1
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Gorman J, Hart SM, John T, Castellanos MA, Harris D, Parsons MF, Banal JL, Willard AP, Schlau-Cohen GS, Bathe M. Sculpting photoproducts with DNA origami. Chem 2024; 10:1553-1575. [PMID: 38827435 PMCID: PMC11138899 DOI: 10.1016/j.chempr.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Natural light-harvesting systems spatially organize densely packed dyes in different configurations to either transport excitons or convert them into charge photoproducts, with high efficiency. In contrast, artificial photosystems like organic solar cells and light-emitting diodes lack this fine structural control, limiting their efficiency. Thus, biomimetic multi-dye systems are needed to organize dyes with the sub-nanometer spatial control required to sculpt resulting photoproducts. Here, we synthesize 11 distinct perylene diimide (PDI) dimers integrated into DNA origami nanostructures and identify dimer architectures that offer discrete control over exciton transport versus charge separation. The large structural-space and site-tunability of origami uniquely provides controlled PDI dimer packing to form distinct excimer photoproducts, which are sensitive to interdye configurations. In the future, this platform enables large-scale programmed assembly of dyes mimicking natural systems to sculpt distinct photophysical products needed for a broad range of optoelectronic devices, including solar energy converters and quantum information processors.
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Affiliation(s)
- Jeffrey Gorman
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- These authors contributed equally
| | - Stephanie M. Hart
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- These authors contributed equally
| | - Torsten John
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Maria A. Castellanos
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Dvir Harris
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Molly F. Parsons
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - James L. Banal
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Adam P. Willard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Lead contact
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2
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Yang F, Li R, Wei W, Ding X, Xu Z, Wang P, Wang G, Xu Y, Fu H, Zhao Y. Water‐Soluble Doubly‐Strapped Isolated Perylene Diimide Chromophore. Angew Chem Int Ed Engl 2022; 61:e202202491. [DOI: 10.1002/anie.202202491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Fei Yang
- Beijing Key Laboratory for Optical Materials and Photonic Devices Department of Chemistry Capital Normal University Beijing 100048 P. R. China
- School of Chemistry and Chemical Engineering Beijing Institute of Technology Beijing 100081 P. R. China
| | - Ran Li
- Beijing Key Laboratory for Optical Materials and Photonic Devices Department of Chemistry Capital Normal University Beijing 100048 P. R. China
| | - Wei Wei
- Beijing Key Laboratory for Optical Materials and Photonic Devices Department of Chemistry Capital Normal University Beijing 100048 P. R. China
- Division of Chemistry and Biological Chemistry School of Physical and Mathematical Sciences Nanyang Technological University 21 Nanyang Link 637371 Singapore Singapore
| | - Xingwei Ding
- Division of Chemistry and Biological Chemistry School of Physical and Mathematical Sciences Nanyang Technological University 21 Nanyang Link 637371 Singapore Singapore
- National Engineering Research Center for Bioengineering Drugs and the Technologies Institute of Translational Medicine, Nanchang University Nanchang Jiangxi 330038 P. R. China
| | - Zhenzhen Xu
- Beijing Key Laboratory for Optical Materials and Photonic Devices Department of Chemistry Capital Normal University Beijing 100048 P. R. China
| | - Ping Wang
- Beijing Key Laboratory for Optical Materials and Photonic Devices Department of Chemistry Capital Normal University Beijing 100048 P. R. China
| | - Guo Wang
- Beijing Key Laboratory for Optical Materials and Photonic Devices Department of Chemistry Capital Normal University Beijing 100048 P. R. China
| | - Yanqing Xu
- School of Chemistry and Chemical Engineering Beijing Institute of Technology Beijing 100081 P. R. China
| | - Hongbing Fu
- Beijing Key Laboratory for Optical Materials and Photonic Devices Department of Chemistry Capital Normal University Beijing 100048 P. R. China
| | - Yanli Zhao
- Division of Chemistry and Biological Chemistry School of Physical and Mathematical Sciences Nanyang Technological University 21 Nanyang Link 637371 Singapore Singapore
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3
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Kihal N, Nazemi A, Bourgault S. Supramolecular Nanostructures Based on Perylene Diimide Bioconjugates: From Self-Assembly to Applications. NANOMATERIALS 2022; 12:nano12071223. [PMID: 35407341 PMCID: PMC9000806 DOI: 10.3390/nano12071223] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 03/31/2022] [Accepted: 04/02/2022] [Indexed: 12/18/2022]
Abstract
Self-assembling π-conjugated systems constitute efficient building blocks for the construction of supramolecular structures with tailored functional properties. In this context, perylene diimide (PDI) has attracted attention owing to its chemical robustness, thermal and photo-stability, and outstanding optical and electronic properties. Recently, the conjugation of PDI derivatives to biological molecules, including oligonucleotides and peptides, has opened new avenues for the design of nanoassemblies with unique structures and functionalities. In the present review, we offer a comprehensive summary of supramolecular bio-assemblies based on PDI. After briefly presenting the physicochemical, structural, and optical properties of PDI derivatives, we discuss the synthesis, self-assembly, and applications of PDI bioconjugates.
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Affiliation(s)
- Nadjib Kihal
- Department of Chemistry, Université du Québec, Montreal, QC H2X 2J6, Canada;
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, Quebec City, QC G1V 0A6, Canada
- Centre Québécois sur les Matériaux Fonctionnels/Québec Centre for Advanced Materials, CQMF/QCAM, Montreal, QC H3A 2A7, Canada
| | - Ali Nazemi
- Department of Chemistry, Université du Québec, Montreal, QC H2X 2J6, Canada;
- Centre Québécois sur les Matériaux Fonctionnels/Québec Centre for Advanced Materials, CQMF/QCAM, Montreal, QC H3A 2A7, Canada
- Correspondence: (A.N.); (S.B.)
| | - Steve Bourgault
- Department of Chemistry, Université du Québec, Montreal, QC H2X 2J6, Canada;
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, Quebec City, QC G1V 0A6, Canada
- Correspondence: (A.N.); (S.B.)
