1
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Wang Y, Ji H, Ma J, Luo H, He Y, Tang X, Wu L. Reversible On-Off Photoswitching of DNA Replication Using a Dumbbell Oligodeoxynucleotide. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248992. [PMID: 36558127 PMCID: PMC9785685 DOI: 10.3390/molecules27248992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/09/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
In most organisms, DNA extension is highly regulated; however, most studies have focused on controlling the initiation of replication, and few have been done to control the regulation of DNA extension. In this study, we adopted a new strategy for azODNs to regulate DNA extension, which is based on azobenzene oligonucleotide chimeras regulated by substrate binding affinity, and the conformation of the chimera can be regulated by a light source with a light wavelength of 365 nm. The results showed that the primer was extended with Taq DNA polymerase after visible light treatment, and DNA extension could be effectively hindered with UV light treatment. We also verify the reversibility of the photoregulation of primer extension through photoswitching of dumbbell asODNs by alternate irradiation with UV and visible light. Our method has the advantages of fast and simple, green response and reversible operations, providing a new strategy for regulating gene replication.
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Affiliation(s)
- Yu Wang
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Heming Ji
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Zhejiang Institute of Mechanical and Electrical Technician, Yiwu 322000, China
| | - Jian Ma
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hang Luo
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yujian He
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
- Correspondence: (X.T.); (L.W.)
| | - Li Wu
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Zhejiang Institute of Mechanical and Electrical Technician, Yiwu 322000, China
- Correspondence: (X.T.); (L.W.)
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2
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Wu Z, Zhang L. Photoregulation between small DNAs and reversible photochromic molecules. Biomater Sci 2019; 7:4944-4962. [PMID: 31650136 DOI: 10.1039/c9bm01305a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Oligonucleotides are widely used biological materials in the fields of biomedicine, nanotechnology, and materials science. Due to the demands for the photoregulation of DNA activities, scientists are placing more and more research interest in the interactions between reversible photochromic molecules and DNAs. Photochromic molecules can work as switches for regulating the DNAs' behavior under light irradiation; meanwhile, DNAs also exert influence over the photochromic molecules. The photochromic molecules can be attached to DNAs either by covalent bonds or by noncovalent forces, which results in different regulative functions. Azobenzenes, spiropyrans, diarylethenes, and stilbene-like compounds are important photochromic molecules working as photoswitches. By summarizing their interactions with oligonucleotides, this review intends to facilitate the relevant research on oligonucleotides/photochromic molecules in the biological and medicinal fields and in materials science.
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Affiliation(s)
- Zhongtao Wu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53 Zhengzhou Rd, Qingdao, 266042, PR China.
| | - Lei Zhang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53 Zhengzhou Rd, Qingdao, 266042, PR China.
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3
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Grebenovsky N, Luma L, Müller P, Heckel A. Introducing LNAzo: More Rigidity for Improved Photocontrol of Oligonucleotide Hybridization. Chemistry 2019; 25:12298-12302. [PMID: 31386225 DOI: 10.1002/chem.201903240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/05/2019] [Indexed: 12/15/2022]
Abstract
Oligonucleotide-based therapeutics have made rapid progress in clinical treatment of a variety of disease indications. Since most therapeutic oligonucleotides serve more than just one function and tend to have a prolonged lifetime, spatio-temporal control of these functions would be desirable. Photoswitches like azobenzene have proven themselves as useful tools in this matter. Upon irradiation, the photoisomerization of the azobenzene moiety causes destabilization in adjacent base pairs, leading to a decreased hybridization affinity. Since the way the azobenzene is incorporated in the oligonucleotide is of utmost importance, we synthesized locked azobenzene C-nucleosides and compared their photocontrol capabilities to established azobenzene C-nucleosides in oligonucleotide test-sequences by means of fluorescence-, UV/Vis-, and CD-spectroscopy.
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Affiliation(s)
- Nikolai Grebenovsky
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Larita Luma
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Patricia Müller
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
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4
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Strauss MA, Wegner HA. Influence of an Ammonium Tag on the Switching Dynamics of Azobenzenes in Polar Solvents. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201800264] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Marcel A. Strauss
- Institute of Organic ChemistryJustus Liebig University Giessen Heinrich-Buff-Ring 17 35392 Giessen Germany
- Center for Materials Research (LaMa)Justus Liebig University Giessen Heinrich-Buff-Ring 16 35392 Giessen Germany
| | - Hermann A. Wegner
- Institute of Organic ChemistryJustus Liebig University Giessen Heinrich-Buff-Ring 17 35392 Giessen Germany
- Center for Materials Research (LaMa)Justus Liebig University Giessen Heinrich-Buff-Ring 16 35392 Giessen Germany
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5
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Wu D, Wang YT, Fang WH, Cui G, Thiel W. QM/MM Studies on Photoisomerization Dynamics of Azobenzene Chromophore Tethered to a DNA Duplex: Local Unpaired Nucleobase Plays a Crucial Role. Chem Asian J 2018; 13:780-784. [PMID: 29446260 DOI: 10.1002/asia.201800006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 02/07/2018] [Indexed: 01/10/2023]
Abstract
The photoresponsive azobenzene-tethered DNAs have received growing experimental attention because of their potential applications in biotechnology and nanotechnology; however, little is known about the initial photoisomerization of azobenzene in these systems. Herein we have employed quantum mechanics/molecular mechanics (QM/MM) methods to explore the photoisomerization dynamics of an azobenzene-tethered DNA duplex. We find that in the S1 state the trans-cis photoisomerization path is much steeper in DNA than in vacuo, which makes the photoisomerization much faster in the DNA environment. This acceleration is primarily caused by complex steric interactions between azobenzene and the nearby unpaired thymine nucleobase, which also change the photoisomerization mechanism of azobenzene in the DNA duplex.
