11/14/2022] Open
Abstract
DNA has recently emerged as a promising material for the construction of nanosized architectures. Chemically modified DNA has been suggested to be an important component of such architectural building blocks. We have designed and synthesized a novel H-shaped DNA oligonucleotide dimer that is cross-linked with a structurally rigid linker composed of phenylene and ethynylene groups. A rotatable DNA unit was constructed through the self-assembly of this H-shaped DNA component and two complementary DNA oligonucleotides. In addition to the rotatable unit, a locked DNA unit containing two H-shaped DNA components was also constructed. As an example of an extended locked structure, a hexagonal DNA origami dimer and oligomer were constructed by using H-shaped DNA as linkers.
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Affiliation(s)
- Ryu Tashiro
- Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science, 3500-3 Minamitamagaki-cho, Suzuka-shi, Mie 513-8670, Japan
| | - Masahiro Iwamoto
- Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science, 3500-3 Minamitamagaki-cho, Suzuka-shi, Mie 513-8670, Japan
| | - Hironobu Morinaga
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Tomoko Emura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Masayuki Endo
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
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24
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Qi XJ, Lu CH, Cecconello A, Yang HH, Willner I. A two-ring interlocked DNA catenane rotor undergoing switchable transitions across three states. Chem Commun (Camb) 2015; 50:4717-20. [PMID: 24676286 DOI: 10.1039/c4cc00880d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A two-ring (α/β) interlocked DNA catenane rotor system is described. Using appropriate fuel and anti-fuel strands, the triggered switchable rotation across three states S1, S2 and S3 associated with the circular track of ring α is demonstrated.
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Affiliation(s)
- Xiu-Juan Qi
- The Key Laboratory of Analysis and Detection Technology for Food Safety of the MOE, College of Chemistry, Fuzhou University, Fuzhou 350002, China
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25
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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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26
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Li D, Wang X, Shi F, Sha R, Seeman NC, Canary JW. Templated DNA ligation with thiol chemistry. Org Biomol Chem 2014; 12:8823-7. [DOI: 10.1039/c4ob01552e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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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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28
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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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29
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Suzuki T, Yamamoto T, Tezuka Y. Constructing a Macromolecular K3,3 Graph through Electrostatic Self-Assembly and Covalent Fixation with a Dendritic Polymer Precursor. J Am Chem Soc 2014; 136:10148-55. [DOI: 10.1021/ja504891x] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Takuya Suzuki
- Department
of Organic and
Polymeric Materials, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Takuya Yamamoto
- Department
of Organic and
Polymeric Materials, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Yasuyuki Tezuka
- Department
of Organic and
Polymeric Materials, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
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30
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Lu CH, Qi XJ, Cecconello A, Jester SS, Famulok M, Willner I. Switchable reconfiguration of an interlocked DNA olympiadane nanostructure. Angew Chem Int Ed Engl 2014; 53:7499-503. [PMID: 24889855 DOI: 10.1002/anie.201403202] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Indexed: 12/27/2022]
Abstract
Interlocked DNA rings (catenanes) are interesting reconfigurable nanostructures. The synthesis of catenanes with more than two rings is, however, hampered, owing to low yields of these systems. We report a new method for the synthesis of catenanes with a controlled number of rings in satisfactory yields. Our approach is exemplified by the synthesis of a five-ring DNA catenane that exists in four different configurations. By the use of nucleic acids as "fuels" and "antifuels", the cyclic reconfiguration of the system across four states is demonstrated. One of the states, olympiadane, corresponds to the symbol of the Olympic Games. The five-ring catenane was implemented as a mechanical scaffold for the reconfiguration of Au NPs. The advantages of DNA catenanes over supramolecular catenanes include the possibility of generating highly populated defined states and the feasibility of tethering nanoobjects to the catenanes, which act as a mechanical scaffold to reconfigure the nanoobjects.
