151
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Meng FN, Li ZY, Ying YL, Liu SC, Zhang J, Long YT. Structural stability of the photo-responsive DNA duplexes containing one azobenzene via a confined pore. Chem Commun (Camb) 2017; 53:9462-9465. [DOI: 10.1039/c7cc04599a] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Herein, the structural stability of single azobenzene modified DNA duplexes, including the trans form and cis form, has been examined separately based on their distinguishable unzipping kinetics from the mixture by an α-hemolysin nanopore.
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Affiliation(s)
- Fu-Na Meng
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering
- Shanghai
- China
| | - Zi-Yuan Li
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering
- Shanghai
- China
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering
- Shanghai
- China
| | - Shao-Chuang Liu
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering
- Shanghai
- China
| | - Junji Zhang
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering
- Shanghai
- China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering
- Shanghai
- China
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152
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Design of photofunctional oligonucleotides by copolymerization of natural nucleobases with base surrogates prepared from acyclic scaffolds. Polym J 2016. [DOI: 10.1038/pj.2016.120] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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153
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Murayama K, Asanuma H. Effect of Methyl Group on Acyclic Serinol Scaffold for Tethering Dyes on the DNA Duplex Stability. Chembiochem 2016; 18:142-149. [DOI: 10.1002/cbic.201600558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Keiji Murayama
- Graduate School of Engineering; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8603 Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8603 Japan
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154
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Li P, Xie G, Kong XY, Zhang Z, Xiao K, Wen L, Jiang L. Light-Controlled Ion Transport through Biomimetic DNA-Based Channels. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201609161] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Pei Li
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education School of Chemistry and Environment; Beihang University; Beijing 100191 P.R. China
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science; Technical Institute of Physics and Chemistry; Chinese Academy of Sciences; Beijing 100190 P.R. China
| | - Ganhua Xie
- Beijing National Laboratory for Molecular Sciences (BNLMS); Key Laboratory of Green Printing; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 P.R. China
- University of Chinese Academy of Sciences; Beijing 100049 P.R. China
| | - Xiang-Yu Kong
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science; Technical Institute of Physics and Chemistry; Chinese Academy of Sciences; Beijing 100190 P.R. China
- University of Chinese Academy of Sciences; Beijing 100049 P.R. China
| | - Zhen Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS); Key Laboratory of Green Printing; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 P.R. China
- University of Chinese Academy of Sciences; Beijing 100049 P.R. China
| | - Kai Xiao
- Beijing National Laboratory for Molecular Sciences (BNLMS); Key Laboratory of Green Printing; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 P.R. China
- University of Chinese Academy of Sciences; Beijing 100049 P.R. China
| | - Liping Wen
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science; Technical Institute of Physics and Chemistry; Chinese Academy of Sciences; Beijing 100190 P.R. China
- University of Chinese Academy of Sciences; Beijing 100049 P.R. China
| | - Lei Jiang
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education School of Chemistry and Environment; Beihang University; Beijing 100191 P.R. China
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science; Technical Institute of Physics and Chemistry; Chinese Academy of Sciences; Beijing 100190 P.R. China
- University of Chinese Academy of Sciences; Beijing 100049 P.R. China
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155
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Li P, Xie G, Kong XY, Zhang Z, Xiao K, Wen L, Jiang L. Light-Controlled Ion Transport through Biomimetic DNA-Based Channels. Angew Chem Int Ed Engl 2016; 55:15637-15641. [DOI: 10.1002/anie.201609161] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Indexed: 01/23/2023]
Affiliation(s)
- Pei Li
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education School of Chemistry and Environment; Beihang University; Beijing 100191 P.R. China
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science; Technical Institute of Physics and Chemistry; Chinese Academy of Sciences; Beijing 100190 P.R. China
| | - Ganhua Xie
- Beijing National Laboratory for Molecular Sciences (BNLMS); Key Laboratory of Green Printing; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 P.R. China
- University of Chinese Academy of Sciences; Beijing 100049 P.R. China
| | - Xiang-Yu Kong
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science; Technical Institute of Physics and Chemistry; Chinese Academy of Sciences; Beijing 100190 P.R. China
- University of Chinese Academy of Sciences; Beijing 100049 P.R. China
| | - Zhen Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS); Key Laboratory of Green Printing; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 P.R. China
- University of Chinese Academy of Sciences; Beijing 100049 P.R. China
| | - Kai Xiao
- Beijing National Laboratory for Molecular Sciences (BNLMS); Key Laboratory of Green Printing; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 P.R. China
- University of Chinese Academy of Sciences; Beijing 100049 P.R. China
| | - Liping Wen
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science; Technical Institute of Physics and Chemistry; Chinese Academy of Sciences; Beijing 100190 P.R. China
- University of Chinese Academy of Sciences; Beijing 100049 P.R. China
| | - Lei Jiang
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education School of Chemistry and Environment; Beihang University; Beijing 100191 P.R. China
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science; Technical Institute of Physics and Chemistry; Chinese Academy of Sciences; Beijing 100190 P.R. China
- University of Chinese Academy of Sciences; Beijing 100049 P.R. China
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156
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Rossetti M, Ranallo S, Idili A, Palleschi G, Porchetta A, Ricci F. Allosteric DNA nanoswitches for controlled release of a molecular cargo triggered by biological inputs. Chem Sci 2016; 8:914-920. [PMID: 28572901 PMCID: PMC5452262 DOI: 10.1039/c6sc03404g] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/03/2016] [Indexed: 12/14/2022] Open
Abstract
A rationally designed new class of DNA-based nanoswitches allosterically regulated by specific biological targets, antibodies and transcription factors, can load and release a molecular cargo in a controlled fashion.