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Affiliation(s)
- Dan Wu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Ya-Ting Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
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6
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Bagheri Novir S. Theoretical study of Z- and E-isomers of some hemithioindigo-based peptide-switches. J Photochem Photobiol A Chem 2018. [DOI: 10.1016/j.jphotochem.2018.01.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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7
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8
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Wang R, Jin C, Zhu X, Zhou L, Xuan W, Liu Y, Liu Q, Tan W. Artificial Base zT as Functional "Element" for Constructing Photoresponsive DNA Nanomolecules. J Am Chem Soc 2017; 139:9104-9107. [PMID: 28585836 PMCID: PMC5877792 DOI: 10.1021/jacs.7b02865] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In contrast to small molecules, DNA and RNA macromolecules can be accurately formulated with base "elements" abbreviated as A, T, U, C, and G. However, the development of functionally artificial bases can result in the generation of new biomaterials with unique properties and applications. Therefore, we herein report the design and synthesis of a photoresponsive base as a new functional or molecular "element" for constructing DNA nanomolecules. The new base is made by fusion of an azobenzene with a natural T base (zT). zT, a new molecular element, is not only the most size-expanded T analogue but also a photoresponsive base capable of specific self-assembly through hydrogen bonding. Our results showed that stable and selective self-assembly of double-stranded DNAs occurred through zT-A base pairing, but it could still be efficiently dissociated by light irradiation. The photoresponsive DNA bases will provide the versatility required for constructing desired DNA nanomolecules and nanodevices.
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Affiliation(s)
- Ruowen Wang
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Departments of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, University Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Cheng Jin
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Xiaoyan Zhu
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Liyi Zhou
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Wenjing Xuan
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Yuan Liu
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Departments of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, University Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Qiaoling Liu
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Departments of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, University Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Weihong Tan
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Departments of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, University Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
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9
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Kingsland A, Samai S, Yan Y, Ginger DS, Maibaum L. Local Density Fluctuations Predict Photoisomerization Quantum Yield of Azobenzene-Modified DNA. J Phys Chem Lett 2016; 7:3027-3031. [PMID: 27428569 DOI: 10.1021/acs.jpclett.6b00956] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Azobenzene incorporated into DNA has a photoisomerization quantum yield that depends on the DNA sequence near the azobenzene attachment site. We use Molecular Dynamics computer simulations to elucidate which physical properties of the modified DNA determine the quantum yield. We show for a wide range of DNA sequences that the photoisomerization quantum yield is strongly correlated with the variance of the number of atoms in close proximity to the outer phenyl ring of the azobenzene group. We infer that quantum yield is controlled by the availability of fluctuations that enable the conformational change. We demonstrate that these simulations can be used as a qualitative predictive tool by calculating the quantum yield for several novel DNA sequences, and confirming these predictions using UV-vis spectroscopy. Our results will be useful for the development of a wide range of applications of photoresponsive DNA nanotechnology.
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Affiliation(s)
- Addie Kingsland
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Soumyadyuti Samai
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Yunqi Yan
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - David S Ginger
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Lutz Maibaum
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
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10
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Yan Y, Samai S, Bischoff KL, Zhang J, Ginger DS. Photocontrolled DNA Hybridization Stringency with Fluorescence Detection in Heterogeneous Assays. ACS Sens 2016. [DOI: 10.1021/acssensors.5b00233] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | | | - Kristi L. Bischoff
- Mel
and Enid Zuckerman College of Public Heath, University of Arizona, Tucson, Arizona 85724, United States
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11
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Tian T, Song Y, Wang J, Fu B, He Z, Xu X, Li A, Zhou X, Wang S, Zhou X. Small-Molecule-Triggered and Light-Controlled Reversible Regulation of Enzymatic Activity. J Am Chem Soc 2016; 138:955-61. [DOI: 10.1021/jacs.5b11532] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Tian Tian
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies,
Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei
Province, China
| | - Yanyan Song
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies,
Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei
Province, China
| | - Jiaqi Wang
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies,
Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei
Province, China
| | - Boshi Fu
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies,
Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei
Province, China
| | - Zhiyong He
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies,
Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei
Province, China
| | - Xianqun Xu
- Zhongnan
Hospital, Wuhan University, Wuhan 430071, Hubei Province, China
| | - Anling Li
- Zhongnan
Hospital, Wuhan University, Wuhan 430071, Hubei Province, China
| | - Xin Zhou
- Zhongnan
Hospital, Wuhan University, Wuhan 430071, Hubei Province, China
| | - Shaoru Wang
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies,
Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei
Province, China
| | - Xiang Zhou
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies,
Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei
Province, China
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12
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Bergen A, Rudiuk S, Morel M, Le Saux T, Ihmels H, Baigl D. Photodependent Melting of Unmodified DNA Using a Photosensitive Intercalator: A New and Generic Tool for Photoreversible Assembly of DNA Nanostructures at Constant Temperature. NANO LETTERS 2016; 16:773-80. [PMID: 26652690 DOI: 10.1021/acs.nanolett.5b04762] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
External control of DNA melting and hybridization, a key step in bio- and DNA nanotechnology, is commonly achieved with temperature. The use of light to direct this process is a challenging alternative, which has been only possible with a DNA modification, such as covalent grafting or mismatch introduction, so far. Here we describe the first photocontrol of DNA melting that relies on the addition of a molecule that noncovalently interacts with unmodified DNA and affects its melting properties in a photoreversible and highly robust manner, without any prerequisite in the length or sequence of the target DNA molecule. We synthesize azobenzene-containing guanidinium derivatives and show that a bivalent molecule with a conformation-dependent binding mode, AzoDiGua, strongly increases the melting temperature (Tm) of DNA under dark conditions because its trans isomer intercalates in the DNA double helix. Upon UV irradiation at 365 nm, the trans-cis isomerization induced the ejection of AzoDiGua from the intercalation binding sites, resulting in a decrease in Tm up to 18 °C. This illumination-dependent Tm shift is observed on many types of DNA, from self-complementary single-stranded or double-stranded oligonucleotides to long genomic duplex DNA molecules. Finally, we show that simply adding AzoDiGua allows us to photoreversibly control the assembly/disassembly of a DNA nanostructure at constant temperature, as demonstrated here with a self-hybridized DNA hairpin. We anticipate that this strategy will be the key ingredient in a new and generic way of placing DNA-based bio- and nanotechnologies under dynamic control by light.