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Affiliation(s)
- Chun-Hua Lu
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904 (Israel)
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31
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Lu CH, Qi XJ, Cecconello A, Jester SS, Famulok M, Willner I. Switchable Reconfiguration of an Interlocked DNA Olympiadane Nanostructure. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403202] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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32
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Onizuka K, Nagatsugi F, Ito Y, Abe H. Automatic pseudorotaxane formation targeting on nucleic acids using a pair of reactive oligodeoxynucleotides. J Am Chem Soc 2014; 136:7201-4. [PMID: 24807826 DOI: 10.1021/ja5018283] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here we report a novel method to form a pseudorotaxane architecture using only a pair of reactive oligodeoxyribonucleotides (ODNs), which we designed and synthesized, and then performed the pseudorotaxane formation reaction with both DNA and RNA oligonucleotides. The reaction proceeded smoothly without any extra reagents at 37 °C and pH 7.2, leading to the formation of a stable complex on a denaturing polyacrylamide gel. Interestingly, the pseudorotaxane was formed with the cyclized ODN reversibly by the slipping process. This new pseudorotaxane formation represents a promising method for developing new DNA nanotechnologies and antisense oligonucleotides.
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Affiliation(s)
- Kazumitsu Onizuka
- Nano Medical Engineering Laboratory, RIKEN , 2-1, Hirosawa, Wako, Saitama 351-0198, Japan
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33
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Powering the programmed nanostructure and function of gold nanoparticles with catenated DNA machines. Nat Commun 2013; 4:2000. [PMID: 23759797 PMCID: PMC3709512 DOI: 10.1038/ncomms3000] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 05/13/2013] [Indexed: 12/21/2022] Open
Abstract
DNA nanotechnology is a rapidly developing research area in nanoscience. It includes the development of DNA machines, tailoring of DNA nanostructures, application of DNA nanostructures for computing, and more. Different DNA machines were reported in the past and DNA-guided assembly of nanoparticles represents an active research effort in DNA nanotechnology. Several DNA-dictated nanoparticle structures were reported, including a tetrahedron, a triangle or linear nanoengineered nanoparticle structures; however, the programmed, dynamic reversible switching of nanoparticle structures and, particularly, the dictated switchable functions emerging from the nanostructures, are missing elements in DNA nanotechnology. Here we introduce DNA catenane systems (interlocked DNA rings) as molecular DNA machines for the programmed, reversible and switchable arrangement of different-sized gold nanoparticles. We further demonstrate that the machine-powered gold nanoparticle structures reveal unique emerging switchable spectroscopic features, such as plasmonic coupling or surface-enhanced fluorescence.
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Cecconello A, Lu CH, Elbaz J, Willner I. Au nanoparticle/DNA rotaxane hybrid nanostructures exhibiting switchable fluorescence properties. NANO LETTERS 2013; 13:6275-6280. [PMID: 24245996 DOI: 10.1021/nl403884w] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The preparation of a DNA rotaxane consisting of a circular nucleic acid interlocked, through hybridization, on a nucleic acid axle and stoppered by two 10-nm-sized Au nanoparticles (NPs) is described. By the tethering of 5-nm- or 15-nm-sized Au NPs on the ring, the supramolecular structure of the rotaxane is confirmed. Using nucleic acids as "fuels" and "anti-fuels", the cyclic and reversible transition of the rotaxane ring across two states is demonstrated. By the functionalization of the ring with fluorophore-modified nucleic acids in different orientations, the transitions of the rings between the sites are followed by fluorescence quenching or surface-enhanced fluorescence. The experimental results are supported by theoretical modeling.
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Affiliation(s)
- Alessandro Cecconello
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
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Lu CH, Cecconello A, Elbaz J, Credi A, Willner I. A three-station DNA catenane rotary motor with controlled directionality. NANO LETTERS 2013; 13:2303-8. [PMID: 23557381 DOI: 10.1021/nl401010e] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The assembly of DNA machines represents a central effort in DNA nanotechnology. We report on the first DNA rotor system composed of a two-ring catenane. The DNA rotor ring rotates in dictated directions along a wheel, and it occupies three distinct sites. Hg(2+)/cysteine or pH (H(+)/OH(-)) act as fuels or antifuels in positioning the rotor ring. Analysis of the kinetics reveals directional clockwise or anticlockwise population of the target-sites (>85%), and the rotor's direction is controlled by the shortest path on the wheel.