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4
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Yang F, Li R, Wei W, Ding X, Xu Z, Wang P, Wang G, Xu Y, Fu H, Zhao Y. Water‐Soluble Doubly‐Strapped Isolated Perylene Diimide Chromophore. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202202491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Fei Yang
- Beijing Key Laboratory for Optical Materials and Photonic Devices Department of Chemistry Capital Normal University Beijing 100048 P. R. China
- School of Chemistry and Chemical Engineering Beijing Institute of Technology Beijing 100081 P. R. China
| | - Ran Li
- Beijing Key Laboratory for Optical Materials and Photonic Devices Department of Chemistry Capital Normal University Beijing 100048 P. R. China
| | - Wei Wei
- Beijing Key Laboratory for Optical Materials and Photonic Devices Department of Chemistry Capital Normal University Beijing 100048 P. R. China
- Division of Chemistry and Biological Chemistry School of Physical and Mathematical Sciences Nanyang Technological University 21 Nanyang Link 637371 Singapore Singapore
| | - Xingwei Ding
- Division of Chemistry and Biological Chemistry School of Physical and Mathematical Sciences Nanyang Technological University 21 Nanyang Link 637371 Singapore Singapore
- National Engineering Research Center for Bioengineering Drugs and the Technologies Institute of Translational Medicine, Nanchang University Nanchang Jiangxi 330038 P. R. China
| | - Zhenzhen Xu
- Beijing Key Laboratory for Optical Materials and Photonic Devices Department of Chemistry Capital Normal University Beijing 100048 P. R. China
| | - Ping Wang
- Beijing Key Laboratory for Optical Materials and Photonic Devices Department of Chemistry Capital Normal University Beijing 100048 P. R. China
| | - Guo Wang
- Beijing Key Laboratory for Optical Materials and Photonic Devices Department of Chemistry Capital Normal University Beijing 100048 P. R. China
| | - Yanqing Xu
- School of Chemistry and Chemical Engineering Beijing Institute of Technology Beijing 100081 P. R. China
| | - Hongbing Fu
- Beijing Key Laboratory for Optical Materials and Photonic Devices Department of Chemistry Capital Normal University Beijing 100048 P. R. China
| | - Yanli Zhao
- Division of Chemistry and Biological Chemistry School of Physical and Mathematical Sciences Nanyang Technological University 21 Nanyang Link 637371 Singapore Singapore
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5
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Gao X, Zhang H, Shen Y, Li Y, Xiao K, Xu H, Zhang L, Yao Z. Visual detection of fluoride based on supramolecular aggregates of perylene diimide in 100% aqueous media. Mikrochim Acta 2021; 188:331. [PMID: 34498134 DOI: 10.1007/s00604-021-04990-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/16/2021] [Indexed: 11/25/2022]
Abstract
A water-soluble perylene imide derivative (PDI-Glu) was synthesized and their supramolecular aggregates composed of PDI-Glu and Al3+ were prepared as a "turn on" fluorometric probe to monitor F- in a purely aqueous system. Based on an "indicator displacement assay" (IDA) approach, the sensing performance and mechanism of PDI-Glu/Al3+ complex toward F- were investigated by absorption and emission spectra. It was suggested that disassembly of PDI-Glu/Al3+ aggregates was promoted by addition of F- through the competitive binding between Al3+ and F-. The detection limit is 240 nmol/L. This method featured simple preparation, excellent water solubility, adjustable self-assembly performance, ease of observation and operation, and high selectivity and sensitivity. It was used for monitoring F- in toothpaste and tap water samples with excellent accuracy and recovery. To the best of our knowledge, this is the first water-soluble perylene diimide-based probe for F- detection in 100% aqueous media. We believe this work could not only extend the sensing scope of water-soluble perylene diimide, but also bring some useful information for the rapid detection of anionic analytes in aqueous media. The disassembly of supramolecular aggregates of PDI-Glu/Al3+ along with significant fluorescence recovery enable a rapid and visual detection of F- based on an "indicator displacement assay" strategy.
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Affiliation(s)
- Xiao Gao
- Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Hao Zhang
- Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Yao Shen
- Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Yining Li
- Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Keren Xiao
- Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Huimin Xu
- Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Li Zhang
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, China
| | - Zhiyi Yao
- Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
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6
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Lin K, Burke A, King NB, Kahanda D, Mazaheripour A, Bartlett A, Dibble DJ, McWilliams MA, Taylor DW, Jocson J, Minary‐Jolandan M, Gorodetsky AA, Slinker JD. Enhancement of the Electrical Properties of DNA Molecular Wires through Incorporation of Perylenediimide DNA Base Surrogates. Chempluschem 2019; 84:416-419. [DOI: 10.1002/cplu.201800661] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/27/2019] [Indexed: 01/30/2023]
Affiliation(s)
- Kuo‐Yao Lin
- Department of Physics The University of Texas at Dallas 800 West Campbell Road, PHY 36 Richardson TX 75080-3021 USA
| | - Anthony Burke
- Department of Chemical Engineering and Materials Science 916 Engineering Tower University of California, Irvine Irvine CA 92697 USA
| | - Nolan B. King
- Department of Physics The University of Texas at Dallas 800 West Campbell Road, PHY 36 Richardson TX 75080-3021 USA
| | - Dimithree Kahanda
- Department of Physics The University of Texas at Dallas 800 West Campbell Road, PHY 36 Richardson TX 75080-3021 USA
| | - Amir Mazaheripour
- Department of Chemical Engineering and Materials Science 916 Engineering Tower University of California, Irvine Irvine CA 92697 USA
| | - Andrew Bartlett
- Department of Chemical Engineering and Materials Science 916 Engineering Tower University of California, Irvine Irvine CA 92697 USA
| | - David J. Dibble
- Department of Chemical Engineering and Materials Science 916 Engineering Tower University of California, Irvine Irvine CA 92697 USA
| | - Marc A. McWilliams
- Department of Physics The University of Texas at Dallas 800 West Campbell Road, PHY 36 Richardson TX 75080-3021 USA
| | - David W. Taylor
- Department of Physics The University of Texas at Dallas 800 West Campbell Road, PHY 36 Richardson TX 75080-3021 USA
| | - Jonah‐Micah Jocson
- Department of Chemical Engineering and Materials Science 916 Engineering Tower University of California, Irvine Irvine CA 92697 USA
| | - Majid Minary‐Jolandan
- Department of Mechanical Engineering The University of Texas at Dallas 800 W. Campbell Road, EC 38 Richardson TX 75080-3020 USA
| | - Alon A. Gorodetsky
- Department of Chemical Engineering and Materials Science 916 Engineering Tower University of California, Irvine Irvine CA 92697 USA
| | - Jason D. Slinker
- Department of Physics The University of Texas at Dallas 800 West Campbell Road, PHY 36 Richardson TX 75080-3021 USA
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7
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Zhao Z, Du T, Liang F, Liu S. Amphiphilic DNA Organic Hybrids: Functional Materials in Nanoscience and Potential Application in Biomedicine. Int J Mol Sci 2018; 19:E2283. [PMID: 30081520 PMCID: PMC6121482 DOI: 10.3390/ijms19082283] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 07/23/2018] [Accepted: 07/30/2018] [Indexed: 12/13/2022] Open
Abstract
Due to the addressability and programmability, DNA has been applied not merely in constructing static elegant nanostructures such as two dimensional and three dimensional DNA nanostructures but also in designing dynamic nanodevices. Moreover, DNA could combine with hydrophobic organic molecules to be a new amphiphilic building block and then self-assemble into nanomaterials. Of particular note, a recent state-of-the-art research has turned our attention to the amphiphilic DNA organic hybrids including small molecule modified DNA (lipid-DNA, fluorescent molecule-DNA, etc.), DNA block copolymers, and DNA-dendron hybrids. This review focuses mainly on the development of their self-assembly behavior and their potential application in nanomaterial and biomedicine. The potential challenges regarding of the amphiphilic DNA organic hybrids are also briefly discussed, aiming to advance their practical applications in nanoscience and biomedicine.
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Affiliation(s)
- Zhiyong Zhao
- The State Key Laboratory of Refractories and Metallurgy, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, China.
| | - Ting Du
- The State Key Laboratory of Refractories and Metallurgy, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, China.
| | - Feng Liang
- The State Key Laboratory of Refractories and Metallurgy, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, China.
| | - Simin Liu
- The State Key Laboratory of Refractories and Metallurgy, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, China.
