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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Hart SM, Gorman J, Bathe M, Schlau-Cohen GS. Engineering Exciton Dynamics with Synthetic DNA Scaffolds. Acc Chem Res 2023; 56:2051-2061. [PMID: 37345736 DOI: 10.1021/acs.accounts.3c00086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2023]
Abstract
Excitons are the molecular-scale currency of electronic energy. Control over excitons enables energy to be directed and harnessed for light harvesting, electronics, and sensing. Excitonic circuits achieve such control by arranging electronically active molecules to prescribe desired spatiotemporal dynamics. Photosynthetic solar energy conversion is a canonical example of the power of excitonic circuits, where chromophores are positioned in a protein scaffold to perform efficient light capture, energy transport, and charge separation. Synthetic systems that aim to emulate this functionality include self-assembled aggregates, molecular crystals, and chromophore-modified proteins. While the potential of this approach is clear, these systems lack the structural precision to control excitons or even test the limits of their power. In recent years, DNA origami has emerged as a designer material that exploits biological building blocks to construct nanoscale architectures. The structural precision afforded by DNA origami has enabled the pursuit of naturally inspired organizational principles in a highly precise and scalable manner. In this Account, we describe recent developments in DNA-based platforms that spatially organize chromophores to construct tunable excitonic systems. The high fidelity of DNA base pairing enables the formation of programmable nanoscale architectures, and sequence-specific placement allows for the precise positioning of chromophores within the DNA structure. The integration of a wide range of chromophores across the visible spectrum introduces spectral tunability. These excitonic DNA-chromophore assemblies not only serve as model systems for light harvesting, solar conversion, and sensing but also lay the groundwork for the integration of coupled chromophores into larger-scale nucleic acid architectures.We have used this approach to generate DNA-chromophore assemblies of strongly coupled delocalized excited states through both sequence-specific self-assembly and the covalent attachment of chromophores. These strategies have been leveraged to independently control excitonic coupling and system-bath interaction, which together control energy transfer. We then extended this framework to identify how scaffold configurations can steer the formation of symmetry-breaking charge transfer states, paving the way toward the design of dual light-harvesting and charge separation DNA machinery. In an orthogonal application, we used the programmability of DNA chromophore assemblies to change the optical emission properties of strongly coupled dimers, generating a series of fluorophore-modified constructs with separable emission properties for fluorescence assays. Upcoming advances in the chemical modification of nucleotides, design of large-scale DNA origami, and predictive computational methods will aid in constructing excitonic assemblies for optical and computing applications. Collectively, the development of DNA-chromophore assemblies as a platform for excitonic circuitry offers a pathway to identifying and applying design principles for light harvesting and molecular electronics.
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Affiliation(s)
- Stephanie M Hart
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jeffrey Gorman
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Gabriela S Schlau-Cohen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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3
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Maity D, Bhaumik SK, Banerjee S. Contrasting luminescence in heparin and DNA-templated co-assemblies of dimeric cyanostilbenes: efficient energy transfer in heparin-based co-assemblies. Phys Chem Chem Phys 2023; 25:12810-12819. [PMID: 37129214 DOI: 10.1039/d3cp00709j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Dimeric cationic cyanostilbenes with peripheral alkyl chains demonstrated aggregation in aqueous media depending on the length of the hydrophobic segment and produced luminescent spherical nano-assemblies in the case of long alkyl chain derivatives. In the presence of heparin, a bio-polyanion that is routinely used as an anticoagulant, the self-assembled structures obtained from the amphiphilic dimers showed the formation of higher-order structures whereas the non-assembling dimers exhibited heparin-induced supramolecular structure formation. In both cases, a significant enhancement in the emission was observed. This led to the detection of heparin in aqueous buffer, serum and plasma with a "turn-on" fluorescence response. Interestingly, these derivatives also exhibited luminescence variation in the presence of ctDNA. However, the response towards DNA was opposite to that observed in the case of heparin i.e., "turn-off'' fluorescence response. Notably, depending on the length of the alkyl segment, divergent DNA binding modes of these derivatives were observed. Due to their enhanced luminescence, the heparin-based co-assemblies were further explored as artificial light-harvesting systems exhibiting an efficient energy transfer process to embedded acceptor dyes with a high antenna effect.
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Affiliation(s)
- Dhananjoy Maity
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, Nadia, India.
| | - Shubhra Kanti Bhaumik
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, Nadia, India.
| | - Supratim Banerjee
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, Nadia, India.
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4
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Takada T, Shimobaki N, Naruo M, Nakamura M, Yamana K. Photoresponsive porphyrin‐DNA complexes constructed through intercalation‐like binding. CHEMPHOTOCHEM 2022. [DOI: 10.1002/cptc.202200093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Tadao Takada
- University of Hyogo: Hyogo Kenritsu Daigaku Department of applied chemistry 2167 Shosha 671-2280 Himeji, Hyogo JAPAN
| | - Nao Shimobaki
- University of Hyogo: Hyogo Kenritsu Daigaku Department of applied chemistry JAPAN
| | - Moe Naruo
- University of Hyogo: Hyogo Kenritsu Daigaku Department of applied chemistry JAPAN
| | - Mitsunobu Nakamura
- University of Hyogo: Hyogo Kenritsu Daigaku Department of applied chemistry JAPAN
| | - Kazushige Yamana
- University of Hyogo: Hyogo Kenritsu Daigaku Department of applied chemistry JAPAN
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5
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Simeth NA, de Mendoza P, Dubach VRA, Stuart MCA, Smith JW, Kudernac T, Browne WR, Feringa BL. Photoswitchable architecture transformation of a DNA-hybrid assembly at the microscopic and macroscopic scale. Chem Sci 2022; 13:3263-3272. [PMID: 35414864 PMCID: PMC8926171 DOI: 10.1039/d1sc06490h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 02/16/2022] [Indexed: 01/01/2023] Open
Abstract
Molecular recognition-driven self-assembly employing single-stranded DNA (ssDNA) as a template is a promising approach to access complex architectures from simple building blocks. Oligonucleotide-based nanotechnology and soft-materials benefit from the high information storage density, self-correction, and memory function of DNA. Here we control these beneficial properties with light in a photoresponsive biohybrid hydrogel, adding an extra level of function to the system. An ssDNA template was combined with a complementary photo-responsive unit to reversibly switch between various functional states of the supramolecular assembly using a combination of light and heat. We studied the structural response of the hydrogel at both the microscopic and macroscopic scale using a combination of UV-vis absorption and CD spectroscopy, as well as fluorescence, transmission electron, and atomic force microscopy. The hydrogels grown from these supramolecular self-assembly systems show remarkable shape-memory properties and imprinting shape-behavior while the macroscopic shape of the materials obtained can be further manipulated by irradiation. Molecular recognition-driven self-assembly employing single-stranded DNA (ssDNA) as a template is a promising approach to access complex architectures from simple building blocks.![]()
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Affiliation(s)
- Nadja A Simeth
- Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Paula de Mendoza
- Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Victor R A Dubach
- Groningen Biomolecular Sciences and Biotechnology, Faculty for Science and Engineering, University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Marc C A Stuart
- Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands .,Groningen Biomolecular Sciences and Biotechnology, Faculty for Science and Engineering, University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Julien W Smith
- Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Tibor Kudernac
- Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Wesley R Browne
- Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Ben L Feringa
- Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
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6
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Dietzsch J, Bialas D, Bandorf J, Würthner F, Höbartner C. Tuning Exciton Coupling of Merocyanine Nucleoside Dimers by RNA, DNA and GNA Double Helix Conformations. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116783] [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)
- Julia Dietzsch
- Institute of Organic Chemistry University of Würzburg Germany
| | - David Bialas
- Institute of Organic Chemistry University of Würzburg Germany
- Center for Nanosystems Chemistry University of Würzburg Am Hubland 97074 Würzburg Germany
| | | | - Frank Würthner
- Institute of Organic Chemistry University of Würzburg Germany
- Center for Nanosystems Chemistry University of Würzburg Am Hubland 97074 Würzburg Germany
| | - Claudia Höbartner
- Institute of Organic Chemistry University of Würzburg Germany
- Center for Nanosystems Chemistry University of Würzburg Am Hubland 97074 Würzburg Germany
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7
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Gorman J, Orsborne SRE, Sridhar A, Pandya R, Budden P, Ohmann A, Panjwani NA, Liu Y, Greenfield JL, Dowland S, Gray V, Ryan ST, De Ornellas S, El-Sagheer AH, Brown T, Nitschke JR, Behrends J, Keyser UF, Rao A, Collepardo-Guevara R, Stulz E, Friend RH, Auras F. Deoxyribonucleic Acid Encoded and Size-Defined π-Stacking of Perylene Diimides. J Am Chem Soc 2022; 144:368-376. [PMID: 34936763 PMCID: PMC8759064 DOI: 10.1021/jacs.1c10241] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Indexed: 02/04/2023]
Abstract
Natural photosystems use protein scaffolds to control intermolecular interactions that enable exciton flow, charge generation, and long-range charge separation. In contrast, there is limited structural control in current organic electronic devices such as OLEDs and solar cells. We report here the DNA-encoded assembly of π-conjugated perylene diimides (PDIs) with deterministic control over the number of electronically coupled molecules. The PDIs are integrated within DNA chains using phosphoramidite coupling chemistry, allowing selection of the DNA sequence to either side, and specification of intermolecular DNA hybridization. In this way, we have developed a "toolbox" for construction of any stacking sequence of these semiconducting molecules. We have discovered that we need to use a full hierarchy of interactions: DNA guides the semiconductors into specified close proximity, hydrophobic-hydrophilic differentiation drives aggregation of the semiconductor moieties, and local geometry and electrostatic interactions define intermolecular positioning. As a result, the PDIs pack to give substantial intermolecular π wave function overlap, leading to an evolution of singlet excited states from localized excitons in the PDI monomer to excimers with wave functions delocalized over all five PDIs in the pentamer. This is accompanied by a change in the dominant triplet forming mechanism from localized spin-orbit charge transfer mediated intersystem crossing for the monomer toward a delocalized excimer process for the pentamer. Our modular DNA-based assembly reveals real opportunities for the rapid development of bespoke semiconductor architectures with molecule-by-molecule precision.