Here we demonstrate the rational design of a new class of DNA-based nanoswitches which are allosterically regulated by specific biological targets, antibodies and transcription factors, and are able to load and release a molecular cargo (i.e. doxorubicin) in a controlled fashion. In our first model system we rationally designed a stem-loop DNA-nanoswitch that adopts two mutually exclusive conformations: a “Load” conformation containing a doxorubicin-intercalating domain and a “Release” conformation containing a duplex portion recognized by a specific transcription-factor (here Tata Binding Protein). The binding of the transcription factor pushes this conformational equilibrium towards the “Release” state thus leading to doxorubicin release from the nanoswitch. In our second model system we designed a similar stem-loop DNA-nanoswitch for which conformational change and subsequent doxorubicin release can be triggered by a specific antibody. Our approach augments the current tool kit of smart drug release mechanisms regulated by different biological inputs.
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Affiliation(s)
- Marianna Rossetti
- Chemistry Department , University of Rome Tor Vergata , Via della Ricerca Scientifica , Rome 00133 , Italy . ;
| | - Simona Ranallo
- Chemistry Department , University of Rome Tor Vergata , Via della Ricerca Scientifica , Rome 00133 , Italy . ;
| | - Andrea Idili
- Chemistry Department , University of Rome Tor Vergata , Via della Ricerca Scientifica , Rome 00133 , Italy . ;
| | - Giuseppe Palleschi
- Chemistry Department , University of Rome Tor Vergata , Via della Ricerca Scientifica , Rome 00133 , Italy . ;
| | - Alessandro Porchetta
- Chemistry Department , University of Rome Tor Vergata , Via della Ricerca Scientifica , Rome 00133 , Italy . ;
| | - Francesco Ricci
- Chemistry Department , University of Rome Tor Vergata , Via della Ricerca Scientifica , Rome 00133 , Italy . ;
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157
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Probst M, Aeschimann W, Chau TTH, Langenegger SM, Stocker A, Häner R. Structural insight into DNA-assembled oligochromophores: crystallographic analysis of pyrene- and phenanthrene-modified DNA in complex with BpuJI endonuclease. Nucleic Acids Res 2016; 44:7079-89. [PMID: 27422870 PMCID: PMC5009758 DOI: 10.1093/nar/gkw644] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 07/07/2016] [Accepted: 07/08/2016] [Indexed: 01/13/2023] Open
Abstract
The use of the DNA duplex as a supramolecular scaffold is an established approach for the assembly of chromophore aggregates. In the absence of detailed structural insight, the characterization of thus assembled oligochromophores is, today, largely based on solution-phase spectroscopy. Here, we describe the crystal structures of three DNA-organized chromophore aggregates. DNA hybrids containing non-nucleosidic pyrene and phenanthrene building blocks were co-crystallized with the recently described binding domain of the restriction enzyme BpuJI. Crystal structures of these complexes were determined at 2.7, 1.9 and 1.6 Å resolutions. The structures reveal aromatic stacking interactions between pyrene and/or phenanthrene units within the framework of the B-DNA duplex. In hybrids containing a single modification in each DNA strand near the end of the duplex, the two polyaromatic hydrocarbons are engaged in a face-to-face stacking orientation. Due to crystal packing and steric effects, the terminal GC base pair is disrupted in all three crystal structures, which results in a non-perfect stacking arrangement of the aromatic chromophores in two of the structures. In a hybrid containing a total of three pyrenes, crystal lattice induced end-to-end stacking of individual DNA duplexes leads to the formation of an extended aromatic π-stack containing four co-axially arranged pyrenes. The aromatic planes of the stacked pyrenes are oriented in a parallel way. The study demonstrates the value of co-crystallization of chemically modified DNA with the recombinant binding domain of the restriction enzyme BpuJI for obtaining detailed structural insight into DNA-assembled oligochromophores.
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Affiliation(s)
- Markus Probst
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Walter Aeschimann
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Thi T H Chau
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Simon M Langenegger
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Achim Stocker
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Robert Häner
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
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158
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Nakasone Y, Ooi H, Kamiya Y, Asanuma H, Terazima M. Dynamics of Inter-DNA Chain Interaction of Photoresponsive DNA. J Am Chem Soc 2016; 138:9001-4. [DOI: 10.1021/jacs.6b02525] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yusuke Nakasone
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | | | | | | | - Masahide Terazima
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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159
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Jiménez-Sánchez A, Santillan R. A photochromic-acidochromic HCl fluorescent probe. An unexpected chloride-directed recognition. Analyst 2016; 141:4108-20. [PMID: 27156709 DOI: 10.1039/c6an00509h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Non-classical protomerism of Schiff bases offers several advantages; for example, specific interactions in the -C[double bond, length as m-dash]N- linkage can be controlled and differentiated because the interactions are not governed by keto-enol tautomerism. Herein, the pH sensing properties of a new protomeric Schiff base probe () are reported. In particular, among several acids, the probe displays significant optical responses upon interaction with hydrochloric acid (HCl). X-ray structural analysis confirmed the existence of an intermolecular interaction with HCl through a -C[double bond, length as m-dash]NH-ClO- linkage. Moreover, an optical response via a second channel is manifested as photochromic fluorescence behavior. The properties of were investigated by UV-vis and fluorescence spectroscopy in a solution and the solid state. Its strong acidofluorochromic behavior was analyzed and its pKa and values were determined, which revealed a photobasic character. Positive solvatochromism that resulted from specific interactions taking place in was studied using four different solvent scales, namely, Lippert-Mataga, Kamlet-Taft, Catalán and the recently proposed scale of Laurence et al., which yielded consistent results. Finally, theoretical calculations were conducted to analyze the mechanism of the probe in terms of natural transition orbitals (NTOs) and the spatial extent of charge transfer excitations.