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8
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Takada T, Ishino S, Takata A, Nakamura M, Fujitsuka M, Majima T, Yamana K. Rapid Electron Transfer of Stacked Heterodimers of Perylene Diimide Derivatives in a DNA Duplex. Chemistry 2018; 24:8228-8232. [DOI: 10.1002/chem.201800947] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Indexed: 01/11/2023]
Affiliation(s)
- Tadao Takada
- Department of Applied Chemistry; Graduate School of Engineering; University of Hyogo; 2167 Shosha Himeji Hyogo 671-2280 Japan
| | - Syunya Ishino
- Department of Applied Chemistry; Graduate School of Engineering; University of Hyogo; 2167 Shosha Himeji Hyogo 671-2280 Japan
| | - Ami Takata
- Department of Applied Chemistry; Graduate School of Engineering; University of Hyogo; 2167 Shosha Himeji Hyogo 671-2280 Japan
| | - Mitsunobu Nakamura
- Department of Applied Chemistry; Graduate School of Engineering; University of Hyogo; 2167 Shosha Himeji Hyogo 671-2280 Japan
| | - Mamoru Fujitsuka
- The Institute of Scientific and Industrial Research (SANKEN); Osaka University; Mihogaoka 8-1 Ibaraki, Osaka 567-0047 Japan
| | - Tetsuro Majima
- The Institute of Scientific and Industrial Research (SANKEN); Osaka University; Mihogaoka 8-1 Ibaraki, Osaka 567-0047 Japan
| | - Kazushige Yamana
- Department of Applied Chemistry; Graduate School of Engineering; University of Hyogo; 2167 Shosha Himeji Hyogo 671-2280 Japan
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9
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Fujii T, K. Thazhathveetil A, Yildirim I, Young RM, Wasielewski MR, Schatz GC, Lewis FD. Structure and Dynamics of Electron Injection and Charge Recombination in i-Motif DNA Conjugates. J Phys Chem B 2017; 121:8058-8068. [DOI: 10.1021/acs.jpcb.7b04996] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Taiga Fujii
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Arun K. Thazhathveetil
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Ilyas Yildirim
- Department
of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, Florida 33458, United States
| | - Ryan M. Young
- Argonne-Northwestern Solar Energy Research (ANSER) Center and Institute for Sustainability and Energy at Northwestern, Evanston, Illinois 60208-3113, United States
| | - Michael R. Wasielewski
- Argonne-Northwestern Solar Energy Research (ANSER) Center and Institute for Sustainability and Energy at Northwestern, Evanston, Illinois 60208-3113, United States
| | - George C. Schatz
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Frederick D. Lewis
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, United States
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10
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Abendroth JM, Nakatsuka N, Ye M, Kim D, Fullerton EE, Andrews AM, Weiss PS. Analyzing Spin Selectivity in DNA-Mediated Charge Transfer via Fluorescence Microscopy. ACS NANO 2017; 11:7516-7526. [PMID: 28672111 DOI: 10.1021/acsnano.7b04165] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Understanding spin-selective interactions between electrons and chiral molecules is critical to elucidating the significance of electron spin in biological processes and to assessing the potential of chiral assemblies for organic spintronics applications. Here, we use fluorescence microscopy to visualize the effects of spin-dependent charge transport in self-assembled monolayers of double-stranded DNA on ferromagnetic substrates. Patterned DNA arrays provide background regions for every measurement to enable quantification of substrate magnetization-dependent fluorescence due to the chiral-induced spin selectivity effect. Fluorescence quenching of photoexcited dye molecules bound within DNA duplexes is dependent upon the rate of charge separation/recombination upon photoexcitation and the efficiency of DNA-mediated charge transfer to the surface. The latter process is modulated using an external magnetic field to switch the magnetization orientation of the underlying ferromagnetic substrates. We discuss our results in the context of the current literature on the chiral-induced spin selectivity effect across various systems.
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Affiliation(s)
| | | | | | - Dokyun Kim
- Center for Memory and Recording Research, University of California, San Diego , La Jolla, California 92093, United States
| | - Eric E Fullerton
- Center for Memory and Recording Research, University of California, San Diego , La Jolla, California 92093, United States
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11
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Mishra AK, Weissman H, Krieg E, Votaw KA, McCullagh M, Rybtchinski B, Lewis FD. Self‐Assembly of Perylenediimide–Single‐Strand‐DNA Conjugates: Employing Hydrophobic Interactions and DNA Base‐Pairing To Create a Diverse Structural Space. Chemistry 2017; 23:10328-10337. [DOI: 10.1002/chem.201700752] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Indexed: 01/05/2023]
Affiliation(s)
| | - Haim Weissman
- Department of Organic ChemistryWeizmann Institute of Science Rehovot 76100 Israel
| | - Elisha Krieg
- Department of Organic ChemistryWeizmann Institute of Science Rehovot 76100 Israel
| | - Kevin A. Votaw
- Department of ChemistryColorado State University Fort Collins Colorado 80523 USA
| | - Martin McCullagh
- Department of ChemistryColorado State University Fort Collins Colorado 80523 USA
| | - Boris Rybtchinski
- Department of Organic ChemistryWeizmann Institute of Science Rehovot 76100 Israel
| | - Frederick D. Lewis
- Department of ChemistryNorthwestern University Evanston Illinois 60208-3113 USA
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12
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Xiang Y, Zhang Q, Li Z, Chen H. Role of electrostatic complementarity between perylenediimide and porphyrin in highly stabilized GNA. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2017; 70:1156-1162. [DOI: 10.1016/j.msec.2016.03.111] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/03/2016] [Accepted: 03/30/2016] [Indexed: 10/22/2022]
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13
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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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14
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Takada T, Ido M, Ashida A, Nakamura M, Yamana K. DNA-Templated Synthesis of Perylenediimide Stacks Utilizing Abasic Sites as Binding Pockets and Reactive Sites. Chembiochem 2016; 17:2230-2233. [DOI: 10.1002/cbic.201600454] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Tadao Takada
- Department of Applied Chemistry; Graduate School of Engineering; University of Hyogo; 2167 Shosha Himeji Hyogo 671-2280 Japan
| | - Misa Ido
- Department of Applied Chemistry; Graduate School of Engineering; University of Hyogo; 2167 Shosha Himeji Hyogo 671-2280 Japan
| | - Akane Ashida
- Department of Applied Chemistry; Graduate School of Engineering; University of Hyogo; 2167 Shosha Himeji Hyogo 671-2280 Japan
| | - Mitsunobu Nakamura
- Department of Applied Chemistry; Graduate School of Engineering; University of Hyogo; 2167 Shosha Himeji Hyogo 671-2280 Japan
| | - Kazushige Yamana
- Department of Applied Chemistry; Graduate School of Engineering; University of Hyogo; 2167 Shosha Himeji Hyogo 671-2280 Japan
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15
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Wardrip AG, Mazaheripour A, Hüsken N, Jocson J, Bartlett A, Lopez RC, Frey N, Markegard CB, Kladnik G, Cossaro A, Floreano L, Verdini A, Burke AM, Dickson MN, Kymissis I, Cvetko D, Morgante A, Sharifzadeh S, Nguyen HD, Gorodetsky AA. Length‐Independent Charge Transport in Chimeric Molecular Wires. Angew Chem Int Ed Engl 2016; 55:14267-14271. [DOI: 10.1002/anie.201605411] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 07/14/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Austin G. Wardrip