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Affiliation(s)
- Jeffrey Gorman
- Cavendish
Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Sarah R. E. Orsborne
- Cavendish
Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Akshay Sridhar
- Department
of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, 171 21 Solna, Sweden
| | - Raj Pandya
- Cavendish
Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Peter Budden
- Cavendish
Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Alexander Ohmann
- Cavendish
Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Naitik A. Panjwani
- Berlin
Joint EPR Lab, Fachbereich Physik, Freie
Universität Berlin, 14195 Berlin, Germany
| | - Yun Liu
- Cavendish
Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Jake L. Greenfield
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Simon Dowland
- Cavendish
Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Victor Gray
- Department
of Chemistry, Ångström Laboratory, Uppsala University, 751
20 Uppsala, Sweden
| | - Seán T.
J. Ryan
- Cavendish
Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Sara De Ornellas
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Afaf H. El-Sagheer
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Tom Brown
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Jonathan R. Nitschke
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Jan Behrends
- Berlin
Joint EPR Lab, Fachbereich Physik, Freie
Universität Berlin, 14195 Berlin, Germany
| | - Ulrich F. Keyser
- Cavendish
Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Akshay Rao
- Cavendish
Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | | | - Eugen Stulz
- Department
of Chemistry & Institute for Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Richard H. Friend
- Cavendish
Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Florian Auras
- Cavendish
Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
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8
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Dietzsch J, Bialas D, Bandorf J, Würthner F, Höbartner C. Tuning exciton coupling of merocyanine nucleoside dimers by RNA, DNA and GNA double helix conformations. Angew Chem Int Ed Engl 2021; 61:e202116783. [PMID: 34937127 PMCID: PMC9302137 DOI: 10.1002/anie.202116783] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Indexed: 12/02/2022]
Abstract
Exciton coupling between two or more chromophores in a specific environment is a key mechanism associated with color tuning and modulation of absorption energies. This concept is well exemplified by natural photosynthetic proteins, and can also be achieved in synthetic nucleic acid nanostructures. Here we report the coupling of barbituric acid merocyanine (BAM) nucleoside analogues and show that exciton coupling can be tuned by the double helix conformation. BAM is a nucleobase mimic that was incorporated in the phosphodiester backbone of RNA, DNA and GNA oligonucleotides. Duplexes with different backbone constitutions and geometries afforded different mutual dye arrangements, leading to distinct optical signatures due to competing modes of chromophore organization via electrostatic, dipolar, π–π‐stacking and hydrogen‐bonding interactions. The realized supramolecular motifs include hydrogen‐bonded BAM–adenine base pairs and antiparallel as well as rotationally stacked BAM dimer aggregates with distinct absorption, CD and fluorescence properties.
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Affiliation(s)
- Julia Dietzsch
- Julius-Maximilians-Universität Würzburg Fakultät für Chemie und Pharmazie: Julius-Maximilians-Universitat Wurzburg Fakultat fur Chemie und Pharmazie, Organic Chemistry, GERMANY
| | - David Bialas
- Julius-Maximilians-Universität Würzburg Fakultät für Chemie und Pharmazie: Julius-Maximilians-Universitat Wurzburg Fakultat fur Chemie und Pharmazie, Organic Chemistry, GERMANY
| | - Johannes Bandorf
- Julius-Maximilians-Universität Würzburg Fakultät für Chemie und Pharmazie: Julius-Maximilians-Universitat Wurzburg Fakultat fur Chemie und Pharmazie, Organic Chemistry, GERMANY
| | - Frank Würthner
- Julius-Maximilians-Universität Würzburg Fakultät für Chemie und Pharmazie: Julius-Maximilians-Universitat Wurzburg Fakultat fur Chemie und Pharmazie, Organic Chemistry, GERMANY
| | - Claudia Höbartner
- Universität Würzburg, Institute für Organische Chemie, Am Hubland, 97074, Würzburg, GERMANY
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9
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Pathak P, Zarandi MA, Zhou X, Jayawickramarajah J. Synthesis and Applications of Porphyrin-Biomacromolecule Conjugates. Front Chem 2021; 9:764137. [PMID: 34820357 PMCID: PMC8606752 DOI: 10.3389/fchem.2021.764137] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/25/2021] [Indexed: 01/10/2023] Open
Abstract
With potential applications in materials and especially in light-responsive biomedicine that targets cancer tissue selectively, much research has focused on developing covalent conjugation techniques to tether porphyrinoid units to various biomacromolecules. This review details the key synthetic approaches that have been employed in the recent decades to conjugate porphyrinoids with oligonucleotides and peptides/proteins. In addition, we provide succinct discussions on the subsequent applications of such hybrid systems and also give a brief overview of the rapidly progressing field of porphyrin-antibody conjugates. Since nucleic acid and peptide systems vary in structure, connectivity, functional group availability and placement, as well as stability and solubility, tailored synthetic approaches are needed for conjugating to each of these biomacromolecule types. In terms of tethering to ONs, porphyrins are typically attached by employing bioorthogonal chemistry (e.g., using phosphoramidites) that drive solid-phase ON synthesis or by conducting post-synthesis modifications and subsequent reactions (such as amide couplings, hydrazide-carbonyl reactions, and click chemistry). In contrast, peptides and proteins are typically conjugated to porphyrinoids using their native functional groups, especially the thiol and amine side chains. However, bioorthogonal reactions (e.g., Staudinger ligations, and copper or strain promoted alkyne-azide cycloadditions) that utilize de novo introduced functional groups onto peptides/proteins have seen vigorous development, especially for site-specific peptide-porphyrin tethering. While the ON-porphyrin conjugates have largely been explored for programmed nanostructure self-assembly and artificial light-harvesting applications, there are some reports of ON-porphyrin systems targeting clinically translational applications (e.g., antimicrobial biomaterials and site-specific nucleic acid cleavage). Conjugates of porphyrins with proteinaceous moieties, on the other hand, have been predominantly used for therapeutic and diagnostic applications (especially in photodynamic therapy, photodynamic antimicrobial chemotherapy, and photothermal therapy). The advancement of the field of porphyrinoid-bioconjugation chemistry from basic academic research to more clinically targeted applications require continuous fine-tuning in terms of synthetic strategies and hence there will continue to be much exciting work on porphyrinoid-biomacromolecule conjugation.