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Affiliation(s)
- Chun-Hua Lu
- Institute of Chemistry and The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Ye M, Guillaume J, Liu Y, Sha R, Wang R, Seeman NC, Canary JW. Site-specific inter-strand cross-links of DNA duplexes. Chem Sci 2013; 4:1319-1329. [PMID: 23894693 PMCID: PMC3719409 DOI: 10.1039/c2sc21775a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We report the development of technology that allows inter-strand coupling across various positions within one turn of DNA. Four 2'-modified nucleotides were synthesized as protected phosphoramidites and incorporated into DNA oligonucleotides. The modified nucleotides contain either 5-atom or 16-atom linker components, with either amine or carboxylic acid functional groups at their termini, forming 10 or 32 atom (11 or 33 bond) linkages. Chemical coupling of the amine and carboxylate groups in designed strands resulted in the formation of an amide bond. Coupling efficiency as a function of trajectory distance between the individual linker components was examined. For those nucleotides capable of forming inter-strand cross-links (ICLs), coupling yields were found to depend on temperature, distance, and linker length, enabling several approaches that can control regioselective linkage. In the most favorable cases, the coupling yields are quantitative. Spectroscopic measurements of strands that were chemically cross-linked indicate that the global structure of the DNA duplex does not appear to be distorted from the B form after coupling. Thermal denaturing profiles of those strands were shifted to somewhat higher temperatures than those of their respective control duplexes. Thus, the robust amide ICLs formed by this approach are site-specific, do not destabilize the rest of the duplex, and only minimally perturb the secondary structure.
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Affiliation(s)
- Miao Ye
- Department of Chemistry, New York University, New York, NY 10003, USA. Fax: +1 212 995 4367; Tel: +1 212 998 8422
| | - Johan Guillaume
- Department of Chemistry, New York University, New York, NY 10003, USA. Fax: +1 212 995 4367; Tel: +1 212 998 8422
| | - Yu Liu
- Department of Chemistry, New York University, New York, NY 10003, USA. Fax: +1 212 995 4367; Tel: +1 212 998 8422
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY 10003, USA. Fax: +1 212 995 4367; Tel: +1 212 998 8422
| | - Risheng Wang
- Department of Chemistry, New York University, New York, NY 10003, USA. Fax: +1 212 995 4367; Tel: +1 212 998 8422
| | - Nadrian C. Seeman
- Department of Chemistry, New York University, New York, NY 10003, USA. Fax: +1 212 995 4367; Tel: +1 212 998 8422
| | - James W. Canary
- Department of Chemistry, New York University, New York, NY 10003, USA. Fax: +1 212 995 4367; Tel: +1 212 998 8422
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Kunishima M, Ujigawa T, Nagaoka Y, Kawachi C, Hioki K, Shiro M. Study on 1,3,5-triazine chemistry in dehydrocondensation: gauche effect on the generation of active triazinylammonium species. Chemistry 2012; 18:15856-67. [PMID: 23059753 DOI: 10.1002/chem.201202236] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Indexed: 01/09/2023]
Abstract
The reaction of 2-chloro-4,6-dimethoxy-1,3,5-triazine (CDMT) with various nitrogen-containing compounds, particularly tertiary amines (tert-amines), has been studied for the preparation of 2-(4,6-dimethoxy-1,3,5-triazinyl)trialkylammonium salts [DMT-Am(s)]. DMT-Ams derived from aliphatic tert-amines exhibited activity for the dehydrocondensation between a carboxylic acid and an amine to form an amide in a model reaction. Based on a conformational analysis of DMT-Ams and tert-amines by NMR and X-ray diffraction methods, we concluded that a β-alkyl group maintained in a gauche relationship with the nitrogen lone pair of tert-amines significantly hinders the approach of CDMT to the nitrogen. Thus, trimethylamine and quinuclidine without such alkyl groups readily react with CDMT whereas triethylamine, possessing two or three such gauche β-alkyl groups in the stable conformations, does not react at all. The theory of "gauche β-alkyl group effect" proposed here provides useful guidelines for the preparation of DMT-Ams possessing various tertiary amine moieties. An investigation of the dehydrocondensation activity of tert-amines in a CDMT/tert-amine system that involves in situ generation of DMT-Am, showed that the gauche effect of the β-alkyl group becomes quite pronounced; the yield of the amide decreases significantly with tert-amines possessing an unavoidable gauche β-alkyl group. Thus, the tert-amine/CDMT systems are useful for judging whether tert-amines can readily react with CDMT without isolation of DMT-Ams.