- Department of Chemistry University of California, Irvine Irvine CA 92697 USA
| | - Amir Mazaheripour
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Nina Hüsken
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Jonah‐Micah Jocson
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Andrew Bartlett
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Robert C. Lopez
- Department of Chemistry University of California, Irvine Irvine CA 92697 USA
| | - Nathan Frey
- Department of Electrical and Computer Engineering Boston University Boston MA 02215 USA
| | - Cade B. Markegard
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Gregor Kladnik
- CNR-IOM Laboratorio TASC Trieste 34149 Italy
- Faculty for Mathematics and Physics University of Ljubljana Jadranska 19 1000 Ljubljana Slovenia
| | | | | | | | - Anthony M. Burke
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Mary N. Dickson
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Ioannis Kymissis
- Department of Electrical Engineering Columbia University New York NY 10027 USA
| | - Dean Cvetko
- CNR-IOM Laboratorio TASC Trieste 34149 Italy
- Faculty for Mathematics and Physics University of Ljubljana Jadranska 19 1000 Ljubljana Slovenia
- Institut J. Stefan Jamova 39 1000 Ljubljana Slovenia
| | - Alberto Morgante
- CNR-IOM Laboratorio TASC Trieste 34149 Italy
- Department of Physics University of Trieste Trieste 34128 Italy
| | - Sahar Sharifzadeh
- Department of Electrical and Computer Engineering Boston University Boston MA 02215 USA
| | - Hung D. Nguyen
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Alon A. Gorodetsky
- Department of Chemistry University of California, Irvine Irvine CA 92697 USA
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
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16
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Wardrip AG, Mazaheripour A, Hüsken N, Jocson J, Bartlett A, Lopez RC, Frey N, Markegard CB, Kladnik G, Cossaro A, Floreano L, Verdini A, Burke AM, Dickson MN, Kymissis I, Cvetko D, Morgante A, Sharifzadeh S, Nguyen HD, Gorodetsky AA. Length‐Independent Charge Transport in Chimeric Molecular Wires. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Austin G. Wardrip
- Department of Chemistry University of California, Irvine Irvine CA 92697 USA
| | - Amir Mazaheripour
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Nina Hüsken
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Jonah‐Micah Jocson
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Andrew Bartlett
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Robert C. Lopez
- Department of Chemistry University of California, Irvine Irvine CA 92697 USA
| | - Nathan Frey
- Department of Electrical and Computer Engineering Boston University Boston MA 02215 USA
| | - Cade B. Markegard
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Gregor Kladnik
- CNR-IOM Laboratorio TASC Trieste 34149 Italy
- Faculty for Mathematics and Physics University of Ljubljana Jadranska 19 1000 Ljubljana Slovenia
| | | | | | | | - Anthony M. Burke
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Mary N. Dickson
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Ioannis Kymissis
- Department of Electrical Engineering Columbia University New York NY 10027 USA
| | - Dean Cvetko
- CNR-IOM Laboratorio TASC Trieste 34149 Italy
- Faculty for Mathematics and Physics University of Ljubljana Jadranska 19 1000 Ljubljana Slovenia
- Institut J. Stefan Jamova 39 1000 Ljubljana Slovenia
| | - Alberto Morgante
- CNR-IOM Laboratorio TASC Trieste 34149 Italy
- Department of Physics University of Trieste Trieste 34128 Italy
| | - Sahar Sharifzadeh
- Department of Electrical and Computer Engineering Boston University Boston MA 02215 USA
| | - Hung D. Nguyen
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
| | - Alon A. Gorodetsky
- Department of Chemistry University of California, Irvine Irvine CA 92697 USA
- Department of Chemical Engineering and Materials Science University of California, Irvine Irvine CA 92697 USA
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17
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Berndl S, Dimitrov SD, Menacher F, Fiebig T, Wagenknecht HA. Thiazole Orange Dimers in DNA: Fluorescent Base Substitutions with Hybridization Readout. Chemistry 2016; 22:2386-95. [DOI: 10.1002/chem.201503849] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Indexed: 01/03/2023]
Affiliation(s)
- Sina Berndl
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
- Institute of Organic Chemistry; University of Regensburg; 93040 Regensburg Germany
| | - Stoichko D. Dimitrov
- Centre for Plastic Electronics; Department of Chemistry; Imperial College London; Exhibition Road London SW7 2AZ UK
| | - Florian Menacher
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
- Institute of Organic Chemistry; University of Regensburg; 93040 Regensburg Germany
| | - Torsten Fiebig
- Feinberg School of Medicine; Department of Otolaryngology; Northwestern University; 420 East Superior Street Chicago IL 60611 USA
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
- Institute of Organic Chemistry; University of Regensburg; 93040 Regensburg Germany
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18
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Singleton DG, Hussain R, Siligardi G, Kumar P, Hrdlicka PJ, Berova N, Stulz E. Increased duplex stabilization in porphyrin-LNA zipper arrays with structure dependent exciton coupling. Org Biomol Chem 2016; 14:149-57. [PMID: 26416024 PMCID: PMC4766578 DOI: 10.1039/c5ob01681a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 09/18/2015] [Indexed: 12/23/2022]
Abstract
Porphyrins were attached to LNA uridine building blocks via rigid 5-acetylene or more flexible propargyl-amide linkers and incorporated into DNA strands. The systems show a greatly increased thermodynamic stability when using as little as three porphyrins in a zipper arrangement. Thermodynamic analysis reveals clustering of the strands into more ordered duplexes with both greater negative ΔΔS and ΔΔH values, and less ordered duplexes with small positive ΔΔS differences, depending on the combination of linkers used. The exciton coupling between the porphyrins is dependent on the flanking DNA sequence in the single stranded form, and on the nature of the linker between the nucleobase and the porphyrin in the double stranded form; it is, however, also strongly influenced by intermolecular interactions. This system is suitable for the formation of stable helical chromophore arrays with sequence and structure dependent exciton coupling.
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Affiliation(s)
- Daniel G. Singleton
- School of Chemistry and Institute for Life Sciences , University of Southampton , Highfield , Southampton , SO17 1BJ , UK . ; http://www.southampton.ac.uk/chemistry/about/staff/est.page?
| | - Rohanah Hussain
- Diamond Light Source , Harwell Science and Innovation Campus , Didcot , Oxfordshire OX11 0DE , UK
| | - Giuliano Siligardi
- Diamond Light Source , Harwell Science and Innovation Campus , Didcot , Oxfordshire OX11 0DE , UK
| | - Pawan Kumar
- Department of Chemistry , University of Idaho , Moscow , ID 83844 , USA
| | | | - Nina Berova
- Department of Chemistry , Columbia University , 3000 Broadway , New York , NY 10027 , USA
| | - Eugen Stulz
- School of Chemistry and Institute for Life Sciences , University of Southampton , Highfield , Southampton , SO17 1BJ , UK . ; http://www.southampton.ac.uk/chemistry/about/staff/est.page?