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Affiliation(s)
- Pravin Pathak
- Department of Chemistry, Tulane University, New Orleans, LA, United States
| | | | - Xiao Zhou
- Department of Chemistry, Tulane University, New Orleans, LA, United States
| | - Janarthanan Jayawickramarajah
- Department of Chemistry, Tulane University, New Orleans, LA, United States
- Department of Biochemistry and Molecular Biology, Tulane University, New Orleans, LA, United States
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10
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Pérez‐Romero A, Domínguez‐Martín A, Galli S, Santamaría‐Díaz N, Palacios O, Dobado JA, Nyman M, Galindo MA. Single‐Stranded DNA as Supramolecular Template for One‐Dimensional Palladium(II) Arrays. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Antonio Pérez‐Romero
- Departamento de Química Inorgánica. Unidad de Excelencia de Química Aplicada a Biomedicina y, Medioambiente Universidad de Granada Avda Fuentenueva s/n 18071 Granada Spain
| | - Alicia Domínguez‐Martín
- Departamento de Química Inorgánica. Unidad de Excelencia de Química Aplicada a Biomedicina y, Medioambiente Universidad de Granada Avda Fuentenueva s/n 18071 Granada Spain
| | - Simona Galli
- 2 Dipartimento di Scienza e Alta Tecnologia Università dell'Insubria Via Valleggio 11 22100 Como Italy
| | - Noelia Santamaría‐Díaz
- Departamento de Química Inorgánica. Unidad de Excelencia de Química Aplicada a Biomedicina y, Medioambiente Universidad de Granada Avda Fuentenueva s/n 18071 Granada Spain
| | - Oscar Palacios
- Departament de Química Facultat de Ciències Universitat Autònoma de Barcelona Campus Bellaterra s/n 08193 Cerdanyola del Vallès, Barcelona Spain
| | - José A. Dobado
- Grupo de Modelización y Diseño Molecular Departamento de Química Orgánica Universidad de Granada Avda Fuentenueva s/n 18071 Granada Spain
| | - May Nyman
- Department of Chemistry Oregon State University Corvallis OR 97331-4003 USA
| | - Miguel A. Galindo
- Departamento de Química Inorgánica. Unidad de Excelencia de Química Aplicada a Biomedicina y, Medioambiente Universidad de Granada Avda Fuentenueva s/n 18071 Granada Spain
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11
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Pérez‐Romero A, Domínguez‐Martín A, Galli S, Santamaría‐Díaz N, Palacios O, Dobado JA, Nyman M, Galindo MA. Single‐Stranded DNA as Supramolecular Template for One‐Dimensional Palladium(II) Arrays. Angew Chem Int Ed Engl 2021; 60:10089-10094. [DOI: 10.1002/anie.202015554] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 01/15/2021] [Indexed: 12/27/2022]
Affiliation(s)
- Antonio Pérez‐Romero
- Departamento de Química Inorgánica. Unidad de Excelencia de Química Aplicada a Biomedicina y, Medioambiente Universidad de Granada Avda Fuentenueva s/n 18071 Granada Spain
| | - Alicia Domínguez‐Martín
- Departamento de Química Inorgánica. Unidad de Excelencia de Química Aplicada a Biomedicina y, Medioambiente Universidad de Granada Avda Fuentenueva s/n 18071 Granada Spain
| | - Simona Galli
- 2 Dipartimento di Scienza e Alta Tecnologia Università dell'Insubria Via Valleggio 11 22100 Como Italy
| | - Noelia Santamaría‐Díaz
- Departamento de Química Inorgánica. Unidad de Excelencia de Química Aplicada a Biomedicina y, Medioambiente Universidad de Granada Avda Fuentenueva s/n 18071 Granada Spain
| | - Oscar Palacios
- Departament de Química Facultat de Ciències Universitat Autònoma de Barcelona Campus Bellaterra s/n 08193 Cerdanyola del Vallès, Barcelona Spain
| | - José A. Dobado
- Grupo de Modelización y Diseño Molecular Departamento de Química Orgánica Universidad de Granada Avda Fuentenueva s/n 18071 Granada Spain
| | - May Nyman
- Department of Chemistry Oregon State University Corvallis OR 97331-4003 USA
| | - Miguel A. Galindo
- Departamento de Química Inorgánica. Unidad de Excelencia de Química Aplicada a Biomedicina y, Medioambiente Universidad de Granada Avda Fuentenueva s/n 18071 Granada Spain
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12
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Coste M, Kotras C, Bessin Y, Gervais V, Dellemme D, Leclercq M, Fossépré M, Richeter S, Clément S, Surin M, Ulrich S. Synthesis, Self‐Assembly, and Nucleic Acid Recognition of an Acylhydrazone‐Conjugated Cationic Tetraphenylethene Ligand. European J Org Chem 2021. [DOI: 10.1002/ejoc.202001420] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Maëva Coste
- IBMM Université de Montpellier, CNRS, ENSCM Montpellier France
| | - Clément Kotras
- ICGM Institut Charles Gerhardt Montpellier UMR 5253 Université de Montpellier CNRS, ENSCM Montpellier France
- Laboratory for Chemistry of Novel Materials Center of Innovation and Research in Materials and Polymers (CIRMAP) University of Mons-UMONS 7000 Mons Belgium
| | - Yannick Bessin
- IBMM Université de Montpellier, CNRS, ENSCM Montpellier France
| | - Virginie Gervais
- CNRS Institut de Pharmacologie et de Biologie Structurale (IPBS) Université de Toulouse, UPS 205 route de Narbonne 31077 Toulouse France
| | - David Dellemme
- Laboratory for Chemistry of Novel Materials Center of Innovation and Research in Materials and Polymers (CIRMAP) University of Mons-UMONS 7000 Mons Belgium
| | - Maxime Leclercq
- Laboratory for Chemistry of Novel Materials Center of Innovation and Research in Materials and Polymers (CIRMAP) University of Mons-UMONS 7000 Mons Belgium
| | - Mathieu Fossépré
- Laboratory for Chemistry of Novel Materials Center of Innovation and Research in Materials and Polymers (CIRMAP) University of Mons-UMONS 7000 Mons Belgium
| | - Sébastien Richeter
- ICGM Institut Charles Gerhardt Montpellier UMR 5253 Université de Montpellier CNRS, ENSCM Montpellier France
| | - Sébastien Clément
- ICGM Institut Charles Gerhardt Montpellier UMR 5253 Université de Montpellier CNRS, ENSCM Montpellier France
| | - Mathieu Surin
- Laboratory for Chemistry of Novel Materials Center of Innovation and Research in Materials and Polymers (CIRMAP) University of Mons-UMONS 7000 Mons Belgium
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13
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Surin M, Ulrich S. From Interaction to Function in DNA-Templated Supramolecular Self-Assemblies. ChemistryOpen 2020; 9:480-498. [PMID: 32328404 PMCID: PMC7175023 DOI: 10.1002/open.202000013] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/24/2020] [Indexed: 12/13/2022] Open
Abstract
DNA-templated self-assembly represents a rich and growing subset of supramolecular chemistry where functional self-assemblies are programmed in a versatile manner using nucleic acids as readily-available and readily-tunable templates. In this review, we summarize the different DNA recognition modes and the basic supramolecular interactions at play in this context. We discuss the recent results that report the DNA-templated self-assembly of small molecules into complex yet precise nanoarrays, going from 1D to 3D architectures. Finally, we show their emerging functions as photonic/electronic nanowires, sensors, gene delivery vectors, and supramolecular catalysts, and their growing applications in a wide range of area from materials to biological sciences.
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Affiliation(s)
- Mathieu Surin
- Laboratory for Chemistry of Novel MaterialsCenter of Innovation and Research in Materials and Polymers (CIRMAP)University of Mons-UMONS7000MonsBelgium
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14
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Burns JR, Wood JW, Stulz E. A Porphyrin-DNA Chiroptical Molecular Ruler With Base Pair Resolution. Front Chem 2020; 8:113. [PMID: 32175308 PMCID: PMC7054460 DOI: 10.3389/fchem.2020.00113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/06/2020] [Indexed: 11/13/2022] Open
Abstract
DNA-based molecular rulers enable scientists to determine important parameters across biology, from the measurement of protein binding interactions, to the study of membrane dynamics in cells. However, existing rulers can suffer from poor nanometre resolution due to the flexible nature of linkers used to tether to the DNA framework. We aimed to overcome this problem using zinc and free-base porphyrin chromophores attached via short and rigid acetylene linkers. This connectivity enables the distance and angle between the porphyrins to be fine-tuned along the DNA scaffold. The porphyrins undergo favorable energy transfer and chiral exciton coupling interactions to act as highly sensitive molecular ruler probes. To validate the system, we monitored the detection of small changes in DNA structure upon intercalation of ethidium bromide. CD spectroscopy showed the porphyrins undergo highly sensitive changes in excitation coupling to facilitate base pair resolution of the novel system.