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Affiliation(s)
- Anna Bergen
- Department of Chemistry, Ecole Normale Supérieure-PSL Research University , 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, PASTEUR, 75005 Paris, France
- CNRS, UMR 8640 PASTEUR, 75005 Paris, France
| | - Sergii Rudiuk
- Department of Chemistry, Ecole Normale Supérieure-PSL Research University , 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, PASTEUR, 75005 Paris, France
- CNRS, UMR 8640 PASTEUR, 75005 Paris, France
| | - Mathieu Morel
- Department of Chemistry, Ecole Normale Supérieure-PSL Research University , 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, PASTEUR, 75005 Paris, France
- CNRS, UMR 8640 PASTEUR, 75005 Paris, France
| | - Thomas Le Saux
- Department of Chemistry, Ecole Normale Supérieure-PSL Research University , 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, PASTEUR, 75005 Paris, France
- CNRS, UMR 8640 PASTEUR, 75005 Paris, France
| | - Heiko Ihmels
- Department of Chemistry-Biology, University of Siegen , Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Damien Baigl
- Department of Chemistry, Ecole Normale Supérieure-PSL Research University , 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, PASTEUR, 75005 Paris, France
- CNRS, UMR 8640 PASTEUR, 75005 Paris, France
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13
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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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14
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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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15
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Yu J, Yang L, Liang X, Dong T, Liu H. Reversible regulation of thrombin adsorption and desorption based on photoresponsive-aptamer modified gold nanoparticles. Talanta 2015; 144:312-7. [PMID: 26452827 DOI: 10.1016/j.talanta.2015.06.053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 06/11/2015] [Accepted: 06/20/2015] [Indexed: 10/23/2022]
Abstract
In the protein separation, adsorption and desorption of target protein have been using different buffer condition. Different buffer will change the structure and activity of target protein in some cases. This work describes the use of different wavelength light for remote regulation of adsorption and desorption of target protein in the same buffer solutions. A dynamic system that captured and released protein in response to light is reported. Matrix gold nanoparticles and light-responsive affinity ligand comprising thrombin aptamer (APT15), polyethylene glycol linker, and azobenzene-modified complementary sequence were used. UV light induced a trans-cis isomerization of the azobenzene that destabilized the duplex of aptamer and azobenzene-modified complementary sequence, resulting in thrombin binding to aptamer sequence. Visible light irradiation resulted in DNA duplex rehybridization and thrombin released. Our work demonstrates that different light wavelengths effectively regulated the adsorption and desorption of thrombin in the same buffer, and this system also can capture and release prothrombin from plasma with different wavelength light. Furthermore, this method can be widely applied to a variety of different protein separation process.
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Affiliation(s)
- Jiemiao Yu
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; Graduate University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Liangrong Yang
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
| | - Xiangfeng Liang
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Tingting Dong
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; Graduate University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Huizhou Liu
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
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16
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Díaz-Lobo M, Garcia-Amorós J, Fita I, Velasco D, Guinovart JJ, Ferrer JC. Selective photoregulation of the activity of glycogen synthase and glycogen phosphorylase, two key enzymes in glycogen metabolism. Org Biomol Chem 2015; 13:7282-8. [PMID: 26055498 DOI: 10.1039/c5ob00796h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Glycogen is a polymer of α-1,4- and α-1,6-linked glucose units that provides a readily available source of energy in living organisms. Glycogen synthase (GS) and glycogen phosphorylase (GP) are the two enzymes that control, respectively, the synthesis and degradation of this polysaccharide and constitute adequate pharmacological targets to modulate cellular glycogen levels, by means of inhibition of their catalytic activity. Here we report on the synthesis and biological evaluation of a selective inhibitor that consists of an azobenzene moiety glycosidically linked to the anomeric carbon of a glucose molecule. In the ground state, the more stable (E)-isomer of the azobenzene glucoside had a slight inhibitory effect on rat muscle GP (RMGP, IC50 = 4.9 mM) and Escherichia coli GS (EcGS, IC50 = 1.6 mM). After irradiation and subsequent conversion to the (Z)-form, the inhibitory potency of the azobenzene glucoside did not significantly change for RMGP (IC50 = 2.4 mM), while its effect on EcGS increased 50-fold (IC50 = 32 μM). Sucrose synthase 4 from potatoes, a glycosyltransferase that does not operate on glycogen, was only slightly inhibited by the (E)-isomer (IC50 = 0.73 mM). These findings could be rationalized on the basis of kinetic and computer-aided docking analysis, which indicated that both isomers of the azobenzene glucoside mimic the EcGS acceptor substrate and exert their inhibitory effect by binding to the glycogen subsite in the active center of the enzyme. The ability to selectively photoregulate the catalytic activity of key enzymes of glycogen metabolism may represent a new approach for the treatment of glycogen metabolism disorders.