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19
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Mutsamwira S, Ainscough EW, Partridge AC, Derrick PJ, Filichev VV. DNA-Based Assemblies for Photochemical Upconversion. J Phys Chem B 2015; 119:14045-52. [DOI: 10.1021/acs.jpcb.5b07489] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Saymore Mutsamwira
- Institute
of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand
| | - Eric W. Ainscough
- Institute
of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand
| | - Ashton C. Partridge
- Institute
of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand
- Department
of Physics and School of Engineering, The University of Auckland, 20 Symonds Street, Auckland 1010, New Zealand
| | - Peter J. Derrick
- Institute
of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand
- Department
of Physics and School of Engineering, The University of Auckland, 20 Symonds Street, Auckland 1010, New Zealand
| | - Vyacheslav V. Filichev
- Institute
of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand
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20
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Markegard CB, Mazaheripour A, Jocson JM, Burke AM, Dickson MN, Gorodetsky AA, Nguyen HD. Molecular Dynamics Simulations of Perylenediimide DNA Base Surrogates. J Phys Chem B 2015; 119:11459-65. [DOI: 10.1021/acs.jpcb.5b03874] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Cade B. Markegard
- Department of Chemical Engineering and Materials Science and ‡Department of
Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Amir Mazaheripour
- Department of Chemical Engineering and Materials Science and ‡Department of
Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Jonah-Micah Jocson
- Department of Chemical Engineering and Materials Science and ‡Department of
Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Anthony M. Burke
- Department of Chemical Engineering and Materials Science and ‡Department of
Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Mary N. Dickson
- Department of Chemical Engineering and Materials Science and ‡Department of
Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Alon A. Gorodetsky
- Department of Chemical Engineering and Materials Science and ‡Department of
Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Hung D. Nguyen
- Department of Chemical Engineering and Materials Science and ‡Department of
Chemistry, University of California, Irvine, Irvine, California 92697, United States
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21
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Würthner F, Saha-Möller CR, Fimmel B, Ogi S, Leowanawat P, Schmidt D. Perylene Bisimide Dye Assemblies as Archetype Functional Supramolecular Materials. Chem Rev 2015; 116:962-1052. [PMID: 26270260 DOI: 10.1021/acs.chemrev.5b00188] [Citation(s) in RCA: 948] [Impact Index Per Article: 105.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Frank Würthner
- Institut für Organische Chemie and Center for Nanosystems Chemistry, Universität Würzburg , Am Hubland, 97074 Würzburg, Germany
| | - Chantu R Saha-Möller
- Institut für Organische Chemie and Center for Nanosystems Chemistry, Universität Würzburg , Am Hubland, 97074 Würzburg, Germany
| | - Benjamin Fimmel
- Institut für Organische Chemie and Center for Nanosystems Chemistry, Universität Würzburg , Am Hubland, 97074 Würzburg, Germany
| | - Soichiro Ogi
- Institut für Organische Chemie and Center for Nanosystems Chemistry, Universität Würzburg , Am Hubland, 97074 Würzburg, Germany
| | - Pawaret Leowanawat
- Institut für Organische Chemie and Center for Nanosystems Chemistry, Universität Würzburg , Am Hubland, 97074 Würzburg, Germany
| | - David Schmidt
- Institut für Organische Chemie and Center for Nanosystems Chemistry, Universität Würzburg , Am Hubland, 97074 Würzburg, Germany
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22
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Al Ouahabi A, Charles L, Lutz JF. Synthesis of Non-Natural Sequence-Encoded Polymers Using Phosphoramidite Chemistry. J Am Chem Soc 2015; 137:5629-35. [DOI: 10.1021/jacs.5b02639] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Abdelaziz Al Ouahabi
- Precision Macromolecular Chemistry, Institut Charles Sadron, UPR-22 CNRS, BP 84047, 23 rue du Loess, 67034 Strasbourg Cedex 2, France
| | - Laurence Charles
- Aix-Marseille Université, CNRS, Institute of Radical Chemistry, UMR 7273, 13397 Marseille Cedex 20, France
| | - Jean-François Lutz
- Precision Macromolecular Chemistry, Institut Charles Sadron, UPR-22 CNRS, BP 84047, 23 rue du Loess, 67034 Strasbourg Cedex 2, France
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23
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Gershberg J, Radić Stojković M, Škugor M, Tomić S, Rehm TH, Rehm S, Saha-Möller CR, Piantanida I, Würthner F. Sensing of Double-Stranded DNA/RNA Secondary Structures by Water Soluble Homochiral Perylene Bisimide Dyes. Chemistry 2015; 21:7886-95. [DOI: 10.1002/chem.201500184] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Indexed: 12/12/2022]
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24
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Takada T, Ido M, Ashida A, Nakamura M, Fujitsuka M, Kawai K, Majima T, Yamana K. Photocurrent Generation through Charge-Transfer Processes in Noncovalent Perylenediimide/DNA Complexes. Chemistry 2015; 21:6846-51. [DOI: 10.1002/chem.201406592] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Indexed: 12/30/2022]
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25
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Weiser M, Wagenknecht HA. Dynamic DNA architectures: spontaneous DNA strand exchange and self-sorting driven by perylene bisimide interactions. Chem Commun (Camb) 2015; 51:16530-3. [DOI: 10.1039/c5cc06491k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Three differently bay-substituted perylene bisimides together with the conventional unsubstituted chromophore were synthetically incorporated as homodimers in DNA double strands and undergo spontaneous strand exchange if mixed together.
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Affiliation(s)
- Martin Weiser
- Institute of Organic Chemistry
- Karlsruhe Institute of Technology (KIT)
- 76131 Karlsruhe
- Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry
- Karlsruhe Institute of Technology (KIT)
- 76131 Karlsruhe
- Germany
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26
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Doluca O, Withers JM, Loo TS, Edwards PJB, González C, Filichev VV. Interdependence of pyrene interactions and tetramolecular G4-DNA assembly. Org Biomol Chem 2015; 13:3742-8. [DOI: 10.1039/c4ob02499k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Our results demonstrate the expanded capabilities of G-quadruplex DNAs for directed chromophore arrangements and show new perspectives in the design of G-quadruplexes governed by non-guanine moieties.
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Affiliation(s)
- Osman Doluca
- College of Sciences
- Institute of Fundamental Sciences
- Massey University
- 4442 Palmerston North
- New Zealand
| | - Jamie M. Withers
- College of Sciences
- Institute of Fundamental Sciences
- Massey University
- 4442 Palmerston North
- New Zealand
| | - Trevor S. Loo
- College of Sciences
- Institute of Fundamental Sciences
- Massey University
- 4442 Palmerston North
- New Zealand
| | - Patrick J. B. Edwards
- College of Sciences
- Institute of Fundamental Sciences
- Massey University
- 4442 Palmerston North
- New Zealand
| | | | - Vyacheslav V. Filichev
- College of Sciences
- Institute of Fundamental Sciences
- Massey University
- 4442 Palmerston North
- New Zealand
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27
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Jalilov AS, Young RM, Eaton SW, Wasielewski MR, Lewis FD. Electronic Interactions of Michler's Ketone with DNA Bases in Synthetic Hairpins. Photochem Photobiol 2014; 91:739-47. [PMID: 25296568 DOI: 10.1111/php.12360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 09/30/2014] [Indexed: 11/26/2022]
Abstract
The mechanism and dynamics of photoinduced electron transfer in two families of DNA hairpins possessing Michler's ketone linkers have been investigated by means of steady state and time-resolved transient absorption and emission spectroscopies. The excited state behavior of the diol linker employed in hairpin synthesis is similar to that of Michler's ketone in methanol solution. Hairpins possessing only a Michler's ketone linker undergo fast singlet state charge separation and charge recombination with an adjacent purine base, attributed to well-stacked ground state conformations, and intersystem crossing to the triplet state, attributed to poorly stacked ground state conformations. The failure of the triplet to undergo electron transfer reactions on the 7 ns time scale of our measurements is attributed to the low triplet energy and reduction potential of the twisted triplet state. Hairpins possessing both a Michler's ketone linker and a perylenediimide base surrogate separated by four base pairs undergo photoinduced hole transport from the diimide to Michler's ketone upon excitation of the diimide. The efficiency of hole transport is dependent upon the sequence of the intervening purine bases.