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Affiliation(s)
- Arturo Jiménez-Sánchez
- Facultad de Química, Universidad Nacional Autónoma de México, México, D. F. 04510, México.
| | - Rosa Santillan
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del IPN, CINVESTAV, Apdo. Postal 14-740, México, D. F. 07000, México
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160
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Doi T, Kawai H, Murayama K, Kashida H, Asanuma H. Visible-Light-Triggered Cross-Linking of DNA Duplexes by Reversible [2+2] Photocycloaddition of Styrylpyrene. Chemistry 2016; 22:10533-8. [DOI: 10.1002/chem.201602006] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Tetsuya Doi
- Graduate School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Hayato Kawai
- Graduate School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Keiji Murayama
- Graduate School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Hiromu Kashida
- Graduate School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
- PRESTO (Japan) Science and Technology Agency; 4-1-8 Honcho, Kawaguchi Saitama 332-0012 Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
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161
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Deo C, Bogliotti N, Métivier R, Retailleau P, Xie J. A Visible-Light-Triggered Conformational Diastereomer Photoswitch in a Bridged Azobenzene. Chemistry 2016; 22:9092-6. [DOI: 10.1002/chem.201601400] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Claire Deo
- PPSM, ENS Cachan, CNRS; Université Paris-Saclay; 94235 Cachan France
| | - Nicolas Bogliotti
- PPSM, ENS Cachan, CNRS; Université Paris-Saclay; 94235 Cachan France
| | - Rémi Métivier
- PPSM, ENS Cachan, CNRS; Université Paris-Saclay; 94235 Cachan France
| | - Pascal Retailleau
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301; Univ. Paris-Sud, Université Paris-Saclay; Gif-Sur-Yvette 91198 France
| | - Juan Xie
- PPSM, ENS Cachan, CNRS; Université Paris-Saclay; 94235 Cachan France
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162
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Kasyanenko N, Lysyakova L, Ramazanov R, Nesterenko A, Yaroshevich I, Titov E, Alexeev G, Lezov A, Unksov I. Conformational and phase transitions in DNA--photosensitive surfactant solutions: Experiment and modeling. Biopolymers 2016; 103:109-22. [PMID: 25302479 DOI: 10.1002/bip.22575] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 10/07/2014] [Accepted: 10/07/2014] [Indexed: 01/17/2023]
Abstract
DNA binding to trans- and cis-isomers of azobenzene containing cationic surfactant in 5 mM NaCl solution was investigated by the methods of dynamic light scattering (DLS), low-gradient viscometry (LGV), atomic force microscopy (AFM), circular dichroism (CD), gel electrophoresis (GE), flow birefringence (FB), UV-Vis spectrophotometry. Light-responsive conformational transitions of DNA in complex with photosensitive surfactant, changes in DNA optical anisotropy and persistent length, phase transition of DNA into nanoparticles induced by high surfactant concentration, as well as transformation of surfactant conformation under its binding to macromolecule were studied. Computer simulations of micelles formation for cis- and trans-isomers of azobenzene containing surfactant, as well as DNA-surfactant interaction, were carried out. Phase diagram for DNA-surfactant solutions was designed. The possibility to reverse the DNA packaging induced by surfactant binding with the dilution and light irradiation was shown.
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Affiliation(s)
- N Kasyanenko
- Faculty of Physics, Department of Molecular Biophysics, Saint Petersburg State University, Petrodvorets, Ulyanovskaya str. 1, 198504, St. Petersburg, Russia
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163
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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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164
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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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165
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Jiang H, Pan V, Vivek S, Weeks ER, Ke Y. Programmable DNA Hydrogels Assembled from Multidomain DNA Strands. Chembiochem 2016; 17:1156-62. [PMID: 26888015 DOI: 10.1002/cbic.201500686] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Indexed: 01/09/2023]
Abstract
Hydrogels are important in biological and medical applications, such as drug delivery and tissue engineering. DNA hydrogels have attracted significant attention due to the programmability and biocompatibility of the material. We developed a series of low-cost one-strand DNA hydrogels self-assembled from single-stranded DNA monomers containing multiple palindromic domains. This new hydrogel design is simple and programmable. Thermal stability, mechanical properties, and loading capacity of these one-strand DNA hydrogels can be readily regulated by simply adjusting the DNA domains.
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Affiliation(s)
- Huiling Jiang
- Wallace H. Coulter Department of Biomedical Engineering, Emory School of Medicine, 1760 Haygood Drive, Atlanta, Georgia, 30322, USA
| | - Victor Pan
- Wallace H. Coulter Department of Biomedical Engineering, Emory School of Medicine, 1760 Haygood Drive, Atlanta, Georgia, 30322, USA
| | - Skanda Vivek
- Emory University, Department of Physics, 400 Dowman Drive, Atlanta, GA, 30322-2430, USA
| | - Eric R Weeks
- Emory University, Department of Physics, 400 Dowman Drive, Atlanta, GA, 30322-2430, USA
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Emory School of Medicine, 1760 Haygood Drive, Atlanta, Georgia, 30322, USA.
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166
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Uematsu R, Inagaki M, Asai M, Sugai H, Maeda Y, Nagami A, Sato H, Sakamoto S, Araki Y, Nishijima M, Inoue Y, Wada T. Module Strategy for Peptide Ribonucleic Acid (PRNA)–DNA and PRNA–Peptide Nucleic Acid (PNA)–DNA Chimeras: Synthesis and Interaction of Chimeras with DNA and RNA. CHEM LETT 2016. [DOI: 10.1246/cl.151157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Ryohei Uematsu
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University
| | - Masahito Inagaki
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University
| | - Mitsuo Asai
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University
| | - Hiroka Sugai
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University
| | | | - Akira Nagami
- Department of Applied Chemistry, Osaka University
| | | | - Seiji Sakamoto
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University
| | - Yasuyuki Araki
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University
| | | | | | - Takehiko Wada
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University
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167
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Abstract
The past quarter of a century has witnessed an increasing engagement on the part of physicists and chemists in the design and synthesis of molecular machines de novo. This minireview traces the development of artificial molecular machines from their prototypes in the form of shuttles and switches to their emergence as motors and pumps where supplies of energy in the form of chemical fuel, electrochemical potential and light activation become a minimum requirement for them to function away from equilibrium. The challenge facing this rapidly growing community of scientists and engineers today is one of putting wholly synthetic molecules to work, both individually and as collections. Here, we highlight some of the recent conceptual and practical advances relating to the operation of wholly synthetic rotary and linear motors.