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Affiliation(s)
- Mireia Díaz-Lobo
- Departament de Bioquímica i Biologia Molecular, Universitat de Barcelona, Av. Diagonal 645, E-08028, Barcelona, Spain.
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17
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Wu L, He Y, Tang X. Photoregulating RNA digestion using azobenzene linked dumbbell antisense oligodeoxynucleotides. Bioconjug Chem 2015; 26:1070-9. [PMID: 25961679 DOI: 10.1021/acs.bioconjchem.5b00125] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Introduction of 4,4'-bis(hydroxymethyl)-azobenzene (azo) to dumbbell hairpin oligonucleotides at the loop position was able to reversibly control the stability of the whole hairpin structure via UV or visible light irradiation. Here, we designed and synthesized a series of azobenzene linked dumbbell antisense oligodeoxynucleotides (asODNs) containing two terminal hairpins that are composed of an asODN and a short inhibitory sense strand. Thermal melting studies of these azobenzene linked dumbbell asODNs indicated that efficient trans to cis photoisomerization of azobenzene moieties induced large difference in thermal stability (ΔTm = 12.1-21.3 °C). In addition, photomodulation of their RNA binding abilities and RNA digestion by RNase H was investigated. The trans-azobenzene linked asODNs with the optimized base pairs between asODN strands and inhibitory sense strands could only bind few percentage of the target RNA, while it was able to recover their binding to the target RNA and degrade it by RNase H after light irradiation. Upon optimization, it is promising to use these azobenzene linked asODNs for reversible spatial and temporal regulation of antisense activities based on both steric binding and RNA digestion by RNase H.
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Affiliation(s)
- Li Wu
- †School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, China.,‡State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yujian He
- †School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, China.,‡State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xinjing Tang
- ‡State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
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18
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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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19
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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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20
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Kovaliov M, Wachtel C, Yavin E, Fischer B. Synthesis and evaluation of a photoresponsive quencher for fluorescent hybridization probes. Org Biomol Chem 2014; 12:7844-58. [PMID: 25177827 DOI: 10.1039/c4ob01185f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nowadays, most nucleic acid detections using fluorescent probes rely on quenching of fluorescence by energy transfer from one fluorophore to another or to a non-fluorescent molecule (quencher). The most widely used quencher in fluorescent probes is 4-((4-(dimethylamino)phenyl)azo)benzoic acid (DABCYL). We targeted a nucleoside-DABCYL analogue which could be incorporated anywhere in an oligonucleotide sequence and in any number, and used as a quencher in different hybridization sensitive probes. Specifically, we introduced a 5-(4-((dimethylamino)phenyl)azo)benzene)-2'-deoxy-uridine (dU(DAB)) quencher. The photoisomerization and dU(DAB)'s ability to quench fluorescein emission have been investigated. We incorporated dU(DAB) into a series of oligonucleotide (ON) probes including strand displacement probes, labeled with both fluorescein (FAM) and dU(DAB), and TaqMan probes bearing one or two dU(DAB) and a FAM fluorophore. We used these probes for the detection of a DNA target in real-time PCR (RT-PCR). All probes showed amplification of targeted DNA. A dU(DAB) modified TaqMan RT-PCR probe was more efficient as compared to a DABCYL bearing probe (93% vs. 87%, respectively). Furthermore, dU(DAB) had a stabilizing effect on the duplex, causing an increase in Tm up to 11 °C. In addition we showed the photoisomerisation of the azobenzene moiety of dU(DAB) and the dU(DAB) triply-labeled oligonucleotide upon irradiation. These findings suggest that dU(DAB) modified probes are promising probes for gene quantification in real-time PCR detection and as photoswitchable devices.
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Affiliation(s)
- Marina Kovaliov
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel.
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21
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Biswas M, Burghardt I. Azobenzene photoisomerization-induced destabilization of B-DNA. Biophys J 2014; 107:932-40. [PMID: 25140428 PMCID: PMC4142232 DOI: 10.1016/j.bpj.2014.06.044] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 06/20/2014] [Accepted: 06/25/2014] [Indexed: 11/24/2022] Open
Abstract
Molecular photoswitches provide a promising way for selective regulation of nanoscaled biological systems. It has been shown that conformational changes of azobenzene, one of the widely used photoswitches, can be used to reversibly control DNA duplex formation. Here, we investigate the conformational response of DNA upon azobenzene binding and isomerization, using a threoninol linker that has been experimentally investigated recently. To this end, nonequilibrium molecular dynamics simulations are carried out using a switching potential describing the photoinduced isomerization. Attachment of azobenzene leads to a distortion of the DNA helical conformation that is similar for the trans and cis forms. However, the trans form is stabilized by favorable stacking interactions whereas the cis form is found to remain flipped out of the basepair-stacked position. Multiple azobenzene attachment augments the distortion in DNA helical conformation. The distorted DNA retains nativelike pairing of bases at ambient temperatures, but shows weaker basepairing compared to native DNA at an elevated temperature.