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Affiliation(s)
- Almaz S Jalilov
- Department of Chemistry and Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, IL
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28
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Stubinitzky C, Bijeljanin A, Antusch L, Ebeling D, Hölscher H, Wagenknecht HA. Bifunctional DNA architectonics: three-way junctions with sticky perylene bisimide caps and a central metal lock. Chemistry 2014; 20:12009-14. [PMID: 25098549 DOI: 10.1002/chem.201402956] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Indexed: 12/23/2022]
Abstract
A new type of a bifunctional DNA architecture based on a three way junction is developed that combines the structural motif of sticky perylene bisimide caps with a tris-bipyridyl metal ion lock in the center part. A clear stabilizing effect was observed in the presence of Fe(3+), Ni(2+) and Zn(2+) by the formation of corresponding bipyridyl complexes in the branching part of the DNA three way junctions. The dimerization of the 5'-terminally attached perylene diimides (PDI) chromophores by hydrophobic interactions can be followed by significant changes in the UV/Vis absorption and steady-state fluorescence. The PDI-mediated DNA assembly occurs at temperatures below the melting temperature and is not influenced by the metal-ion bipyridyl locks in the central part. The corresponding AFM images revealed the formation of higher-ordered structures as the result of DNA assemblies mediated by the PDI interactions.
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Affiliation(s)
- Claudia Stubinitzky
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe (Germany), Fax: (+49)-721-608-44825
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29
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Takada T, Yamaguchi K, Tsukamoto S, Nakamura M, Yamana K. Light-up fluorescent probes utilizing binding behavior of perylenediimide derivatives to a hydrophobic pocket within DNA. Analyst 2014; 139:4016-21. [DOI: 10.1039/c4an00493k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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Neelakandan PP, Zeidan TA, McCullagh M, Schatz GC, Vura-Weis J, Kim CH, Wasielewski MR, Lewis FD. Ground and excited state electronic spectra of perylenediimide dimers with flexible and rigid geometries in DNA conjugates. Chem Sci 2014. [DOI: 10.1039/c3sc52908h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Ground and excited state spectra of co-facial PDI dimers embedded in DNA constructs depend on the geometry imposed by the construct.
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Affiliation(s)
- Prakash P. Neelakandan
- Department of Chemistry and Argonne-Northwestern Solar Energy Research (ANSER) Center
- Northwestern University
- Evanston, USA
| | - Tarek A. Zeidan
- Department of Chemistry and Argonne-Northwestern Solar Energy Research (ANSER) Center
- Northwestern University
- Evanston, USA
| | - Martin McCullagh
- Department of Chemistry and Argonne-Northwestern Solar Energy Research (ANSER) Center
- Northwestern University
- Evanston, USA
| | - George C. Schatz
- Department of Chemistry and Argonne-Northwestern Solar Energy Research (ANSER) Center
- Northwestern University
- Evanston, USA
| | - Josh Vura-Weis
- Department of Chemistry and Argonne-Northwestern Solar Energy Research (ANSER) Center
- Northwestern University
- Evanston, USA
| | - Chul Hoon Kim
- Department of Chemistry and Argonne-Northwestern Solar Energy Research (ANSER) Center
- Northwestern University
- Evanston, USA
| | - Michael R. Wasielewski
- Department of Chemistry and Argonne-Northwestern Solar Energy Research (ANSER) Center
- Northwestern University
- Evanston, USA
| | - Frederick D. Lewis
- Department of Chemistry and Argonne-Northwestern Solar Energy Research (ANSER) Center
- Northwestern University
- Evanston, USA
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31
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Takada T, Ashida A, Nakamura M, Yamana K. Cationic perylenediimide as a specific fluorescent binder to mismatch containing DNA. Bioorg Med Chem 2013; 21:6011-4. [PMID: 23953688 DOI: 10.1016/j.bmc.2013.07.040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 07/17/2013] [Accepted: 07/19/2013] [Indexed: 11/15/2022]
Abstract
Small ligand molecules, which can recognize thermodynamically unstable site within DNA, such as mismatch base pair, abasic site, and single-bulge, have attracted much attention because of their potential diagnostics and biological applications. In this paper, we describe the binding of cationic perylenediimide (cPDI) molecules to thymine-containing mismatch base pair in DNA and the formation of cPDI dimer at the mismatch site. The cPDI dimer exhibits a characteristic excimer emission at 650nm. For T/T mismatch containing DNA, the switching behavior from the PDI dimer (650nm) to the monomer (550nm) emission in specific response to Hg(2+) ion was observed.
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Affiliation(s)
- Tadao Takada
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan.
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32
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Griffith JA, Withers JM, Martin DJ, Rowlands GJ, Filichev VV. Ligand assembly and chirality transfer guided by DNA modified with enantiomerically pure [2.2]paracyclophanes. RSC Adv 2013. [DOI: 10.1039/c3ra41841c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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33
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Tanpure AA, Srivatsan SG. Synthesis and photophysical characterisation of a fluorescent nucleoside analogue that signals the presence of an abasic site in RNA. Chembiochem 2012; 13:2392-9. [PMID: 23070860 DOI: 10.1002/cbic.201200408] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Indexed: 11/07/2022]
Abstract
The synthesis and site-specific incorporation of an environment-sensitive fluorescent nucleoside analogue (2), based on a 5-(benzofuran-2-yl)pyrimidine core, into DNA oligonucleotides (ONs), and its photophysical properties within these ONs are described. Interestingly and unlike 2-aminopurine (a widely used nucleoside analogue probe), when incorporated into an ON and hybridised with a complementary ON, the emissive nucleoside 2 displays significantly higher emission intensity than the free nucleoside. Furthermore, photophysical characterisation shows that the fluorescence properties of the nucleoside analogue within ONs are significantly influenced by flanking bases, especially by guanosine. By utilising the responsiveness of the nucleoside to changes in base environment, a DNA ON reporter labelled with the emissive nucleoside 2 was constructed; this signalled the presence of an abasic site in a model depurinated sarcin/ricin RNA motif of a eukaryotic 28S rRNA.