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Affiliation(s)
- Chuyang Cheng
- Department of Chemistry, Northwestern University, 2145 Sheridan Rd., Evanston, IL, 60208, USA
| | - J Fraser Stoddart
- Department of Chemistry, Northwestern University, 2145 Sheridan Rd., Evanston, IL, 60208, USA.
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168
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Ariga K, Li J, Fei J, Ji Q, Hill JP. Nanoarchitectonics for Dynamic Functional Materials from Atomic-/Molecular-Level Manipulation to Macroscopic Action. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:1251-86. [PMID: 26436552 DOI: 10.1002/adma.201502545] [Citation(s) in RCA: 291] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 07/27/2015] [Indexed: 05/21/2023]
Abstract
Objects in all dimensions are subject to translational dynamism and dynamic mutual interactions, and the ability to exert control over these events is one of the keys to the synthesis of functional materials. For the development of materials with truly dynamic functionalities, a paradigm shift from "nanotechnology" to "nanoarchitectonics" is proposed, with the aim of design and preparation of functional materials through dynamic harmonization of atomic-/molecular-level manipulation and control, chemical nanofabrication, self-organization, and field-controlled organization. Here, various examples of dynamic functional materials are presented from the atom/molecular-level to macroscopic dimensions. These systems, including atomic switches, molecular machines, molecular shuttles, motional crystals, metal-organic frameworks, layered assemblies, gels, supramolecular assemblies of biomaterials, DNA origami, hollow silica capsules, and mesoporous materials, are described according to their various dynamic functions, which include short-term plasticity, long-term potentiation, molecular manipulation, switchable catalysis, self-healing properties, supramolecular chirality, morphological control, drug storage and release, light-harvesting, mechanochemical transduction, molecular tuning molecular recognition, hand-operated nanotechnology.
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Affiliation(s)
- Katsuhiko Ariga
- World Premier International (WPI) Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, 305-0044, Japan
| | - Junbai Li
- Beijing National Laboratory for Molecular Science, CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Science, Beijing, 100190, P. R. China
| | - Jinbo Fei
- Beijing National Laboratory for Molecular Science, CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Science, Beijing, 100190, P. R. China
| | - Qingmin Ji
- World Premier International (WPI) Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, 305-0044, Japan
| | - Jonathan P Hill
- World Premier International (WPI) Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, 305-0044, Japan
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169
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A light-driven three-dimensional plasmonic nanosystem that translates molecular motion into reversible chiroptical function. Nat Commun 2016; 7:10591. [PMID: 26830310 PMCID: PMC4740900 DOI: 10.1038/ncomms10591] [Citation(s) in RCA: 191] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 01/02/2016] [Indexed: 12/23/2022] Open
Abstract
Nature has developed striking light-powered proteins such as bacteriorhodopsin, which can convert light energy into conformational changes for biological functions. Such natural machines are a great source of inspiration for creation of their synthetic analogues. However, synthetic molecular machines typically operate at the nanometre scale or below. Translating controlled operation of individual molecular machines to a larger dimension, for example, to 10-100 nm, which features many practical applications, is highly important but remains challenging. Here we demonstrate a light-driven plasmonic nanosystem that can amplify the molecular motion of azobenzene through the host nanostructure and consequently translate it into reversible chiroptical function with large amplitude modulation. Light is exploited as both energy source and information probe. Our plasmonic nanosystem bears unique features of optical addressability, reversibility and modulability, which are crucial for developing all-optical molecular devices with desired functionalities.
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170
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Morihiro K, Hasegawa O, Mori S, Tsunoda S, Obika S. C5-azobenzene-functionalized locked nucleic acid uridine: isomerization properties, hybridization ability, and enzymatic stability. Org Biomol Chem 2016; 13:5209-14. [PMID: 25853508 DOI: 10.1039/c5ob00477b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Oligonucleotides (ONs) modified with a locked nucleic acid (LNA) are widely used in the fields of therapeutics, diagnosis, and nanotechnology. There have been significant efforts towards developing LNA analogues bearing modified bridges to improve their hybridization ability, nuclease resistance, and pharmacokinetic profiles. Moreover, nucleobase modifications of LNA are useful strategies for the functionalization of ONs. Modifications of the C5-position of pyrimidine nucleobases are particularly interesting because they enable predictable positioning of functional groups in the major groove of the duplex. Here we report the synthesis of C5-azobenzene-functionalized LNA uridine (LNA-U(Az)) and properties of LNA-U(Az)-modified ONs, including isomerization properties, hybridization ability, and enzyme stability. LNA-U(Az) in ON is photo-isomerized effectively and reversibly by irradiation at 365 nm (trans to cis) and 450 nm (cis to trans). LNA-U(Az)-modified ONs show RNA-selective hybridization ability despite the large hydrophobic azobenzene moiety extending into the major groove of the duplex. The enzymatic stability of LNA-U(Az)-modified ONs is higher than that of natural and LNA-modified ONs with or without photo-irradiation. Our results indicate that LNA-U(Az) holds promise for RNA targeting and photo-switchable technologies.
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Affiliation(s)
- K Morihiro
- National Institute of Biomedical Innovation (NIBIO), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan.
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171
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Wang A, Shi W, Huang J, Yan Y. Adaptive soft molecular self-assemblies. SOFT MATTER 2016; 12:337-357. [PMID: 26509717 DOI: 10.1039/c5sm02397a] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Adaptive molecular self-assemblies provide possibility of constructing smart and functional materials in a non-covalent bottom-up manner. Exploiting the intrinsic properties of responsiveness of non-covalent interactions, a great number of fancy self-assemblies have been achieved. In this review, we try to highlight the recent advances in this field. The following contents are focused: (1) environmental adaptiveness, including smart self-assemblies adaptive to pH, temperature, pressure, and moisture; (2) special chemical adaptiveness, including nanostructures adaptive to important chemicals, such as enzymes, CO2, metal ions, redox agents, explosives, biomolecules; (3) field adaptiveness, including self-assembled materials that are capable of adapting to external fields such as magnetic field, electric field, light irradiation, and shear forces.