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Affiliation(s)
- Mithun Biswas
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany.
| | - Irene Burghardt
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany.
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22
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Gupta M, Agarwal N, Arora A, Kumar S, Kumar B, Sheet G, Pal SK. Synthesis and characterization of novel azobenzene-based mesogens and their organization at the air–water and air–solid interfaces. RSC Adv 2014. [DOI: 10.1039/c4ra05572a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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23
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Sengupta E, Yan Y, Wang X, Munechika K, Ginger DS. Dynamic force spectroscopy of photoswitch-modified DNA. ACS NANO 2014; 8:2625-2631. [PMID: 24502655 DOI: 10.1021/nn406334b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We apply a combination of photoswitch-modified DNA and AFM-based pulling measurements to study the force-induced melting of double-stranded DNA in the unzipping geometry. We measure the differences in peak rupture force for azobenzene-modified DNA, as the incorporated azobenzenes are photoswitched reversibly between the trans and the cis form. Fitting our rupture force versus loading rate data, we obtain off rate (koff) at zero force values in the range of ∼10 s(-1). We show that the change in peak rupture force and koff induced by destabilizing the DNA duplex depends on the position of the destabilizing azobenzene photoswitch relative to the force-loading site. When the azobenzenes are proximal to the unzipping end, the decrease in peak force and koff upon azobenzene photoisomerization is significantly larger than when the azobenzene is distal to the site of force loading. We interpret these results as experimental evidence supporting the picture that the destabilization of a double-stranded DNA by a photoswitch isomerization is localized to a small bubble around the photoswitch.
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Affiliation(s)
- Esha Sengupta
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
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24
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Yan Y, Wang X, Chen JIL, Ginger DS. Photoisomerization Quantum Yield of Azobenzene-Modified DNA Depends on Local Sequence. J Am Chem Soc 2013; 135:8382-7. [DOI: 10.1021/ja403249u] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Yunqi Yan
- Department of Chemistry, University of Washington, Seattle, Washington 98195,
United States
| | - Xin Wang
- Department of Chemistry, University of Washington, Seattle, Washington 98195,
United States
| | | | - David S. Ginger
- Department of Chemistry, University of Washington, Seattle, Washington 98195,
United States
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25
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Szymański W, Beierle JM, Kistemaker HAV, Velema WA, Feringa BL. Reversible Photocontrol of Biological Systems by the Incorporation of Molecular Photoswitches. Chem Rev 2013; 113:6114-78. [DOI: 10.1021/cr300179f] [Citation(s) in RCA: 847] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Wiktor Szymański
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The
Netherlands
| | - John M. Beierle
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The
Netherlands
| | - Hans A. V. Kistemaker
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The
Netherlands
| | - Willem A. Velema
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The
Netherlands
| | - Ben L. Feringa
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The
Netherlands
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26
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Ulrich S, Dumy P, Boturyn D, Renaudet O. Engineering of biomolecules for sensing and imaging applications. J Drug Deliv Sci Technol 2013. [DOI: 10.1016/s1773-2247(13)50001-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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27
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Barrois S, Wagenknecht HA. Diarylethene-modified nucleotides for switching optical properties in DNA. Beilstein J Org Chem 2012; 8:905-14. [PMID: 23015841 PMCID: PMC3388881 DOI: 10.3762/bjoc.8.103] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 05/09/2012] [Indexed: 01/03/2023] Open
Abstract
Diarylethenes were attached to the 5-position of 2’-deoxyuridine in order to yield three different photochromic nucleosides. All nucleosides were characterized with respect to their absorption and photochromic properties. Based on these results, the most promising photochromic DNA base modification was incorporated into representative oligonucleotides by using automated phosphoramidite chemistry. The switching of optical properties in DNA can be achieved selectively at 310 nm (forward) and 450 nm (backward); both wavelengths are outside the normal nucleic acid absorption range. Moreover, this nucleoside was proven to be photochemically stable and allows switching back and forth several times. These results open the way for the use of diarylethenes as photochromic compounds in DNA-based architectures.
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Affiliation(s)
- Sebastian Barrois
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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28
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Kördel C, Popeney CS, Haag R. Photoresponsive amphiphiles based on azobenzene-dendritic glycerol conjugates show switchable transport behavior. Chem Commun (Camb) 2011; 47:6584-6. [DOI: 10.1039/c1cc11673h] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Tanabe K, Ito T, Nishimoto SI. Radiolytic Reduction Characteristics of Artificial Oligodeoxynucleotides Possessing 2-Oxoalkyl Group or Disulfide Bonds. J Nucleic Acids 2011; 2011:816207. [PMID: 21860782 PMCID: PMC3153922 DOI: 10.4061/2011/816207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Accepted: 05/20/2011] [Indexed: 11/30/2022] Open
Abstract
A number of advances have been made in the development of modified oligodeoxynucleotides (ODNs), and chemical or physical properties of which are controlled by external stimuli. These intelligent ODNs are promising for the next generation of gene diagnostics and therapy. This paper focuses on the molecular design of artificial ODNs that are activated by X-irradiation and their applications to regulation of hybridization properties, conformation change, radiation-activated DNAzyme, and decoy molecules.