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Affiliation(s)
- Jonathan R Burns
- Department of Chemistry, University College London, London, United Kingdom
| | - James W Wood
- School of Chemistry & Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Eugen Stulz
- School of Chemistry & Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
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15
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Development of functional molecular assemblies based on programmable construction of face-to-face assemblies of metallo-porphyrinoids. J INCL PHENOM MACRO 2020. [DOI: 10.1007/s10847-019-00969-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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16
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Pathak P, Yao W, Hook KD, Vik R, Winnerdy FR, Brown JQ, Gibb BC, Pursell ZF, Phan AT, Jayawickramarajah J. Bright G-Quadruplex Nanostructures Functionalized with Porphyrin Lanterns. J Am Chem Soc 2019; 141:12582-12591. [PMID: 31322869 DOI: 10.1021/jacs.9b03250] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The intricate arrangement of numerous and closely placed chromophores on nanoscale scaffolds can lead to key photonic applications ranging from optical waveguides and antennas to signal-enhanced fluorescent sensors. In this regard, the self-assembly of dye-appended DNA sequences into programmed photonic architectures is promising. However, the dense packing of dyes can result in not only compromised DNA assembly (leading to ill-defined structures and precipitates) but also to essentially nonfluorescent systems (due to π-π aggregation). Here, we introduce a two-step "tether and mask" strategy wherein large porphyrin dyes are first attached to short G-quadruplex-forming sequences and then reacted with per-O-methylated β-cyclodextrin (PMβCD) caps, to form supramolecular synthons featuring the porphyrin fluor fixed into a masked porphyrin lantern (PL) state, due to intramolecular host-guest interactions in water. The PL-DNA sequences can then be self-assembled into cyclic architectures or unprecedented G-wires tethered with hundreds of porphyrin dyes. Importantly, despite the closely arrayed PL units (∼2 nm), the dyes behave as bright chromophores (up to 180-fold brighter than the analogues lacking the PMβCD masks). Since other self-assembling scaffolds, dyes, and host molecules can be used in this modular approach, this work lays out a general strategy for the bottom-up aqueous self-assembly of bright nanomaterials containing densely packed dyes.
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Affiliation(s)
- Pravin Pathak
- Department of Chemistry , Tulane University , 2015 Percival Stern Hall , New Orleans , Louisiana 70118 , United States
| | - Wei Yao
- Department of Chemistry , Tulane University , 2015 Percival Stern Hall , New Orleans , Louisiana 70118 , United States
| | - Katherine Delaney Hook
- Department of Biochemistry and Molecular Biology , Tulane University , New Orleans , Louisiana 70112 , United States
| | - Ryan Vik
- Department of Chemistry , Tulane University , 2015 Percival Stern Hall , New Orleans , Louisiana 70118 , United States
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences , Nanyang Technological University , Singapore 637371 , Singapore
| | - Jonathon Quincy Brown
- Department of Biomedical Engineering , Tulane University , New Orleans , Louisiana 70118 , United States
| | - Bruce C Gibb
- Department of Chemistry , Tulane University , 2015 Percival Stern Hall , New Orleans , Louisiana 70118 , United States
| | - Zachary F Pursell
- Department of Biochemistry and Molecular Biology , Tulane University , New Orleans , Louisiana 70112 , United States
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences , Nanyang Technological University , Singapore 637371 , Singapore
| | - Janarthanan Jayawickramarajah
- Department of Chemistry , Tulane University , 2015 Percival Stern Hall , New Orleans , Louisiana 70118 , United States
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17
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Wang J, Tu T, Chen M, Qian D. Interfacial Self‐Assembly of Closely Packed Nanoparticle Arrays of Silica@Multiporphyrin Hybrids as Light‐Sensitizers for Dye Degradation and Viologen Photochromism. Chem Asian J 2019; 14:3035-3045. [DOI: 10.1002/asia.201900803] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/11/2019] [Indexed: 01/02/2023]
Affiliation(s)
- Jing Wang
- Department of ChemistryFudan University 2005 Songhu Road Shanghai 200438 P. R. China
| | - Tao Tu
- Department of ChemistryFudan University 2005 Songhu Road Shanghai 200438 P. R. China
| | - Meng Chen
- Department of Materials ScienceFudan University 220 Handan Road Shanghai 200433 P. R. China
| | - Dong‐Jin Qian
- Department of ChemistryFudan University 2005 Songhu Road Shanghai 200438 P. R. China
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18
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Tan J, Meeprasert J, Ding Y, Namuangruk S, Ding X, Wang C, Guo J. Cyclomatrix Polyphosphazene Porous Networks with J-Aggregated Multiphthalocyanine Arrays for Dual-Modality Near-Infrared Photosensitizers. ACS APPLIED MATERIALS & INTERFACES 2018; 10:40132-40140. [PMID: 30362706 DOI: 10.1021/acsami.8b13594] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Here, we have developed a kind of cyclomatrix polyphosphazene with excellent photophysical properties and pursued their potential of being organic photosensitizers for dual-modality phototherapy. Briefly, hexachlorocyclophosphazene (HCCP) with D3 h symmetry is adopted as a synthon to attach Zn(II) phthalocyanine (ZnPc) to form dendritic units that are covalently expanded into a soluble porous network through the nucleophilic substitution reaction. Molecular simulation reveals that the multi-ZnPc units around HCCP can be oriented in a side-by-side manner, leading to the remarkably red-shifted and intense absorbance in the near-infrared (NIR) region. To validate the potential in bioapplication, such ZnPc-based polyphosphazenes are assembled by incorporation of polyvinylpyrrolidone (PVP) to produce the uniform nanoparticles with aqueous dispersibility and biocompatibility. From the in vitro results, the PVP-stabilized photosensitizing nanoparticles can undergo the photothermal/photodynamic processes to concurrently generate heat and singlet oxygen for efficiently killing cancer cells upon exposure to a single-bandwidth NIR laser (785 nm). Compared with the known organic photosensitizers, cyclomatrix polyphosphazene would be a promising platform to configure a diversity of reticular arrays with dense and oriented arrangement of dye molecules, leading to their largely enhanced photophysical and photochemical properties.
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Affiliation(s)
- Jing Tan
- State Key Laboratory of Molecular Engineering of Polymers, and Department of Macromolecular Science , Fudan University , Shanghai 200433 , P. R. China
| | - Jittima Meeprasert
- National Nanotechnology Center (NANOTEC) , National Science and Technology Development Agency , Pathumthani 12120 , Thailand
| | - Yuxue Ding
- State Key Laboratory of Molecular Engineering of Polymers, and Department of Macromolecular Science , Fudan University , Shanghai 200433 , P. R. China
| | - Supawadee Namuangruk
- National Nanotechnology Center (NANOTEC) , National Science and Technology Development Agency , Pathumthani 12120 , Thailand
| | - Xuesong Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , P. R. China
| | - Changchun Wang
- State Key Laboratory of Molecular Engineering of Polymers, and Department of Macromolecular Science , Fudan University , Shanghai 200433 , P. R. China
| | - Jia Guo
- State Key Laboratory of Molecular Engineering of Polymers, and Department of Macromolecular Science , Fudan University , Shanghai 200433 , P. R. China
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19
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Ishutkina MV, Berry AR, Hussain R, Khelevina OG, Siligardi G, Stulz E. Self-Assembled Porphyrazine Nucleosides on DNA Templates: Highly Fluorescent Chromophore Arrays and Sizing Forensic Tandem Repeat Sequences. European J Org Chem 2018; 2018:5054-5059. [PMID: 30333712 PMCID: PMC6174987 DOI: 10.1002/ejoc.201800683] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Indexed: 12/15/2022]
Abstract
The formation of chromophore arrays using a DNA templating approach leads to the creation of supramolecular assemblies, where the optical properties of the overall system can be fine-tuned to a large extent. In particular, porphyrin derivatives have been shown to be versatile building blocks; mostly covalent chemistry was used for embedding the units into DNA strands. Self-assembly of porphyrin modified nucleosides, on the other hand, has not been investigated as a simplified approach. We report on the synthesis of a magnesium(II) tetraaza porphine (MgTAP) coupled to deoxyuridine, and array formation on DNA templates which contain well-defined oligo(dA) segments showing strong fluorescence enhancement which is significantly larger than that with a Zn-porphyrin. The use of the deep-eutectic solvent glycholine is essential for successful assembly formation. The system allows for sizing of short tandem repeat markers with multiple adenosines, thus the concept could be adaptable to in vitro forensic DNA profiling with a suitable set of different chromophores on all nucleosides.