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Affiliation(s)
- Arun A Tanpure
- Department of Chemistry, Indian Institute of Science Education and Research, 900, NCL Innovation Park, Dr. Homi Bhabha Road, Pune 411008, India
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34
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Fujii T, Hara Y, Osawa T, Kashida H, Liang X, Yoshida Y, Asanuma H. Bulge-like Asymmetric Heterodye Clustering in DNA Duplex Results in Efficient Quenching of Background Emission Based on the Maximized Excitonic Interaction. Chemistry 2012; 18:10865-72. [DOI: 10.1002/chem.201201365] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Indexed: 11/08/2022]
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35
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Takada T, Otsuka Y, Nakamura M, Yamana K. Molecular Arrangement and Assembly Guided by Hydrophobic Cavities inside DNA. Chemistry 2012; 18:9300-4. [DOI: 10.1002/chem.201201469] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Indexed: 11/07/2022]
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36
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Asanuma H, Fujii T, Kato T, Kashida H. Coherent interactions of dyes assembled on DNA. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2012. [DOI: 10.1016/j.jphotochemrev.2012.04.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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37
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Görl D, Zhang X, Würthner F. Molecular assemblies of perylene bisimide dyes in water. Angew Chem Int Ed Engl 2012; 51:6328-48. [PMID: 22573415 DOI: 10.1002/anie.201108690] [Citation(s) in RCA: 395] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Indexed: 01/28/2023]
Abstract
Perylene bisimides are among the most valuable functional dyes and have numerous potential applications. As a result of their chemical robustness, photostability, and outstanding optical and electronic properties, these dyes have been applied as pigments, fluorescence sensors, and n-semiconductors in organic electronics and photovoltaics. Moreover, the extended quadrupolar π system of this class of dyes has facilitated the construction of numerous supramolecular architectures with fascinating photophysical properties. However, the supramolecular approach to the formation of perylene bisimide aggregates has been restricted mostly to organic media. Pleasingly, considerable progress has been made in the last few years in developing water-soluble perylene bisimides and their application in aqueous media. This Review provides an up-to-date overview on the self-assembly of perylene bisimides through π-π interactions in aqueous media. Synthetic strategies for the preparation of water-soluble perylene bisimides and the influence of water on the π-π stacking of perylene bisimides as well as the resulting applications are discussed.
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Affiliation(s)
- Daniel Görl
- Universität Würzburg, Institut für Organische Chemie and Center for Nanosystems Chemistry, Am Hubland, 97074 Würzburg, Germany
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Görl D, Zhang X, Würthner F. Molekülverbände von Perylenbisimid-Farbstoffen in Wasser. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201108690] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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39
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Affiliation(s)
- Yin Nah Teo
- Department of Chemistry, Stanford University, California 94305, United States
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40
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Astakhova IV, Kumar TS, Wengel J. Fluorescent oligonucleotides containing a novel perylene 2′-amino-α-L-LNA monomer: Synthesis and analytical potential. ACTA ACUST UNITED AC 2011. [DOI: 10.1135/cccc2011096] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Herein, a novel fluorescent nucleotide analogue, perylene-2′-amino-α-L-LNA, has been prepared and studied within synthetic oligonucleotides of different sequences. The phosphoramidite reagent was synthesized in 85% overall yield starting from 2′-amino-α-L-LNA nucleoside. Incorporation efficiency of the resulting perylene-2′-amino-α-L-LNA monomer (T*) into synthetic oligonucleotides was significantly improved by replacement of the typically used 1H-tetrazole activator with pyridine hydrochloride. Generally, oligonucleotides containing monomerT* showed high binding affinity towards complementary DNA and RNA targets, batochromically shifted excitation/emission wavelengths with respect to the often applied polyaromatic hydrocarbon pyrene, high fluorescent quantum yields and very low target detection limits (5–10 nM). Fluorescence of single stranded LNA/DNA mixmer oligonucleotide having two incorporations of monomersT* was quenched (quantum yield ΦF= 0.21) relative to duplexes of this probe with complementary DNA and RNA (ΦF= 0.42 and 0.35, respectively). On the contrary, a strong fluorescence quenching upon target binding was demonstrated by two short oligonucleotides of analogues sequences containing monomersT* at 5′- and 3′-terminal positions. We explain the hybridization-induced light-up effect observed for double-labeled probe by a reduction of fluorescence quenching due to precise positioning of the fluorophores within the double-stranded complexes. Furthermore, we propose that a covalent link between twoT* monomers in the double-labeled probe provides a remarkable degree of rigidity in the double helix which enforces positioning of the bulky perylene moieties in the nonpolar groove resulting in reduced fluorescence quenching.
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41
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Lambertucci C, Buccioni M, Cacciari B, Dal Ben D, Federico S, Klotz KN, Marucci G, Volpini R, Spalluto G, Cristalli G. New 9-methyl-8-(4-hydroxyphenyl)adenine derivatives as A1 adenosine receptor antagonists. ACTA ACUST UNITED AC 2011. [DOI: 10.1135/cccc2011091] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A new series of 9-methyladenines, bearing different bulky groups at the 8-position, were prepared and their affinity for the four human adenosine receptor subtypes were evaluated. All the synthesized compounds showed affinities at the A1, A2A, and A3AR subtypes ranging from nanomolar to micromolar levels with different degrees of A1selectivity, while they resulted nearly inactive at A2BAR. In particular, 9-methyl-8-[4-(4-methylbenzyloxy)phenyl]- adenine showed A1AR affinity in the nanomolar range and good levels of selectivity versus the other receptor subtypes. Furthermore, a functional assay at mouse ileum allowed to assess the potency of selected compounds at A1AR subtype. Results showed that all the tested derivatives are neutral antagonists and theirKbvalues are in good agreement with theKivalues from radioligand binding assay at human A1AR, confirming that the effect is due to inhibition of this subtype.
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42
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Franceschin M, Borbone N, Oliviero G, Casagrande V, Scuotto M, Coppola T, Borioni S, Mayol L, Ortaggi G, Bianco A, Amato J, Varra M. Synthesis of a dibromoperylene phosphoramidite building block and its incorporation at the 5' end of a G-quadruplex forming oligonucleotide: spectroscopic properties and structural studies of the resulting dibromoperylene conjugate. Bioconjug Chem 2011; 22:1309-19. [PMID: 21688831 DOI: 10.1021/bc100526q] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Previous studies indicate that some perylene bisimide derivatives can drive the assembly of DNA G-quadruplexes, thus suggesting the possible advantage in the adoption of perylene-conjugated G-rich oligonucleotides in biological and biotechnological applications. Nevertheless, the typical poor solubility of perylene bisimides strongly limits the number of suitable chemical strategies to prepare perylene-conjugated oligonucleotides. In order to overcome these difficulties, we employed the earlier described core twisted perylene derivatives possessing unique optical and electronic properties, besides good solubility in common solvents. As a first result, the large-scale synthesis of a new dibromoperylene derivative (PEOEBr) phosphoramidite building block is herein reported. Furthermore, the structural behavior of the conjugated PEOEBr-GGGTTAGGG (HTRp2) human telomeric repeat was investigated by using CD, UV, fluorescence, and gel electrophoresis techniques in desalted water and in K(+)- and Na(+)-containing buffers. We observed that the peculiar property of PEOEBr moieties to form dimers instead of extended aggregates drives the HTRp2 strands toward dimerization and mainly promotes the formation of quadruplex species having both the 5'-ends located at the same side of the structures. However, the counterions present in solutions (K(+) or Na(+)) as well as the strand concentration, also contribute to influence the topology and the stoichiometry of formed structures. Furthermore, unlike the unmodified sequence GGGTTAGGG (HTR2), HTRp2 strands quickly associate into G-quadruplexes even in desalted water, as assessed by CD experiments.