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Affiliation(s)
- Kazuhito Tanabe
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura Campus, Kyoto 615-8510, Japan
| | - Takeo Ito
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura Campus, Kyoto 615-8510, Japan
| | - Sei-ichi Nishimoto
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura Campus, Kyoto 615-8510, Japan
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30
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Singer M, Jäschke A. Reversibly photoswitchable nucleosides: synthesis and photochromic properties of diarylethene-functionalized 7-deazaadenosine derivatives. J Am Chem Soc 2010; 132:8372-7. [PMID: 20481531 DOI: 10.1021/ja1024782] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photochromic nucleosides were designed that combine the structural features and molecular recognition properties of nucleic acids with the light-sensitivity of diarylethenes. Target compounds 1a-c consist of a 7-deazaadenosine unit that is linked to a thiophene as the second aryl functionality via a 1,2-cyclopentenyl linker. These nucleoside analogues undergo a reversible electrocyclic rearrangement, generating strongly colored closed-ring isomers upon irradiation with UV-light, while exposure to light in the visible range triggers the cycloreversion to the colorless opened-ring form. UV-vis spectroscopy, HPLC, and (1)H NMR measurements revealed recognition of complementary thymidine and up to 97% conversion to the thermally stable closed-ring isomers after illumination with UV-light. The required wavelength for ring closure was found to vary depending on the substituents attached to the thiophene moiety. In a first design step, we used this important feature of diarylethenes to shift the switching wavelength from initially 300 nm (1a) to 405 nm (1cH(+)). In a second step, we generated a pair of orthogonal switches, differing enough in their respective switching wavelengths to be controlled independently in the same sample. Finally, a molecular switch was developed that showed both photochromism and acidichromism, thereby illustrating the possibility to gate the spectral properties to multiple stimuli. These new photochromic nucleosides represent useful building blocks for the generation of light-sensitive nucleic acids either by inducing conformational changes upon isomerization or by exploring the different spectral properties of the closed and opened isomers, for example, for use as reversible fluorescence quenchers.
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Affiliation(s)
- Marco Singer
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany
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31
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Liang X, Wakuda R, Fujioka K, Asanuma H. Photoregulation of DNA transcription by using photoresponsive T7 promoters and clarification of its mechanism. FEBS J 2010; 277:1551-61. [PMID: 20148969 DOI: 10.1111/j.1742-4658.2010.07583.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
With the use of photoresponsive T7 promoters tethering two 2'-methylazobenzenes or 2',6'-dimethylazobenzenes, highly efficient photoregulation of DNA transcription was obtained. After UV-A light irradiation (320-400 nm), the rate of transcription with T7 RNA polymerase and a photoresponsive promoter involving two 2',6'-dimethylazobenzenes was 10-fold faster than that after visible light irradiation (400-600 nm). By attaching a nonmodified azobenzene and 2',6'-dimethylazobenzene at the two positions, respectively, and by utilizing the different cis-->trans thermal stability between cis-nonmodified azobenzene and cis-2',6'-dimethylazobenzene, four species of T7 promoter (cis-cis, trans-cis, cis-trans, and trans-trans) were obtained. The four species showed transcriptional activity in the order of cis-cis > cis-trans > trans-cis > trans-trans. Kinetic analysis revealed that the K(m) for the cis-cis promoter (both of the introduced azobenzene derivatives were in the cis form) and T7 RNA polymerase was 68 times lower than that for the trans-trans form, indicating that high photoregulatory efficiency was mainly due to a remarkable difference in affinity for RNA polymerase. The present approach is promising for the creation of biological tools for artificially controlling gene expression, and as a photocontrolled system for supplying RNA fuel for RNA-powered molecular nanomachines.
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Affiliation(s)
- Xingguo Liang
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Japan.
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32
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Shao Q, Xing B. Photoactive molecules for applications in molecular imaging and cell biology. Chem Soc Rev 2010; 39:2835-46. [DOI: 10.1039/b915574k] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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33
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Liang X, Mochizuki T, Asanuma H. A supra-photoswitch involving sandwiched DNA base pairs and azobenzenes for light-driven nanostructures and nanodevices. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2009; 5:1761-1768. [PMID: 19572326 DOI: 10.1002/smll.200900223] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A supra-photoswitch is designed for complete ON/OFF switching of DNA hybridization by light irradiation for the purpose of using DNA as a material for building nanostructures. Azobenzenes, attached to D-threoninols that function as scaffolds, are introduced into each DNA strand after every two natural nucleotides (in the form (NNX)n where N and X represent the natural nucleotide and the azobenzene moiety, respectively). Hybridization of these two modified strands forms a supra-photoswitch consisting of alternating natural base pairs and azobenzene moieties. In this newly designed sequence, each base pair is sandwiched between two azobenzene moieties and all the azobenzene moieties are separated by base pairs. When the duplex is irradiated by visible light, the azobenzene moieties take the trans form and this duplex is surprisingly stable compared to the corresponding native duplex composed of only natural oligonucleotides. On the other hand, when the azobenzene moieties are isomerized to the cis form by UV light irradiation, the duplex is completely dissociated. Based on this design, a DNA hairpin structure is synthesized that should be closed by visible light irradiation and opened by UV light irradiation at the level of a single molecule. Indeed, perfect ON/OFF photoregulation is attained. This is a promising strategy for the design of supra-photoswitches such as photoresponsive sticky ends on DNA nanodevices and other nanostructures.