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Affiliation(s)
- Munetaka Kunishima
- Faculty of Pharmaceutical Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Japan.
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Liu Y, Wang R, Ding L, Sha R, Seeman NC, Canary JW. Templated synthesis of nylon nucleic acids and characterization by nuclease digestion. Chem Sci 2012; 3:1930-1937. [PMID: 23125913 PMCID: PMC3486707 DOI: 10.1039/c2sc20129a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Nylon nucleic acids containing oligouridine nucleotides with pendent polyamide linkers and flanked by unmodified heteronucleotide sequences were prepared by DNA templated synthesis. Templation was more efficient than the single-stranded synthesis: Coupling step yields were as high as 99.2%, with up to 7 amide linkages formed in the synthesis of a molecule containing 8 modified nucleotides. Controlled digestion by calf spleen phosphodiesterase enabled the mapping of modified nucleotides in the sequences. A combination of complete degradation of nylon nucleic acids by snake venom phosphodiesterase and dephosphorylation of the resulting nucleotide fragments by bacterial alkaline phosphatase, followed by LCMS analysis, clarified the linear structure of the oligo-amide linkages. The templated synthesis strategy afforded nylon nucleic acids in the target structure and was compatible with the presence heteronucleotides. The complete digestion procedure produced a new species of DNA analogues, nylon ribonucleosides, which display nucleosides attached via a 2'-alkylthio linkage to each diamine and dicarboxylate repeat unit of the original nylon nucleic acids. The binding affinity of a nylon ribonucleoside octamer to the complementary DNA was evaluated by thermal denaturing experiments. The octamer was found to form stable duplexes with an inverse dependence on salt concentration, in contrast to the salt-dependent DNA control.
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Affiliation(s)
- Yu Liu
- Department of Chemistry, New York University, New York, NY 10003, USA, Fax: +1 212 995 4367; Tel: +1 212998 8422
| | - Risheng Wang
- Department of Chemistry, New York University, New York, NY 10003, USA, Fax: +1 212 995 4367; Tel: +1 212998 8422
| | - Liang Ding
- Department of Chemistry, New York University, New York, NY 10003, USA, Fax: +1 212 995 4367; Tel: +1 212998 8422
| | - Roujie Sha
- Department of Chemistry, New York University, New York, NY 10003, USA, Fax: +1 212 995 4367; Tel: +1 212998 8422
| | - Nadrian C. Seeman
- Department of Chemistry, New York University, New York, NY 10003, USA, Fax: +1 212 995 4367; Tel: +1 212998 8422
| | - James W. Canary
- Department of Chemistry, New York University, New York, NY 10003, USA, Fax: +1 212 995 4367; Tel: +1 212998 8422
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Single strand DNA catenane synthesis using the formation of G-quadruplex structure. Bioorg Med Chem 2012; 20:2030-4. [DOI: 10.1016/j.bmc.2012.01.040] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 01/24/2012] [Accepted: 01/25/2012] [Indexed: 11/21/2022]
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40
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Elbaz J, Wang ZG, Wang F, Willner I. Programmed Dynamic Topologies in DNA Catenanes. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201107591] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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41
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Elbaz J, Wang ZG, Wang F, Willner I. Programmed Dynamic Topologies in DNA Catenanes. Angew Chem Int Ed Engl 2012; 51:2349-53. [DOI: 10.1002/anie.201107591] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 12/06/2011] [Indexed: 01/02/2023]
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Cao PF, Bunha A, Mangadlao J, Felipe MJ, Mongcopa KI, Advincula R. A supramolecularly templated catenane initiator and a controlled ring expansion strategy. Chem Commun (Camb) 2012; 48:12094-6. [DOI: 10.1039/c2cc35588d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Abstract
Guanine-rich DNA, which is widely distributed in the human genome, can fold into a supramolecular structure called the G-wire. The G-wire possesses promising characteristics as a functional element for various applications in vitro and in vivo. Here, we describe the preparative procedures for the G-wire and signatures of G-wire formation. Procedures for the regulation of G-wire formation by chemical stimuli will be useful for in vivo and in vitro applications.