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Affiliation(s)
- Mariia V. Ishutkina
- Department of Organic ChemistryIvanovo State University of Chemistry and TechnologySheremetev Av. 7RF‐153000IvanovoRussia
| | - Alice R. Berry
- School of Chemistry & Institute for Life SciencesUniversity of SouthamptonHighfieldSO17 1BJSouthamptonUK
| | - Rohanah Hussain
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOX11 0DEOxfordshireUK
| | - Olga G. Khelevina
- Department of Organic ChemistryIvanovo State University of Chemistry and TechnologySheremetev Av. 7RF‐153000IvanovoRussia
| | - Giuliano Siligardi
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOX11 0DEOxfordshireUK
| | - Eugen Stulz
- School of Chemistry & Institute for Life SciencesUniversity of SouthamptonHighfieldSO17 1BJSouthamptonUK
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20
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Auras BL, De Lucca Meller S, da Silva MP, Neves A, Cocca LH, De Boni L, da Silveira CH, Iglesias BA. Synthesis, spectroscopic/electrochemical characterization and DNA interaction study of novel ferrocenyl-substituted porphyrins. Appl Organomet Chem 2018. [DOI: 10.1002/aoc.4318] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Bruna L. Auras
- Laboratório de Bioinorgânica e Cristalografia (LABINC), Departamento de Química; Universidade Federal de Santa Catarina; 88040-900 Florianópolis SC Brazil
| | - Sheila De Lucca Meller
- Laboratório de Bioinorgânica e Cristalografia (LABINC), Departamento de Química; Universidade Federal de Santa Catarina; 88040-900 Florianópolis SC Brazil
| | - Marcos Paulo da Silva
- Laboratório de Bioinorgânica e Cristalografia (LABINC), Departamento de Química; Universidade Federal de Santa Catarina; 88040-900 Florianópolis SC Brazil
| | - Ademir Neves
- Laboratório de Bioinorgânica e Cristalografia (LABINC), Departamento de Química; Universidade Federal de Santa Catarina; 88040-900 Florianópolis SC Brazil
| | - Leandro H.Z. Cocca
- Instituto de Física de São Carlos; Universidade de São Paulo, CP 369 13560-970 São Carlos SP Brazil
| | - Leonardo De Boni
- Instituto de Física de São Carlos; Universidade de São Paulo, CP 369 13560-970 São Carlos SP Brazil
| | - Carolina Hahn da Silveira
- Departamento de Química, Universidade Federal de Santa Maria - UFSM, 97105-900 Santa Maria RS Brazil
| | - Bernardo A. Iglesias
- Departamento de Química, Universidade Federal de Santa Maria - UFSM, 97105-900 Santa Maria RS Brazil
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21
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Nakamura M, Jomura A, Takada T, Yamana K. Photocurrent Enhancement in DNA-Scaffolded Chromophore-Aggregate-Functionalized Systems Containing Multiple Types of Chromophores. CHEMPHOTOCHEM 2017. [DOI: 10.1002/cptc.201700152] [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)
- Mitsunobu Nakamura
- Department of Applied Chemistry; University of Hyogo; 2167 Shosha, Himeji Hyogo 671-2280 Japan
| | - Ayumi Jomura
- Department of Applied Chemistry; University of Hyogo; 2167 Shosha, Himeji Hyogo 671-2280 Japan
| | - Tadao Takada
- Department of Applied Chemistry; University of Hyogo; 2167 Shosha, Himeji Hyogo 671-2280 Japan
| | - Kazushige Yamana
- Department of Applied Chemistry; University of Hyogo; 2167 Shosha, Himeji Hyogo 671-2280 Japan
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22
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Takada T, Iwaki T, Nakamura M, Yamana K. Photoresponsive Electrodes Modified with DNA Duplexes Possessing a Porphyrin Dimer. Chemistry 2017; 23:18258-18263. [PMID: 29052264 DOI: 10.1002/chem.201704281] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Indexed: 12/29/2022]
Abstract
This work describes the formation of a porphyrin (Por) dimer using a DNA duplex as a scaffold and photocurrent generation from electrodes modified with a monolayer of Por-DNA conjugates. The solid-phase click reaction between an azide-porphyrin and oligonucleotide labeled with an ethynyl group on CPG support was utilized to conjugate the Por to the DNA. UV/Vis absorption and circular dichroism (CD) spectral studies revealed that the Por dimer can be formed through DNA hybridization and that through-space electronic interactions, characterized from the exciton-coupled absorption and the bisignate CD, can occur between the two Por molecules. Photoelectrochemical experiments were performed for the electrodes functionalized with a monolayer composed of the Por-DNA conjugates. It was found that the Por dimer on the electrode, which was designed to resemble the special pair in natural photosynthesis, shows efficient photocurrent generation in the presence of electron-acceptor reagents compared with the Por monomer. These findings strongly support the idea that the DNA structures could be useful to construct Por arrays, which is essential for the design of photo- and bio-electronic devices.
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Affiliation(s)
- Tadao Takada
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo, 671-2280, Japan
| | - Toshihiro Iwaki
- 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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23
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Chiral multichromophoric supramolecular nanostructures assembled by single stranded DNA and RNA templates. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2017.08.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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24
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Kang B, Yang W, Lee S, Mukherjee S, Forstater J, Kim H, Goh B, Kim TY, Voelz VA, Pang Y, Seo J. Precisely tuneable energy transfer system using peptoid helix-based molecular scaffold. Sci Rep 2017; 7:4786. [PMID: 28684782 PMCID: PMC5500559 DOI: 10.1038/s41598-017-04727-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 05/26/2017] [Indexed: 12/27/2022] Open
Abstract
The energy flow during natural photosynthesis is controlled by maintaining the spatial arrangement of pigments, employing helices as scaffolds. In this study, we have developed porphyrin-peptoid (pigment-helix) conjugates (PPCs) that can modulate the donor-acceptor energy transfer efficiency with exceptional precision by controlling the relative distance and orientation of the two pigments. Five donor-acceptor molecular dyads were constructed using zinc porphyrin and free base porphyrin (Zn(i + 2)–Zn(i + 6)), and highly efficient energy transfer was demonstrated with estimated efficiencies ranging from 92% to 96% measured by static fluorescence emission in CH2Cl2 and from 96.3% to 97.6% using femtosecond transient absorption measurements in toluene, depending on the relative spatial arrangement of the donor-acceptor pairs. Our results suggest that the remarkable precision and tunability exhibited by nature can be achieved by mimicking the design principles of natural photosynthetic proteins.
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Affiliation(s)
- Boyeong Kang
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagiro, Buk-gu, Gwangju, 61005, South Korea
| | - Woojin Yang
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagiro, Buk-gu, Gwangju, 61005, South Korea
| | - Sebok Lee
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagiro, Buk-gu, Gwangju, 61005, South Korea
| | - Sudipto Mukherjee
- Department of Chemistry, Temple University, 1901 N. 13th St., Philadelphia, PA 19122, USA
| | - Jonathan Forstater
- Department of Chemistry, Temple University, 1901 N. 13th St., Philadelphia, PA 19122, USA
| | - Hanna Kim
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagiro, Buk-gu, Gwangju, 61005, South Korea
| | - Byoungsook Goh
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagiro, Buk-gu, Gwangju, 61005, South Korea
| | - Tae-Young Kim
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagiro, Buk-gu, Gwangju, 61005, South Korea.,School of Earth Sciences and Engineering, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagiro, Buk-gu, Gwangju, 61005, South Korea
| | - Vincent A Voelz
- Department of Chemistry, Temple University, 1901 N. 13th St., Philadelphia, PA 19122, USA.
| | - Yoonsoo Pang
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagiro, Buk-gu, Gwangju, 61005, South Korea.
| | - Jiwon Seo
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagiro, Buk-gu, Gwangju, 61005, South Korea.
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25
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Fresch B, Remacle F, Levine RD. Implementation of Probabilistic Algorithms by Multi-chromophoric Molecular Networks with Application to Multiple Travelling Pathways. Chemphyschem 2017; 18:1782-1789. [DOI: 10.1002/cphc.201700228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Indexed: 12/17/2022]
Affiliation(s)
- Barbara Fresch
- Department of Chemical Science; University of Padova; Via Marzolo 1 35131 Italy
| | - Françoise Remacle
- Department of Chemistry, B6c; University of Liege; B4000 Liege Belgium
- The Fritz Haber Center for Molecular Dynamics and Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | - Raphael D. Levine
- The Fritz Haber Center for Molecular Dynamics and Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
- Crump Institute for Molecular Imaging and Department of Molecular and Medical Pharmacology; David Geffen School of Medicine and Department of Chemistry and Biochemistry; University of California, Los Angeles; California 90095 USA
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26
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Bousmail D, Amrein L, Fakhoury JJ, Fakih HH, Hsu JCC, Panasci L, Sleiman HF. Precision spherical nucleic acids for delivery of anticancer drugs. Chem Sci 2017; 8:6218-6229. [PMID: 28989655 PMCID: PMC5628336 DOI: 10.1039/c7sc01619k] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/29/2017] [Indexed: 12/31/2022] Open
Abstract
Highly monodisperse sequence-defined spherical nucleic acids (HE12–SNAs) for delivery of small-molecule anticancer drugs.