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Affiliation(s)
- Xingguo Liang
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa, Nagoya 464-8603, Japan
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34
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Richards JL, Tang X, Turetsky A, Dmochowski IJ. RNA bandages for photoregulating in vitro protein synthesis. Bioorg Med Chem Lett 2008; 18:6255-8. [PMID: 18926697 PMCID: PMC2593108 DOI: 10.1016/j.bmcl.2008.09.093] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2008] [Revised: 09/24/2008] [Accepted: 09/26/2008] [Indexed: 11/24/2022]
Abstract
'RNA bandages' are composed of two 6-12-mer 2'-OMe RNA strands complementary to a mRNA target that are joined by a photocleavable linker. These tandem oligonucleotides typically exhibit much higher affinity for the mRNA than the individual strands. An RNA bandage with binding arms of different lengths and a 4-base gap blocked translation in vitro of GFP mRNA; subsequent near-UV irradiation restored translation. This provides a general method of photomodulating hybridization for a variety of oligonucleotide-based technologies.
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Affiliation(s)
- Julia L. Richards
- Department of Chemistry, 231 S. 34 St., University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - XinJing Tang
- Department of Chemistry, 231 S. 34 St., University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Anna Turetsky
- Department of Chemistry, 231 S. 34 St., University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Ivan J. Dmochowski
- Department of Chemistry, 231 S. 34 St., University of Pennsylvania, Philadelphia, PA 19104-6323, USA
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35
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Andersson J, Li S, Lincoln P, Andréasson J. Photoswitched DNA-Binding of a Photochromic Spiropyran. J Am Chem Soc 2008; 130:11836-7. [DOI: 10.1021/ja801968f] [Citation(s) in RCA: 166] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Johanna Andersson
- Department of Chemical and Biological Engineering, Physical Chemistry, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
| | - Shiming Li
- Department of Chemical and Biological Engineering, Physical Chemistry, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
| | - Per Lincoln
- Department of Chemical and Biological Engineering, Physical Chemistry, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
| | - Joakim Andréasson
- Department of Chemical and Biological Engineering, Physical Chemistry, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
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36
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37
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Liang X, Nishioka H, Takenaka N, Asanuma H. A DNA nanomachine powered by light irradiation. Chembiochem 2008; 9:702-5. [PMID: 18253940 DOI: 10.1002/cbic.200700649] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Xingguo Liang
- Core Research for Evolution Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
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38
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Liang X, Takenaka N, Nishioka H, Asanuma H. Molecular Design for Reversing the Photoswitching Mode of Turning ON and OFF DNA Hybridization. Chem Asian J 2008; 3:553-560. [DOI: 10.1002/asia.200700384] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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39
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Dmochowski IJ, Tang X. Taking control of gene expression with light-activated oligonucleotides. Biotechniques 2007; 43:161, 163, 165 passim. [PMID: 17824383 DOI: 10.2144/000112519] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The recent development of caged oligonucletides that are efficiently activated by ultraviolet (UV) light creates opportunities for regulating gene expression with very high spatial and temporal resolution. By selectively modulating gene activity, these photochemical tools will facilitate efforts to elucidate gene function and may eventually serve therapeutic aims. We demonstrate how the incorporation of a photocleavable blocking group within a DNA duplex can transiently arrest DNA polymerase activity. Indeed, caged oligonucleotides make it possible to control many different protein-oligonucleotide interactions. In related experiments, hybridization of a reverse complementary (antisense) oligodeoxynucleotide to target mRNA can inhibit translation by recruiting endogenous RNases or sterically blocking the ribosome. Our laboratory recently synthesized caged antisense oligonucleotides composed of phosphorothioated DNA or peptide nucleic acid (PNA). The antisense oligonucleotide, which was attached to a complementary blocking oligonucleotide strand by a photocleavable linker, was blocked from binding target mRNA. This provided a useful method for photomodulating hybridization of the antisense strand to target mRNA. Caged DNA and PNA oligonucleotides have proven effective at photoregulating gene expression in cells and zebrafish embryos.
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Affiliation(s)
- Ivan J Dmochowski
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
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40
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Patnaik S, Kumar P, Garg BS, Gandhi RP, Gupta KC. Photomodulation of PS-modified oligonucleotides containing azobenzene substituent at pre-selected positions in phosphate backbone. Bioorg Med Chem 2007; 15:7840-9. [PMID: 17870546 DOI: 10.1016/j.bmc.2007.08.042] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2007] [Revised: 08/21/2007] [Accepted: 08/23/2007] [Indexed: 11/20/2022]
Abstract
A new protocol has been developed for incorporation of a photoisomerizable azobenzene moiety into synthetic stereo-enriched [R(p)] and [S(p)] PS-oligonucleotides. The azobenzene pendant is attached at pre-selected positions in internucleotidic phosphorothioate oligonucleotides of both [R(p)] and [S(p)] diastereomers using a novel reagent, N-iodoacetyl-p-aminoazobenzene, 1. The modified oligomers are purified on HPLC, characterized by LC-MS, and examined for their thermal and photoisomerization properties. The azobenzene moiety imparts greater stability to oligomer duplexes in (E) NN configuration as compared to (Z) configuration. The placement of the azobenzene pendant close to 5'-terminus (n-1) and 3'-terminus of the modified PS-oligos contributes maximum stability to the duplex while a gradual decline in stability occurs with azobenzene moving toward middle of the duplex. Circular Dichroism studies reveal that the chiral environment at the phosphorus center of the PS-oligos does not alter the global conformation of the DNA duplex as such, suggesting conservation of conformation of the modified DNA strands.