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Affiliation(s)
- Marco Franceschin
- Dipartimento di Chimica, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Roma, Italy
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43
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Menacher F, Wagenknecht HA. Synthesis of DNA with Green Perylene Bisimides as DNA Base Substitutions. European J Org Chem 2011. [DOI: 10.1002/ejoc.201100519] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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44
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Menacher F, Wagenknecht HA. Ratiometric molecular beacons based on the perylene bisimide as a dimeric internal DNA base substitution. Photochem Photobiol Sci 2011; 10:1275-8. [PMID: 21547330 DOI: 10.1039/c1pp05091e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Molecular beacons with an excitonically interacting perylene bisimide base pair show the presence of the complementary olignucleotide sequence by both absorption and fluorescence changes.
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Affiliation(s)
- Florian Menacher
- University of Regensburg, Institute for Organic Chemistry, D-93040, Regensburg, Germany
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45
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Menacher F, Stepanenko V, Würthner F, Wagenknecht HA. Assembly of DNA triangles mediated by perylene bisimide caps. Chemistry 2011; 17:6683-8. [PMID: 21538613 DOI: 10.1002/chem.201100141] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Indexed: 02/01/2023]
Abstract
Perylene bisimides (PBI) have been synthetically incorporated as caps onto a Y-shaped DNA triple strand. These PBI caps serve as "sticky" ends in the spontaneous assembly of larger DNA ensembles, linking the triangular DNA through stacking interactions. This, in turn, yields a hypsochromic shift in the absorption and a red shift in the fluorescence as characteristic optical readouts. This assembly occurs spontaneously without any enzymatic ligation process and without the use of overhanging DNA as sticky ends. Instead, dimerizations of the PBI chromophores in the assembly are controlled by the DNA as a structural scaffold. Thereby, the PBI-driven assembly is fully reversible. Due to the fact that PBI dimerization does not occur in the single strand, the aggregates can be destroyed by thermal dehybridization of the DNA scaffold and reassembled by reannealing of the DNA construct. In view of the fact that PBI forms stable radical anions, the presented DNA architectures are not only interesting optical biomaterials, but are also promising materials for molecular electronics with DNA.
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Affiliation(s)
- Florian Menacher
- Institute for Organic Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
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46
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Ehrenschwender T, Wagenknecht HA. 4,4-Difluoro-4-bora-3a,4a-diaza-s-indacene as a Bright Fluorescent Label for DNA. J Org Chem 2011; 76:2301-4. [DOI: 10.1021/jo102519k] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Thomas Ehrenschwender
- Institute for Organic Chemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Hans-Achim Wagenknecht
- Institute for Organic Chemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
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47
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Kashida H, Hayashi T, Fujii T, Asanuma H. A cationic dye triplet as a unique "glue" that can connect fully matched termini of DNA duplexes. Chemistry 2011; 17:2614-22. [PMID: 21305625 DOI: 10.1002/chem.201003059] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Indexed: 11/08/2022]
Abstract
In this study, we propose that three consecutive cationic p-methylstilbazoles tethered on D-threoninols (Z residues) at 5' termini act as a unique "glue" connecting DNA duplexes by their interstrand cluster formation. Interstrand clustering of p-methylstilbazoles (ZZZ triplets) induces narrowing and hypsochromic shift of bands at 350 nm, which can be assigned to the absorption of p-methylstilbazole. However, single-stranded DNA conjugates involving a ZZZ triplet at the 5' terminus of 8-mer native nucleotides is found not to induce such large spectral changes, which implies that the intrinsic self-assembling property of ZZZ triplets is weak. Interestingly, when this conjugate is hybridized with a complementary 8-mer native oligonucleotide, a remarkable spectral change is observed, indicating the dimerization of a duplex through the interstrand clustering of ZZZ triplets. Dimerization of the duplex is also evidenced by cold-spray ionization mass spectrometry. This interstrand clustering is observed only when a ZZZ triplet is tethered to a 5' rather than 3' terminus. Furthermore, the stability of the interstrand cluster increases by increasing the number of nucleobases of the DNA portion, and when mismatched base pairs are incorporated or when a base next to the Z residue is deleted, the stability substantially drops. When we apply the ZZZ triplet to the formation of a nanowire using two complementary DNA conjugates, each of which has a ZZZ triplet at the 5' termini as overhang, we demonstrate the successful formation of a nanowire by native PAGE analysis. Since native sticky ends that have three nucleotides do not serve as "glue", ZZZ triplets with their unique glue-like properties are prime candidates for constructing DNA-based nanoarchitectures.
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Affiliation(s)
- Hiromu Kashida
- Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya, Japan
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48
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Wenger D, Malinovskii VL, Häner R. Modulation of chiroptical properties by DNA-guided assembly of fluorenes. Chem Commun (Camb) 2011; 47:3168-70. [PMID: 21283836 DOI: 10.1039/c0cc05125j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The supramolecular organization of fluorene building blocks in a DNA scaffold is described. The molecular assembly into ordered π-aggregates leads to distinct changes in the electronic properties.
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Affiliation(s)
- Daniel Wenger
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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49
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Berndl S, Herzig N, Kele P, Lachmann D, Li X, Wolfbeis OS, Wagenknecht HA. Comparison of a nucleosidic vs non-nucleosidic postsynthetic "click" modification of DNA with base-labile fluorescent probes. Bioconjug Chem 2010; 20:558-64. [PMID: 19220008 DOI: 10.1021/bc8004864] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The azides 1 and 2 bearing a phenoxazinium and a coumarin fluorophore, respectively, were applied in postsynthetic "click"-type bioconjugation and coupled to oligonucleotides modified with alkyne groups using two alternative approaches: (i) as a nucleotide modification at the 2'-position of uridine and (ii) as a nucleotide substitution using (S)-(-)-3-amino-1,2-propanediol as an acyclic linker between the phosphodiester bridges. The corresponding alkynylated phosporamidites 3 and 6 were used as DNA building blocks for the preparation of alkyne-bearing DNA duplexes. The base pairs adjacent to the site of modification and the base opposite to it were varied in the DNA sequences. The modified duplexes were investigated by UV/vis absorption spectroscopy (including melting temperatures) and fluorescence spectroscopy in order to study the different optical properties of the two chromophores and to evaluate their potential for bioanalytical applications. The sequence-selective fluorescence quenching of phenoxazinium 1 differs only slightly and does not depend on the type of modification, meaning whether it has been attached to the 2'-position of uridine or as DNA base surrogate using the acyclic glycol linker. The 2'-chromophore-modified uridine still recognizes adenine as the counterbase, and the duplexes exhibit a sufficient thermal stability that is comparable to that of unmodified duplexes. Thus, the application of the 2'-modification site of uridine is preferred in comparison to glycol-assisted DNA base surrogates. Accordingly, the coumarin dye azide 2 was attached only to the 2'-position of uridine. The significant Stokes shift of approximately 100 nm and the good quantum yields make the coumarin chromophore a powerful fluorescent label for nucleic acids.
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Affiliation(s)
- Sina Berndl
- Institute of Organic Chemistry, University of Regensburg, Regensburg, Germany
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50
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Kashida H, Sekiguchi K, Asanuma H. Insulator Base Pairs for Lighting-up Perylenediimide in a DNA Duplex. Chemistry 2010; 16:11554-7. [DOI: 10.1002/chem.201001638] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Indexed: 11/10/2022]
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