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Affiliation(s)
- Daisuke Miyoshi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), and Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Kobe, Japan
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Sugai N, Heguri H, Ohta K, Meng Q, Yamamoto T, Tezuka Y. Effective Click Construction of Bridged- and Spiro-Multicyclic Polymer Topologies with Tailored Cyclic Prepolymers (kyklo-Telechelics). J Am Chem Soc 2010; 132:14790-802. [DOI: 10.1021/ja103402c] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Naoto Sugai
- Department of Organic and Polymeric Materials, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Hiroyuki Heguri
- Department of Organic and Polymeric Materials, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Kengo Ohta
- Department of Organic and Polymeric Materials, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Qingyuan Meng
- Department of Organic and Polymeric Materials, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Takuya Yamamoto
- Department of Organic and Polymeric Materials, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Yasuyuki Tezuka
- Department of Organic and Polymeric Materials, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
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Ishikawa K, Yamamoto T, Asakawa M, Tezuka Y. Effective Synthesis of Polymer Catenanes by Cooperative Electrostatic/Hydrogen-Bonding Self-Assembly and Covalent Fixation. Macromolecules 2009. [DOI: 10.1021/ma902031j] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Kazuyuki Ishikawa
- Department of Organic and Polymeric Materials, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Takuya Yamamoto
- Department of Organic and Polymeric Materials, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Masumi Asakawa
- Nanotube Research Center, National Instutute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Yasuyuki Tezuka
- Department of Organic and Polymeric Materials, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
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Andersen CS, Knudsen MM, Chhabra R, Liu Y, Yan H, Gothelf KV. Distance dependent interhelical couplings of organic rods incorporated in DNA 4-helix bundles. Bioconjug Chem 2009; 20:1538-46. [PMID: 19572635 PMCID: PMC3412156 DOI: 10.1021/bc900078c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The synthesis of a conjugated linear organic module containing terminal salicylaldehyde groups and a central activated ester, designed for conjugation to amino-modified oligonucleotides, is presented. The organic module has a phenylene-ethynylene backbone and is highly fluorescent. It is conjugated to oligonucleotide sequences and incorporated into specific locations in a well-defined DNA 4-helix bundle (4-HB). The DNA-nanostructure offers precise location control of the organic modules which allows for selective interhelical coupling reactions. In this study, metal-salen formation as well as dihydrazone formation are used to covalently interlink the organic modules. Both coupling reactions are highly dependent on the distances between the organic modules in the 4-HB. Neighboring modules dimerize easier, whereas more distanced modules are less prone to react, even when the linkers are extended. The dimeric products are characterized by denaturing polyacrylamide gel electrophoresis (PAGE), high performance liquid chromatography (HPLC), and matrix assisted laser desorption/absorption ionization time-of-flight (MALDI TOF) mass spectrometry.
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Affiliation(s)
- Casper S. Andersen
- Danish National Research Foundation: Centre for DNA Nanotechnology, Department of Chemistry and Interdisciplinary Nanoscience Center at Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark. Fax: +45 8619 6199; Tel:+45 89423907; Homepage: http://www.cdna.dk
| | - Martin M. Knudsen
- Danish National Research Foundation: Centre for DNA Nanotechnology, Department of Chemistry and Interdisciplinary Nanoscience Center at Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark. Fax: +45 8619 6199; Tel:+45 89423907; Homepage: http://www.cdna.dk
| | - Rahul Chhabra
- Department of Chemistry and Biochemistry & The Biodesign Institute, Arizona State University, Tempe, Az, 85287 (USA)
| | - Yan Liu
- Department of Chemistry and Biochemistry & The Biodesign Institute, Arizona State University, Tempe, Az, 85287 (USA)
| | - Hao Yan
- Department of Chemistry and Biochemistry & The Biodesign Institute, Arizona State University, Tempe, Az, 85287 (USA)
| | - Kurt V. Gothelf
- Danish National Research Foundation: Centre for DNA Nanotechnology, Department of Chemistry and Interdisciplinary Nanoscience Center at Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark. Fax: +45 8619 6199; Tel:+45 89423907; Homepage: http://www.cdna.dk
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