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Affiliation(s)
- Andong Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Wenyue Shi
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Jianbin Huang
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Yun Yan
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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172
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Wu J, Yu F, Zhang Z, Chen Y, Du J. Highly sensitive self-complementary DNA nanoswitches triggered by polyelectrolytes. NANOSCALE 2016; 8:464-470. [PMID: 26627445 DOI: 10.1039/c5nr05193b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Dimerization of two homologous strands of genomic DNA/RNA is an essential feature of retroviral replication. Herein we show that a cationic comb-type copolymer (CCC), poly(L-lysine)-graft-dextran, accelerates the dimerization of self-complementary stem-loop DNA, frequently found in functional DNA/RNA molecules, such as aptamers. Furthermore, an anionic polymer poly(sodium vinylsulfonate) (PVS) dissociates CCC from the duplex shortly within a few seconds. Then single stem-loop DNA spontaneously transforms from its dimer. Thus we can easily control the dimer and stem-loop DNA by switching on/off CCC activity. Both polyelectrolytes and DNA concentrations are in the nanomole per liter range. The polyelectrolyte-assisted transconformation and sequences design strategy ensures the reversible state control with rapid response and effective switching under physiologically relevant conditions. A further application of this sensitive assembly is to construct an aptamer-type drug delivery system, bind or release functional molecules responding to its transconformation.
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Affiliation(s)
- Jincai Wu
- College of Materials and Chemistry Engineering, Hainan University, Haikou 570228, China.
| | - Feng Yu
- College of Materials and Chemistry Engineering, Hainan University, Haikou 570228, China.
| | - Zheng Zhang
- College of Materials and Chemistry Engineering, Hainan University, Haikou 570228, China.
| | - Yong Chen
- College of Materials and Chemistry Engineering, Hainan University, Haikou 570228, China.
| | - Jie Du
- College of Materials and Chemistry Engineering, Hainan University, Haikou 570228, China.
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173
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Wang X, Liang X. Azobenzene-modified antisense oligonucleotides for site-specific cleavage of RNA with photocontrollable property. RSC Adv 2016. [DOI: 10.1039/c6ra20954h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Photoresponsive azobenzene-modified antisense oligonucleotides for site-specific RNA cleavage by RNase H.
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Affiliation(s)
- Xingyu Wang
- School of Food Science and Engineering
- Ocean University of China
- Qingdao
- China
- College of Food Engineering and Nutritional Science
| | - Xingguo Liang
- School of Food Science and Engineering
- Ocean University of China
- Qingdao
- China
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174
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Photocontrolled micellar aggregation of amphiphilic DNA-azobenzene conjugates. Colloids Surf B Biointerfaces 2015; 135:126-132. [DOI: 10.1016/j.colsurfb.2015.07.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 07/05/2015] [Indexed: 11/16/2022]
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175
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Goldau T, Murayama K, Brieke C, Asanuma H, Heckel A. Azobenzene C-Nucleosides for Photocontrolled Hybridization of DNA at Room Temperature. Chemistry 2015; 21:17870-6. [DOI: 10.1002/chem.201503303] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Indexed: 12/26/2022]
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176
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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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177
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Kim K, Guo J, Xu X, Fan DL. Recent Progress on Man-Made Inorganic Nanomachines. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:4037-4057. [PMID: 26114572 DOI: 10.1002/smll.201500407] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 04/17/2015] [Indexed: 06/04/2023]
Abstract
The successful development of nanoscale machinery, which can operate with high controllability, high precision, long lifetimes, and tunable driving powers, is pivotal for the realization of future intelligent nanorobots, nanofactories, and advanced biomedical devices. However, the development of nanomachines remains one of the most difficult research areas, largely due to the grand challenges in fabrication of devices with complex components and actuation with desired efficiency, precision, lifetime, and/or environmental friendliness. In this work, the cutting-edge efforts toward fabricating and actuating various types of nanomachines and their applications are reviewed, with a special focus on nanomotors made from inorganic nanoscale building blocks, which are introduced according to the employed actuation mechanism. The unique characteristics and obstacles for each type of nanomachine are discussed, and perspectives and challenges of this exciting field are presented.
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Affiliation(s)
- Kwanoh Kim
- Department of Mechanical Engineering, the University of Texas at Austin, Austin, TX, 78712, USA
| | - Jianhe Guo
- Materials Science and Engineering Program, the University of Texas at Austin, Austin, TX, 78712, USA
| | - Xiaobin Xu
- Materials Science and Engineering Program, the University of Texas at Austin, Austin, TX, 78712, USA
| | - D L Fan
- Department of Mechanical Engineering, the University of Texas at Austin, Austin, TX, 78712, USA
- Materials Science and Engineering Program, the University of Texas at Austin, Austin, TX, 78712, USA
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178
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Zhou J, Guo X, Katz HE, Bragg AE. Molecular Switching via Multiplicity-Exclusive E/Z Photoisomerization Pathways. J Am Chem Soc 2015; 137:10841-50. [PMID: 26258436 DOI: 10.1021/jacs.5b07348] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Mutual exclusivity in the nature of forward and reserve isomerization pathways holds promise for predictably controlling responses of photoswitchable materials according to molecular structure or external stimuli. Herein we have characterized the E/Z photoisomerization mechanisms of the visible-light-triggered switch 1,2-dithienyl-1,2-dicyanoethene (4TCE) in chlorobenzene with ultrafast transient absorption spectroscopy. We observe that switching mechanisms occur exclusively by relaxation through electronic manifolds of different spin multiplicity: trans-to-cis isomerization only occurs via electronic relaxation within the singlet manifold on a time scale of 40 ps; in contrast, cis-to-trans isomerization is not observed above 440 nm, but occurs via two rapid ISC processes into and out of the triplet manifold on time scales of ∼2 ps and 0.4 ns, respectively, when excited at higher energies (e.g., 420 nm). Observation of ultrafast ISC in cis-4TCE is consistent with photoinduced dynamics of related thiophene-based oligomers. Interpretation of the photophysical pathways underlying these isomerization reactions is supported by the observation that cis-to-trans isomerization occurs efficiently via triplet-sensitized energy transfer, whereas trans-to-cis isomerization does not. Quantum-chemical calculations reveal that the T1 potential energy surface is barrierless along the coordinate of the central ethylene dihedral angle (θ) from the cis Franck-Condon region (θ = 175°) to geometries that are within the region of the trans ground-state well; furthermore, the T1 and S1 surfaces cross with a substantial spin-orbital coupling. In total, we demonstrate that E/Z photoswitching of 4TCE operates by multiplicity-exclusive pathways, enabling additional means for tailoring switch performance by manipulating spin-orbit couplings through variations in molecular structure or physical environment.