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Affiliation(s)
- Satyakam Patnaik
- Nucleic Acids Research Laboratory, Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, Delhi 110 007, India
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Tang X, Dmochowski IJ. Controlling RNA digestion by RNase H with a light-activated DNA hairpin. Angew Chem Int Ed Engl 2007; 45:3523-6. [PMID: 16634105 DOI: 10.1002/anie.200600954] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Xinjing Tang
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104-6323, USA
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42
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Keiper S, Vyle JS. Reversible photocontrol of deoxyribozyme-catalyzed RNA cleavage under multiple-turnover conditions. Angew Chem Int Ed Engl 2007; 45:3306-9. [PMID: 16619331 DOI: 10.1002/anie.200600164] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sonja Keiper
- School of Chemistry and Chemical Engineering, Queen's University Belfast, Belfast BT9 5AG, UK
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43
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Abstract
Biologically active compounds which are light-responsive offer experimental possibilities which are otherwise very difficult to achieve. Since light can be manipulated very precisely, for example, with lasers and microscopes rapid jumps in concentration of the active form of molecules are possible with exact control of the area, time, and dosage. The development of such strategies started in the 1970s. This review summarizes new developments of the last five years and deals with "small molecules", proteins, and nucleic acids which can either be irreversibly activated with light (these compounds are referred to as "caged compounds") or reversibly switched between an active and an inactive state.
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Affiliation(s)
- Günter Mayer
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.
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Nishioka H, Liang X, Kashida H, Asanuma H. 2′,6′-Dimethylazobenzene as an efficient and thermo-stable photo-regulator for the photoregulation of DNA hybridization. Chem Commun (Camb) 2007:4354-6. [DOI: 10.1039/b708952j] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Tang X, Dmochowski IJ. Regulating gene expression with light-activated oligonucleotides. MOLECULAR BIOSYSTEMS 2006; 3:100-10. [PMID: 17245489 DOI: 10.1039/b614349k] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Since the development of light-responsive amino acids, the activity of numerous biomolecules has been photomodulated in biochemical, biophysical, and cellular assays. Biological problems of even greater complexity motivate the development of quantitative methods for controlling gene activity with high spatial and temporal resolution, using light as an external trigger. Photoresponsive DNA and RNA oligonucleotides would optimally serve this purpose, but have proven difficult to expand from proofs-of-concept to in vivo experiments. Until recently, the development of this technology was limited by the synthesis of oligonucleotides whose function could be significantly modulated with near-UV light. New synthetic protocols and strategies for both up- and down-regulating gene activity finally make it possible to address biological considerations. In the near future, we can expect photoresponsive DNA and RNA molecules that are relatively non-toxic, nuclease-resistant, and maintain their specificity and activity in vivo. Quantitative, laser-initiated methods for controlling DNA and RNA function will illuminate new areas in cell and developmental biology.
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Affiliation(s)
- XinJing Tang
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104-6323, USA
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46
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47
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Tang X, Dmochowski IJ. Controlling RNA Digestion by RNase H with a Light-Activated DNA Hairpin. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200600954] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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48
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Keiper S, Vyle JS. Reversible Photocontrol of Deoxyribozyme-Catalyzed RNA Cleavage under Multiple-Turnover Conditions. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200600164] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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49
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Liu M, Asanuma H, Komiyama M. Azobenzene-tethered T7 promoter for efficient photoregulation of transcription. J Am Chem Soc 2006; 128:1009-15. [PMID: 16417393 DOI: 10.1021/ja055983k] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Azobenzene was additionally introduced into side chain of T7 promoter for the photocontrol of transcription reaction by T7 RNA polymerase (T7 RNAP). When a single azobenzene molecule was introduced into the T7 promoter either at the loop-binding region of the RNAP (-7 to -11 position) or at the unwinding region (-1 to -4 position), transcription was suppressed in the trans-form but proceeded faster in the cis-form. The amount of transcripts after UV irradiation with respect to that in the dark was 1.5-2.0-fold. Kinetic analysis of the transcription reaction revealed that the photoregulatory mechanism was different in these positions. The photoisomerization of an azobenzene at the loop-binding region primarily affected Km. On the other hand, the isomerization of an azobenzene at the unwinding region mainly affected kcat. Still more clear-cut photoregulation was achieved when two azobenzenes were introduced into both loop-binding and unwinding regions, respectively: transcription proceeded 7.6-fold faster after UV irradiation than that in the dark. This synergistic effect was observed only when two azobenzenes were introduced into these two different regions, respectively, and introduction of them into the same loop-binding region drastically lowered the transcription activity. The cooperation of two azobenzenes at loop-binding and unwinding regions would contribute to the clear-cut photoregulation of transcription.
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Affiliation(s)
- Mingzhe Liu
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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Tang X, Richards JL, Peritz AE, Dmochowski IJ. Photoregulation of DNA polymerase I (Klenow) with caged fluorescent oligodeoxynucleotides. Bioorg Med Chem Lett 2005; 15:5303-6. [PMID: 16188439 DOI: 10.1016/j.bmcl.2005.08.058] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2005] [Revised: 08/08/2005] [Accepted: 08/10/2005] [Indexed: 10/25/2022]
Abstract
The DNA polymerase reaction by Klenow fragment (KF) was efficiently regulated with UV light using a 25-mer caged fluorescent oligodeoxynucleotide (CFO) as the template. The CFO was functionalized with a fluorescein reporter (Fl) and photocleavable DABSYL quencher moiety (Dab). With Fl and Dab at adjacent cytidines in the middle at the template, KF was blocked from extending a complementary 12-mer primer. Upon UV photolysis of the DABSYL blocking group under aerobic conditions, fluorescein emission was restored and 50% of the primers were fully extended by KF.
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Affiliation(s)
- XinJing Tang
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104-6323, USA
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