We report a spherical nucleic acid (SNA) system for the delivery of BKM120, an anticancer drug for treatment of chronic lymphocytic leukemia (CLL). While promising for cancer treatment, this drug crosses the blood–brain barrier causing significant side-effects in patients. The DNA nanoparticle encapsulates BKM120 in high efficiency, and is unparalleled in its monodispersity, ease of synthesis and stability in different biological media and in serum. These DNA nanostructures demonstrate efficient uptake in human cervical cancer (HeLa) cells, and increased internalization of cargo. In vitro studies show that BKM120-loaded nanoparticles promote apoptosis in primary patient CLL lymphocytes, and act as sensitizers of other antitumor drugs, without causing non-specific inflammation. Evaluation of this drug delivery system in vivo shows long circulation times up to 24 hours, full body distribution, accumulation at tumor sites and minimal leakage through the blood–brain barrier. Our results demonstrate the great potential of these delivery vehicles as a general platform for chemotherapeutic drug delivery.
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Affiliation(s)
- Danny Bousmail
- Department of Chemistry , Centre for Self-Assembled Chemical Structures (CSACS) , McGill University , 801 Sherbrooke St. W. , Montreal , Canada .
| | - Lilian Amrein
- Department of Oncology , Jewish General Hospital , 3755 Cote Sainte-Catherine Rd. , Montreal , Canada .
| | - Johans J Fakhoury
- Department of Chemistry , Centre for Self-Assembled Chemical Structures (CSACS) , McGill University , 801 Sherbrooke St. W. , Montreal , Canada .
| | - Hassan H Fakih
- Department of Chemistry , Centre for Self-Assembled Chemical Structures (CSACS) , McGill University , 801 Sherbrooke St. W. , Montreal , Canada .
| | - John C C Hsu
- Department of Chemistry , Centre for Self-Assembled Chemical Structures (CSACS) , McGill University , 801 Sherbrooke St. W. , Montreal , Canada .
| | - Lawrence Panasci
- Department of Oncology , Jewish General Hospital , 3755 Cote Sainte-Catherine Rd. , Montreal , Canada .
| | - Hanadi F Sleiman
- Department of Chemistry , Centre for Self-Assembled Chemical Structures (CSACS) , McGill University , 801 Sherbrooke St. W. , Montreal , Canada .
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27
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Kim Y, Kang B, Ahn HY, Seo J, Nam KT. Plasmon Enhanced Fluorescence Based on Porphyrin-Peptoid Hybridized Gold Nanoparticle Platform. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1700071. [PMID: 28513982 DOI: 10.1002/smll.201700071] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 03/08/2017] [Indexed: 06/07/2023]
Abstract
A porphyrin-peptoid-hybridized silica-coated gold nanoparticle is developed, which is inspired by the protein-chlorophyll ensemble found in photosynthetic antenna. In the natural antenna, chlorophylls are integrated into dense assemblies that are supported by frameworks of proteins, which ensure optimal pigment arrangement for effective light harvesting. In the subject platform, porphyrins are conjugated to the peptoid helix scaffold in a structurally well-defined alignments and subsequently immobilized on the surface of nanoparticles. This prevents intermolecular aggregation among porphyrins and allows high resolution analysis of the effect of porphyrin configuration on the optical properties of the system. Interestingly, under the influence of plasmon from the gold nanoparticle core, the fluorescence of porphyrin is enhanced up to 24-fold at the wavelength where the plasmon resonance matches the porphyrin excitation wavelength. In addition, differences in porphyrin configuration result in spectral modification of their fluorescence emissions. Particularly, the peptoid bearing two porphyrins at a distance of 6 Å shows the most significant alteration in fluorescence. The platform can facilitate extensive studies on the relationship between porphyrin arrangement design and their photophysical interaction in antenna complexes.
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Affiliation(s)
- Younghye Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul, 151-744, Republic of Korea
| | - Boyeong Kang
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, Gwangju, 500-712, Republic of Korea
| | - Hyo-Yong Ahn
- Department of Materials Science and Engineering, Seoul National University, Seoul, 151-744, Republic of Korea
| | - Jiwon Seo
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, Gwangju, 500-712, Republic of Korea
| | - Ki Tae Nam
- Department of Materials Science and Engineering, Seoul National University, Seoul, 151-744, Republic of Korea
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Kumari R, Khan MI, Bhowmick S, Sinha KK, Das N, Das P. Self-assembly of DNA-porphyrin hybrid molecules for the creation of antimicrobial nanonetwork. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2017; 172:28-35. [DOI: 10.1016/j.jphotobiol.2017.05.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 05/05/2017] [Accepted: 05/09/2017] [Indexed: 12/31/2022]
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Abstract
![]()
DNA is well-known as bearer of the genetic code.
Since its structure
elucidation nearly seven decades ago by Watson, Crick, Wilkins, and
Franklin, much has been learned about its detailed structure, function,
and genetic coding. The development of automated solid-phase synthesis,
and with it the availability of synthetic DNA with any desired sequence
in lengths of up to hundreds of bases in the best case, has contributed
much to the advancement of the field of DNA research. In addition,
classic organic synthesis has allowed introduction of a very large
number of modifications in the DNA in a sequence specific manner,
which have initially been targeted at altering the biological function
of DNA. However, in recent years DNA has become a very attractive
scaffold in supramolecular chemistry, where DNA is taken out of its
biological role and serves as both stick and glue molecule to assemble
novel functional structures with nanometer precision. The attachment
of functionalities to DNA has led to the creation of supramolecular
systems with applications in light harvesting, energy and electron
transfer, sensing, and catalysis. Functional DNA is clearly having
a significant impact in the field of bioinspired nanosystems. Of particular interest is the use of porphyrins in supramolecular
chemistry and bionanotechnology, because they are excellent functional
groups due to their electronic properties that can be tailored through
chemical modifications of the aromatic core or through insertion of
almost any metal of the periodic table into the central cavity. The
porphyrins can be attached either to the nucleobase, to the phosphate
group, or to the ribose moiety. Additionally, noncovalent templating
through Watson–Crick base pairing forms an alternative and
attractive approach. With this, the combination of two seemingly simple
molecules gives rise to a highly complex system with unprecedented
possibilities for modulation of function, and with it applications,
particularly when combined with other functional groups. Here, an
overview is given on the developments of using porphyrin modified
DNA for the construction of functional assemblies. Strategies for
the synthesis and characterization are presented alongside selected
applications where the porphyrin modification has proven to be particularly
useful and superior to other modifiers but also has revealed its limitations.
We also discuss implications on properties and behavior of the porphyrin–DNA,
where similar issues could arise when using other hydrophobic and
bulky substituents on DNA. This includes particularly problems regarding
synthesis of the building blocks, DNA synthesis, yields, solubility,
and intermolecular interactions.
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Affiliation(s)
- Eugen Stulz
- School of Chemistry & Institute for Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, U.K
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30
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Cha YJ, Yoon DK. Control of Periodic Zigzag Structures of DNA by a Simple Shearing Method. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2017; 29:1604247. [PMID: 27862385 DOI: 10.1002/adma.201604247] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/19/2016] [Indexed: 06/06/2023]
Abstract
A periodic zigzag structure of DNA material is successfully fabricated by a simple shearing method. The periodicity of the pattern can be finely controlled by combining the mechanical shearing method with topographic patterns of microchannels. The resultant zigzag patterns can be used as a template to control the alignment of rod-like liquid crystals due to its highly regular periodicity.
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Affiliation(s)
- Yun Jeong Cha
- Graduate School of Nanoscience and Technology and KINC, KAIST, Daejeon, 305-701, Republic of Korea
| | - Dong Ki Yoon
- Graduate School of Nanoscience and Technology and KINC, KAIST, Daejeon, 305-701, Republic of Korea
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31
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Nicoli F, Roos MK, Hemmig EA, Di Antonio M, de Vivie-Riedle R, Liedl T. Proximity-Induced H-Aggregation of Cyanine Dyes on DNA-Duplexes. J Phys Chem A 2016; 120:9941-9947. [PMID: 27934475 PMCID: PMC6544512 DOI: 10.1021/acs.jpca.6b10939] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A wide variety of organic dyes form, under certain conditions, clusters know as J- and H-aggregates. Cyanine dyes are such a class of molecules where the spatial proximity of several dyes leads to overlapping electron orbitals and thus to the creation of a new energy landscape compared to that of the individual units. In this work, we create artificial H-aggregates of exactly two Cyanine 3 (Cy3) dyes by covalently linking them to a DNA molecule with controlled subnanometer distances. The absorption spectra of these coupled systems exhibit a blue-shifted peak, whose intensity varies depending on the distance between the dyes and the rigidity of the DNA template. Simulated vibrational resolved spectra, based on molecular orbital theory, excellently reproduce the experimentally observed features. Circular dichroism spectroscopy additionally reveals distinct signals, which indicates a chiral arrangement of the dye molecules. Molecular dynamic simulations of a Cy3-Cy3 construct including a 14-base pair DNA sequence verified chiral stacking of the dye molecules.