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Affiliation(s)
- Jiawang Zhou
- Department of Chemistry, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Xin Guo
- Department of Materials Science and Engineering, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Howard E Katz
- Department of Chemistry, Johns Hopkins University , Baltimore, Maryland 21218, United States.,Department of Materials Science and Engineering, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Arthur E Bragg
- Department of Chemistry, Johns Hopkins University , Baltimore, Maryland 21218, United States
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179
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Suzuki Y, Endo M, Sugiyama H. Mimicking membrane-related biological events by DNA origami nanotechnology. ACS NANO 2015; 9:3418-3420. [PMID: 25880224 DOI: 10.1021/acsnano.5b01723] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
One of the potential applications of DNA nanotechnology is the construction of two- or three-dimensional nanostructures that mimic the function of existing biological molecules. In this issue of ACS Nano, Kocabey et al. demonstrate that lipid-bilayer-anchored DNA origami structures can be assembled into prescribed superstructures in a programmed manner. The reported DNA-based artificial system can mimic the dynamic assembly of membrane-associated protein clusters that play an essential role in deformation of cellular membranes.
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Affiliation(s)
- Yuki Suzuki
- †Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
- §CREST, Japan Science and Technology Agency (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Masayuki Endo
- ‡Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
- §CREST, Japan Science and Technology Agency (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, 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
- §CREST, Japan Science and Technology Agency (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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180
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Altavilla SF, Segarra-Martí J, Nenov A, Conti I, Rivalta I, Garavelli M. Deciphering the photochemical mechanisms describing the UV-induced processes occurring in solvated guanine monophosphate. Front Chem 2015; 3:29. [PMID: 25941671 PMCID: PMC4403598 DOI: 10.3389/fchem.2015.00029] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 03/30/2015] [Indexed: 01/17/2023] Open
Abstract
The photophysics and photochemistry of water-solvated guanine monophosphate (GMP) are here characterized by means of a multireference quantum-chemical/molecular mechanics theoretical approach (CASPT2//CASSCF/AMBER) in order to elucidate the main photo-processes occurring upon UV-light irradiation. The effect of the solvent and of the phosphate group on the energetics and structural features of this system are evaluated for the first time employing high-level ab initio methods and thoroughly compared to those in vacuo previously reported in the literature and to the experimental evidence to assess to which extent they influence the photoinduced mechanisms. Solvated electronic excitation energies of solvated GMP at the Franck-Condon (FC) region show a red shift for the ππ(*) La and Lb states, whereas the energy of the oxygen lone-pair nπ(*) state is blue-shifted. The main photoinduced decay route is promoted through a ring-puckering motion along the bright lowest-lying La state toward a conical intersection (CI) with the ground state, involving a very shallow stationary point along the minimum energy pathway in contrast to the barrierless profile found in gas-phase, the point being placed at the end of the minimum energy path (MEP) thus endorsing its ultrafast deactivation in accordance with time-resolved transient and photoelectron spectroscopy experiments. The role of the nπ(*) state in the solvated system is severely diminished as the crossings with the initially populated La state and also with the Lb state are placed too high energetically to partake prominently in the deactivation photo-process. The proposed mechanism present in solvated and in vacuo DNA/RNA chromophores validates the intrinsic photostability mechanism through CI-mediated non-radiative processes accompanying the bright excited-state population toward the ground state and subsequent relaxation back to the FC region.
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Affiliation(s)
| | | | - Artur Nenov
- Dipartimento di Chimica “G. Ciamician,” Università di BolognaBologna, Italy
| | - Irene Conti
- Dipartimento di Chimica “G. Ciamician,” Università di BolognaBologna, Italy
| | - Ivan Rivalta
- École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, UMR 5182, Université de LyonLyon, France
| | - Marco Garavelli
- Dipartimento di Chimica “G. Ciamician,” Università di BolognaBologna, Italy
- École Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, UMR 5182, Université de LyonLyon, France
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181
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Synthesis and Properties of 2'-Deoxyuridine Analogues Bearing Various Azobenzene Derivatives at the C5 Position. CHEMOSENSORS 2015. [DOI: 10.3390/chemosensors3020036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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182
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Guo X, Zhou J, Siegler MA, Bragg AE, Katz HE. Visible‐Light‐Triggered Molecular Photoswitch Based on Reversible
E
/
Z
Isomerization of a 1,2‐Dicyanoethene Derivative. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201410945] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Xin Guo
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218 (USA)
| | - Jiawang Zhou
- Department of Chemistry, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218 (USA)
| | - Maxime A. Siegler
- Department of Chemistry, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218 (USA)
| | - Arthur E. Bragg
- Department of Chemistry, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218 (USA)
| | - Howard E. Katz
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218 (USA)
- Department of Chemistry, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218 (USA)
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183
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Guo X, Zhou J, Siegler MA, Bragg AE, Katz HE. Visible‐Light‐Triggered Molecular Photoswitch Based on Reversible
E
/
Z
Isomerization of a 1,2‐Dicyanoethene Derivative. Angew Chem Int Ed Engl 2015; 54:4782-6. [DOI: 10.1002/anie.201410945] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 01/02/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Xin Guo
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218 (USA)
| | - Jiawang Zhou
- Department of Chemistry, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218 (USA)
| | - Maxime A. Siegler
- Department of Chemistry, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218 (USA)
| | - Arthur E. Bragg
- Department of Chemistry, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218 (USA)
| | - Howard E. Katz
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218 (USA)
- Department of Chemistry, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218 (USA)
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184
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Wang L, Pan X, Zhao Y, Chen Y, Zhang W, Tu Y, Zhang Z, Zhu J, Zhou N, Zhu X. A Straightforward Protocol for the Highly Efficient Preparation of Main-Chain Azo Polymers Directly from Bisnitroaromatic Compounds by the Photocatalytic Process. Macromolecules 2015. [DOI: 10.1021/acs.macromol.5b00048] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Laibing Wang
- Suzhou
Key Laboratory of Macromolecular Design and Precision Synthesis, Jiangsu
Key Laboratory of Advanced Functional Polymer Design and Application,
College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou
Industrial Park, Suzhou 215123, China
| | - Xiangqiang Pan
- Suzhou
Key Laboratory of Macromolecular Design and Precision Synthesis, Jiangsu
Key Laboratory of Advanced Functional Polymer Design and Application,
College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou
Industrial Park, Suzhou 215123, China
| | - Yin Zhao
- Suzhou
Key Laboratory of Macromolecular Design and Precision Synthesis, Jiangsu
Key Laboratory of Advanced Functional Polymer Design and Application,
College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou
Industrial Park, Suzhou 215123, China
| | - Yang Chen
- Suzhou
Key Laboratory of Macromolecular Design and Precision Synthesis, Jiangsu
Key Laboratory of Advanced Functional Polymer Design and Application,
College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou
Industrial Park, Suzhou 215123, China
| | - Wei Zhang
- Suzhou
Key Laboratory of Macromolecular Design and Precision Synthesis, Jiangsu
Key Laboratory of Advanced Functional Polymer Design and Application,
College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou
Industrial Park, Suzhou 215123, China
| | - Yingfeng Tu
- Suzhou
Key Laboratory of Macromolecular Design and Precision Synthesis, Jiangsu
Key Laboratory of Advanced Functional Polymer Design and Application,
College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou
Industrial Park, Suzhou 215123, China
| | - Zhengbiao Zhang
- Suzhou
Key Laboratory of Macromolecular Design and Precision Synthesis, Jiangsu
Key Laboratory of Advanced Functional Polymer Design and Application,
College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou
Industrial Park, Suzhou 215123, China
| | - Jian Zhu
- Suzhou
Key Laboratory of Macromolecular Design and Precision Synthesis, Jiangsu
Key Laboratory of Advanced Functional Polymer Design and Application,
College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou
Industrial Park, Suzhou 215123, China
| | - Nianchen Zhou
- Suzhou
Key Laboratory of Macromolecular Design and Precision Synthesis, Jiangsu
Key Laboratory of Advanced Functional Polymer Design and Application,
College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou
Industrial Park, Suzhou 215123, China
| | - Xiulin Zhu
- Suzhou
Key Laboratory of Macromolecular Design and Precision Synthesis, Jiangsu
Key Laboratory of Advanced Functional Polymer Design and Application,
College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou
Industrial Park, Suzhou 215123, China
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185
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Wu L, Wu Y, Jin H, Zhang L, He Y, Tang X. Photoswitching properties of hairpin ODNs with azobenzene derivatives at the loop position. MEDCHEMCOMM 2015. [DOI: 10.1039/c4md00378k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photoisomerization of an azobenzene moiety modulates the thermodynamic stability of hairpin ODNs by interfering with stacking interation between azobenzene and neighbouring base pair and dihedral angle of the neighbouring base pair.
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Affiliation(s)
- Li Wu
- College of Chemistry Chemical Engineering
- University of Chinese Academy of Sciences
- Beijing 100049
- China
- State Key Laboratory of Natural and Biomimetic Drugs
| | - Ya Wu
- College of Chemistry and Chemical Engineering
- Xi'an Shiyou University
- Xi'an 710062
- China
| | - Hongwei Jin
- State Key Laboratory of Natural and Biomimetic Drugs
- School of Pharmaceutical Sciences
- Peking University
- Beijing 100191
- China
| | - Liangren Zhang
- State Key Laboratory of Natural and Biomimetic Drugs
- School of Pharmaceutical Sciences
- Peking University
- Beijing 100191
- China
| | - Yujian He
- College of Chemistry Chemical Engineering
- University of Chinese Academy of Sciences
- Beijing 100049
- China
- State Key Laboratory of Natural and Biomimetic Drugs
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs
- School of Pharmaceutical Sciences
- Peking University
- Beijing 100191
- China
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186
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Wang W, Hu J, Zheng M, Zheng L, Wang H, Zhang Y. Multi-responsive supramolecular hydrogels based on merocyanine–peptide conjugates. Org Biomol Chem 2015; 13:11492-8. [DOI: 10.1039/c5ob01912e] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Stimuli-responsive hydrogels are “smart” materials with diverse applications.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing
- P. R. China
| | - Jing Hu
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing
- P. R. China
| | - Mengmeng Zheng
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing
- P. R. China
| | - Li Zheng
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing
- P. R. China
| | - Huan Wang
- State Key Laboratory of Coordination Chemistry
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing
- P. R. China
| | - Yan Zhang
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing
- P. R. China
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187
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Taura D, Min H, Katan C, Yashima E. Synthesis of a double-stranded spiroborate helicate bearing stilbene units and its photoresponsive behaviour. NEW J CHEM 2015. [DOI: 10.1039/c4nj01669f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The sodium ion-triggered extension and contraction motions along with photo-induced cis–trans isomerisation of a photoresponsive spiroborate-based double-stranded helicate were investigated.