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Affiliation(s)
- Francesca Nicoli
- Faculty of Physics and Center for NanoScience (CENS), Ludwig-Maximilians-Universität München (LMU), Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| | - Matthias K. Roos
- Department Chemie, Ludwig-Maximilians-Universität München (LMU), Butenandt Str. 11, 81377 Munich, Germany
| | - Elisa A. Hemmig
- Cavendish Laboratory, University of Cambridge, JJ Thomson Ave., CB3 0HE Cambridge, United Kingdom
| | - Marco Di Antonio
- Chemistry Department, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
| | - Regina de Vivie-Riedle
- Department Chemie, Ludwig-Maximilians-Universität München (LMU), Butenandt Str. 11, 81377 Munich, Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience (CENS), Ludwig-Maximilians-Universität München (LMU), Geschwister-Scholl-Platz 1, 80539 Munich, Germany
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32
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Orimoto Y, Aoki Y. Computational Study of Cu-Containing Artificial DNA: Twist Angle Dependence of Magnetism. ChemistrySelect 2016. [DOI: 10.1002/slct.201600940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Yuuichi Orimoto
- Department of Material Sciences, Faculty of Engineering Sciences; Kyushu University; 6-1 Kasuga-Park Fukuoka 816-8580 Japan
| | - Yuriko Aoki
- Department of Material Sciences, Faculty of Engineering Sciences; Kyushu University; 6-1 Kasuga-Park Fukuoka 816-8580 Japan
- Japan Science and Technology Agency; CREST; 4-1-8 Hon-chou, Kawaguchi Saitama 332-0012 Japan
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33
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Mejías SH, López-Andarias J, Sakurai T, Yoneda S, Erazo KP, Seki S, Atienza C, Martín N, Cortajarena AL. Repeat protein scaffolds: ordering photo- and electroactive molecules in solution and solid state. Chem Sci 2016; 7:4842-4847. [PMID: 29732049 PMCID: PMC5905405 DOI: 10.1039/c6sc01306f] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 05/23/2016] [Indexed: 01/15/2023] Open
Abstract
The precise control over the organization of photoactive components at the nanoscale is one of the main challenges for the generation of new and sophisticated macroscopically ordered materials with enhanced properties. In this work we present a novel bioinspired approach using protein-based building blocks for the arrangement of photo- and electroactive porphyrin derivatives. We used a designed repeat protein scaffold with demonstrated unique features that allow for the control of their structure, functionality, and assembly. Our designed domains act as exact biomolecular templates to organize porphyrin molecules at the required distance. The hybrid conjugates retain the structure and assembly properties of the protein scaffold and display the spectroscopic features of orderly aggregated porphyrins along the protein structure. Finally, we achieved a solid ordered bio-organic hybrid thin film with anisotropic photoconductivity.
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Affiliation(s)
- Sara H Mejías
- IMDEA-Nanoscience , Campus de Cantoblanco , E-28049 Madrid , Spain
| | - Javier López-Andarias
- Departamento de Química Orgánica I , Facultad de Ciencias Químicas , Universidad Complutense de Madrid , E-28040 Madrid , Spain .
| | - Tsuneaki Sakurai
- Department of Applied Chemistry , Graduate School of Engineering , Osaka University , Japan
| | - Satoru Yoneda
- Department of Applied Chemistry , Graduate School of Engineering , Osaka University , Japan
| | - Kevin P Erazo
- IMDEA-Nanoscience , Campus de Cantoblanco , E-28049 Madrid , Spain
| | - Shu Seki
- Department of Applied Chemistry , Graduate School of Engineering , Osaka University , Japan
| | - Carmen Atienza
- Departamento de Química Orgánica I , Facultad de Ciencias Químicas , Universidad Complutense de Madrid , E-28040 Madrid , Spain .
| | - Nazario Martín
- IMDEA-Nanoscience , Campus de Cantoblanco , E-28049 Madrid , Spain
- Departamento de Química Orgánica I , Facultad de Ciencias Químicas , Universidad Complutense de Madrid , E-28040 Madrid , Spain .
| | - Aitziber L Cortajarena
- IMDEA-Nanoscience , Campus de Cantoblanco , E-28049 Madrid , Spain
- CIC biomaGUNE , Paseo de Miramón 182 , E-20009 Donostia-San Sebastian , Spain
- Ikerbasque , Basque Foundation for Science , Ma Díaz de Haro 3 , E-48013 Bilbao , Spain
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34
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Göpfrich K, Li CY, Mames I, Bhamidimarri SP, Ricci M, Yoo J, Mames A, Ohmann A, Winterhalter M, Stulz E, Aksimentiev A, Keyser UF. Ion Channels Made from a Single Membrane-Spanning DNA Duplex. NANO LETTERS 2016; 16:4665-9. [PMID: 27324157 PMCID: PMC4948918 DOI: 10.1021/acs.nanolett.6b02039] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 06/17/2016] [Indexed: 05/21/2023]
Abstract
Because of their hollow interior, transmembrane channels are capable of opening up pathways for ions across lipid membranes of living cells. Here, we demonstrate ion conduction induced by a single DNA duplex that lacks a hollow central channel. Decorated with six porpyrin-tags, our duplex is designed to span lipid membranes. Combining electrophysiology measurements with all-atom molecular dynamics simulations, we elucidate the microscopic conductance pathway. Ions flow at the DNA-lipid interface as the lipid head groups tilt toward the amphiphilic duplex forming a toroidal pore filled with water and ions. Ionic current traces produced by the DNA-lipid channel show well-defined insertion steps, closures, and gating similar to those observed for traditional protein channels or synthetic pores. Ionic conductances obtained through simulations and experiments are in excellent quantitative agreement. The conductance mechanism realized here with the smallest possible DNA-based ion channel offers a route to design a new class of synthetic ion channels with maximum simplicity.
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Affiliation(s)
- Kerstin Göpfrich
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Chen-Yu Li
- Center for the Physics of Living Cells, Department of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Iwona Mames
- School of
Chemistry and Institute for Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | | | - Maria Ricci
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Jejoong Yoo
- Center for the Physics of Living Cells, Department of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Adam Mames
- School of
Chemistry and Institute for Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Alexander Ohmann
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | | | - Eugen Stulz
- School of
Chemistry and Institute for Life Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
- E-mail: . Phone: +44(0)238059 9369
| | - Aleksei Aksimentiev
- Center for the Physics of Living Cells, Department of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
- E-mail: . Phone: +1(0) 217333 6495
| | - Ulrich F. Keyser
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
- E-mail: . Phone: +44(0)1223
337272
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35
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Rout B. A Miniaturized Therapeutic Chromophore for Multiple Metal Pollutant Sensing, Pathological Metal Diagnosis and Logical Computing. Sci Rep 2016; 6:27115. [PMID: 27271817 PMCID: PMC4895214 DOI: 10.1038/srep27115] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 05/03/2016] [Indexed: 12/23/2022] Open
Abstract
The efficacy of a miniaturized unimolecular analytic system is illustrated. The easily accessible therapeutic chromophore "temoporfin", which responds differentially to bound metals at multiple wavelengths of Q-band absorption using chemometric analysis, expeditiously detects and discriminates a wide range of metals regarded as priority pollutants in water and hence may also be used for diagnosis of medically relevant metals in human urine. The molecule was further investigated as an electronic logic device, e.g. keypad lock device, to authorize multiple highly secure chemical passwords for information protection.