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Affiliation(s)
- Daisuke Taura
- Department of Molecular Design and Engineering
- Graduate School of Engineering
- Nagoya University
- Chikusa-ku
- Japan
| | - Heejun Min
- Department of Molecular Design and Engineering
- Graduate School of Engineering
- Nagoya University
- Chikusa-ku
- Japan
| | - Claudine Katan
- Institut des Sciences Chimiques de Rennes
- UMR 6226 CNRS-Université de Rennes 1
- France
| | - Eiji Yashima
- Department of Molecular Design and Engineering
- Graduate School of Engineering
- Nagoya University
- Chikusa-ku
- Japan
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188
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Goldau T, Murayama K, Brieke C, Steinwand S, Mondal P, Biswas M, Burghardt I, Wachtveitl J, Asanuma H, Heckel A. Reversible photoswitching of RNA hybridization at room temperature with an azobenzene C-nucleoside. Chemistry 2014; 21:2845-54. [PMID: 25537843 DOI: 10.1002/chem.201405840] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Indexed: 12/14/2022]
Abstract
Photoregulation of RNA remains a challenging task as the introduction of a photoswitch entails changes in the shape and the stability of the duplex that strongly depend on the chosen linker strategy. Herein, the influence of a novel nucleosidic linker moiety on the photoregulation efficiency of azobenzene is investigated. To this purpose, two azobenzene C-nucleosides were stereoselectively synthesized, characterized, and incorporated into RNA oligonucleotides. Spectroscopic characterization revealed a reversible and fast switching process, even at 20 °C, and a high thermal stability of the respective cis isomers. The photoregulation efficiency of RNA duplexes upon trans-to-cis isomerization was investigated by using melting point studies and compared with the known D-threoninol-based azobenzene system, revealing a photoswitching amplitude of the new residues exceeding 90 % even at room temperature. Structural changes in the duplexes upon photoisomerization were investigated by using MM/MD calculations. The excellent photoswitching performance at room temperature and the high thermal stability make these new azobenzene residues promising candidates for in-vivo and nanoarchitecture photoregulation applications of RNA.
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Affiliation(s)
- Thomas Goldau
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438 Frankfurt/Main (Germany), Fax: (+49) 69-798-763-42505
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189
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Amodio A, Zhao B, Porchetta A, Idili A, Castronovo M, Fan C, Ricci F. Rational design of pH-controlled DNA strand displacement. J Am Chem Soc 2014; 136:16469-72. [PMID: 25369216 DOI: 10.1021/ja508213d] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Achieving strategies to finely regulate with biological inputs the formation and functionality of DNA-based nanoarchitectures and nanomachines is essential toward a full realization of the potential of DNA nanotechnology. Here we demonstrate an unprecedented, rational approach to achieve control, through a simple change of the solution's pH, over an important class of DNA association-based reactions. To do so we took advantage of the pH dependence of parallel Hoogsteen interactions and rationally designed two triplex-based DNA strand displacement strategies that can be triggered and finely regulated at either basic or acidic pHs. Because pH change represents an important input both in healthy and pathological biological pathways, our findings can have implication for the development of DNA nanostructures whose assembly and functionality can be triggered in the presence of specific biological targets.
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Affiliation(s)
- Alessia Amodio
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome, Tor Vergata , Via della Ricerca Scientifica, 00133, Rome, Italy
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190
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Hernández-Ainsa S, Keyser UF. DNA origami nanopores: developments, challenges and perspectives. NANOSCALE 2014; 6:14121-32. [PMID: 25325422 DOI: 10.1039/c4nr04094e] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
DNA nanotechnology has enabled the construction of DNA origami nanopores; synthetic nanopores that present improved capabilities for the area of single molecule detection. Their extraordinary versatility makes them a new and powerful tool in nanobiotechnology for a wide range of important applications beyond molecular sensing. In this review, we briefly present the recent developments in this emerging field of research. We discuss the current challenges and possible solutions that would enhance the sensing capabilities of DNA origami nanopores. Finally, we anticipate novel avenues for future research and highlight a range of exciting ideas and applications that could be explored in the near future.
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191
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Rodrigues-Correia A, Knapp-Bühle D, Engels JW, Heckel A. Selective uncaging of DNA through reaction rate selectivity. Org Lett 2014; 16:5128-31. [PMID: 25232905 DOI: 10.1021/ol502478g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The synthesis and use of the new nucleobase-caged nucleotides dT(pHP) and dT(NDEACM) is reported. Through a combination of time and wavelength selectivity four levels of selective uncaging with only two cages, and only two wavelengths, were obtained. The new residue dT(pHP) can be uncaged at 313 nm without the formation of unwanted cyclic pyridine dimers.
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Affiliation(s)
- Alexandre Rodrigues-Correia
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt , Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
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192
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Li J, Wang X, Liang X. Modification of Nucleic Acids by Azobenzene Derivatives and Their Applications in Biotechnology and Nanotechnology. Chem Asian J 2014; 9:3344-58. [DOI: 10.1002/asia.201402758] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Indexed: 01/29/2023]
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193
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Asanuma H, Kashida H, Kamiya Y. De novo design of functional oligonucleotides with acyclic scaffolds. CHEM REC 2014; 14:1055-69. [PMID: 25171046 DOI: 10.1002/tcr.201402040] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Indexed: 01/20/2023]
Abstract
In this account, we demonstrate a new methodology for the de novo design of functional oligonucleotides with the acyclic scaffolds threoninol and serinol. Four functional motifs-wedge, interstrand-wedge, dimer, and cluster-have been prepared from natural DNA or RNA and functional base surrogates prepared from d-threoninol. The following applications of these motifs are described: (1) photoregulation of formation and dissociation of a DNA duplex modified with azobenzene, (2) sequence-specific detection of DNA using a fluorescent probe, (3) formation of fluorophore assemblies that mimic quantum dots, (4) improved strand selectivity of siRNA modified with a base surrogate, and (5) in vivo tracing of the RNAi pathway. Finally, we introduce artificial nucleic acids (XNAs) prepared from d-threoninol and serinol functionalized with each of the four nucleobases, which have unique properties compared with other acyclic XNAs. Functional oligonucleotides designed from acyclic scaffolds will be powerful tools for both DNA nanotechnology and biotechnology.
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Affiliation(s)
- Hiroyuki Asanuma
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan.
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