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Affiliation(s)
- Bhimsen Rout
- Organic Chemistry Division, Institute of Chemical and Engineering Sciences, A*STAR, 138665-Singapore
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36
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Santamaría-Díaz N, Méndez-Arriaga JM, Salas JM, Galindo MA. Highly Stable Double-Stranded DNA Containing Sequential Silver(I)-Mediated 7-Deazaadenine/Thymine Watson-Crick Base Pairs. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201600924] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Noelia Santamaría-Díaz
- Facultad de Ciencias; Departamento Química Inorgánica; Universidad de Granada; Avd. Fuentenueva s/n 18071 Granada Spain
| | - José M. Méndez-Arriaga
- Facultad de Ciencias; Departamento Química Inorgánica; Universidad de Granada; Avd. Fuentenueva s/n 18071 Granada Spain
| | - Juan M. Salas
- Facultad de Ciencias; Departamento Química Inorgánica; Universidad de Granada; Avd. Fuentenueva s/n 18071 Granada Spain
| | - Miguel A. Galindo
- Facultad de Ciencias; Departamento Química Inorgánica; Universidad de Granada; Avd. Fuentenueva s/n 18071 Granada Spain
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37
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Santamaría-Díaz N, Méndez-Arriaga JM, Salas JM, Galindo MA. Highly Stable Double-Stranded DNA Containing Sequential Silver(I)-Mediated 7-Deazaadenine/Thymine Watson-Crick Base Pairs. Angew Chem Int Ed Engl 2016; 55:6170-4. [DOI: 10.1002/anie.201600924] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Indexed: 01/18/2023]
Affiliation(s)
- Noelia Santamaría-Díaz
- Facultad de Ciencias; Departamento Química Inorgánica; Universidad de Granada; Avd. Fuentenueva s/n 18071 Granada Spain
| | - José M. Méndez-Arriaga
- Facultad de Ciencias; Departamento Química Inorgánica; Universidad de Granada; Avd. Fuentenueva s/n 18071 Granada Spain
| | - Juan M. Salas
- Facultad de Ciencias; Departamento Química Inorgánica; Universidad de Granada; Avd. Fuentenueva s/n 18071 Granada Spain
| | - Miguel A. Galindo
- Facultad de Ciencias; Departamento Química Inorgánica; Universidad de Granada; Avd. Fuentenueva s/n 18071 Granada Spain
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38
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Duprey JLHA, Carr-Smith J, Horswell SL, Kowalski J, Tucker JHR. Macrocyclic Metal Complex-DNA Conjugates for Electrochemical Sensing of Single Nucleobase Changes in DNA. J Am Chem Soc 2016; 138:746-9. [PMID: 26694542 DOI: 10.1021/jacs.5b11319] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The direct incorporation of macrocyclic cyclidene complexes into DNA via automated synthesis results in a new family of metal-functionalized DNA derivatives that readily demonstrate their utility through the ability of one redox-active copper(II)-containing strand to distinguish electrochemically between all four canonical DNA nucleobases at a single site within a target sequence of DNA.
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Affiliation(s)
- Jean-Louis H A Duprey
- School of Chemistry, University of Birmingham , Edgbaston, Birmingham, West Midlands B15 2TT, U.K
| | - James Carr-Smith
- School of Chemistry, University of Birmingham , Edgbaston, Birmingham, West Midlands B15 2TT, U.K
| | - Sarah L Horswell
- School of Chemistry, University of Birmingham , Edgbaston, Birmingham, West Midlands B15 2TT, U.K
| | - Jarosław Kowalski
- Insitute of Organic Chemistry, Polish Academy of Sciences , Kasprzaka 44/52, Warsaw, 01-224, Poland
| | - James H R Tucker
- School of Chemistry, University of Birmingham , Edgbaston, Birmingham, West Midlands B15 2TT, U.K
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39
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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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40
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Rodríguez-Vázquez N, Fuertes A, Amorín M, Granja JR. Bioinspired Artificial Sodium and Potassium Ion Channels. Met Ions Life Sci 2016; 16:485-556. [DOI: 10.1007/978-3-319-21756-7_14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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41
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Albert SK, Golla M, Thelu HVP, Krishnan N, Deepak P, Varghese R. Synthesis and self-assembly of DNA–chromophore hybrid amphiphiles. Org Biomol Chem 2016; 14:6960-9. [DOI: 10.1039/c6ob00681g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA based amphiphiles are synthesized through a modular “click” chemistry approach, and the DNA–chromophore hybrid amphiphiles undergo amphiphilicity-driven self-assembly into vesicular or micellar nanostructures having a DNA shell and functional core.
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Affiliation(s)
- Shine K. Albert
- School of Chemistry
- Indian Institute of Science Education and Research-Thiruvananthapuram (IISER-TVM)
- Trivandrum-695016
- India
| | - Murali Golla
- School of Chemistry
- Indian Institute of Science Education and Research-Thiruvananthapuram (IISER-TVM)
- Trivandrum-695016
- India
| | - Hari Veera Prasad Thelu
- School of Chemistry
- Indian Institute of Science Education and Research-Thiruvananthapuram (IISER-TVM)
- Trivandrum-695016
- India
| | - Nithiyanandan Krishnan
- School of Chemistry
- Indian Institute of Science Education and Research-Thiruvananthapuram (IISER-TVM)
- Trivandrum-695016
- India
| | - Perapaka Deepak
- School of Chemistry
- Indian Institute of Science Education and Research-Thiruvananthapuram (IISER-TVM)
- Trivandrum-695016
- India
| | - Reji Varghese
- School of Chemistry
- Indian Institute of Science Education and Research-Thiruvananthapuram (IISER-TVM)
- Trivandrum-695016
- India
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42
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Ensslen P, Wagenknecht HA. One-Dimensional Multichromophor Arrays Based on DNA: From Self-Assembly to Light-Harvesting. Acc Chem Res 2015; 48:2724-33. [PMID: 26411920 DOI: 10.1021/acs.accounts.5b00314] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Light-harvesting complexes collect light energy and deliver it by a cascade of energy and electron transfer processes to the reaction center where charge separation leads to storage as chemical energy. The design of artificial light-harvesting assemblies faces enormous challenges because several antenna chromophores need to be kept in close proximity but self-quenching needs to be avoided. Double stranded DNA as a supramolecular scaffold plays a promising role due to its characteristic structural properties. Automated DNA synthesis allows incorporation of artificial chromophore-modified building blocks, and sequence design allows precise control of the distances and orientations between the chromophores. The helical twist between the chromophores, which is induced by the DNA framework, controls energy and electron transfer and thereby reduces the self-quenching that is typically observed in chromophore aggregates. This Account summarizes covalently multichromophore-modified DNA and describes how such multichromophore arrays were achieved by Watson-Crick-specific and DNA-templated self-assembly. The covalent DNA systems were prepared by incorporation of chromophores as DNA base substitutions (either as C-nucleosides or with acyclic linkers as substitutes for the 2'-deoxyribofuranoside) and as DNA base modifications. Studies with DNA base substitutions revealed that distances but more importantly relative orientations of the chromophores govern the energy transfer efficiencies and thereby the light-harvesting properties. With DNA base substitutions, duplex stabilization was faced and could be overcome, for instance, by zipper-like placement of the chromophores in both strands. For both principal structural approaches, DNA-based light-harvesting antenna could be realized. The major disadvantages, however, for covalent multichromophore DNA conjugates are the poor yields of synthesis and the solubility issues for oligonucleotides with more than 5-10 chromophore modifications in a row. A logical alternative approach is to leave out the phosphodiester bridges between the chromophores and let chromophore-nucleoside conjugates self-assemble specifically along single stranded DNA as template. The self-organization of chromophores along the DNA template based on canonical base pairing would be advantageous because sequence selective base pairing could provide a structural basis for programmed complexity within the chromophore assembly. The self-assembly is governed by two interactions. The chromophore-nucleoside conjugates as guest molecules are recognized via hydrogen bonds to the corresponding counter bases in the single stranded DNA template. Moreover, the π-π interactions between the stacked chromophores stabilize these self-assembled constructs with increasing length. Longer DNA templates are more attractive for self-assembled antenna. The helicity in the stack of porphyrins as guest molecules assembled on the DNA template can be switched by environmental changes, such as pH variations. DNA-templated stacks of ethynyl pyrene and nile red exhibit left-handed chirality, which stands in contrast to similar covalent multichromophore-DNA conjugates with enforced right-handed helicity. With ethynyl nile red, it is possible to occupy every available binding site on the templates. Mixed assemblies of ethynyl pyrene and nile red show energy transfer and thereby provide a proof-of-principle that simple light-harvesting antennae can be obtained in a noncovalent and self-assembled fashion. With respect to the next important step, chemical storage of the absorbed light energy, future research has to focus on the coupling of sophisticated DNA-based light-harvesting antenna to reaction centers.
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Affiliation(s)
- Philipp Ensslen
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Hans-Achim Wagenknecht
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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43
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Seifert A, Göpfrich K, Burns JR, Fertig N, Keyser UF, Howorka S. Bilayer-spanning DNA nanopores with voltage-switching between open and closed state. ACS NANO 2015; 9:1117-26. [PMID: 25338165 PMCID: PMC4508203 DOI: 10.1021/nn5039433] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Membrane-spanning nanopores from folded DNA are a recent example of biomimetic man-made nanostructures that can open up applications in biosensing, drug delivery, and nanofluidics. In this report, we generate a DNA nanopore based on the archetypal six-helix-bundle architecture and systematically characterize it via single-channel current recordings to address several fundamental scientific questions in this emerging field. We establish that the DNA pores exhibit two voltage-dependent conductance states. Low transmembrane voltages favor a stable high-conductance level, which corresponds to an unobstructed DNA pore. The expected inner width of the open channel is confirmed by measuring the conductance change as a function of poly(ethylene glycol) (PEG) size, whereby smaller PEGs are assumed to enter the pore. PEG sizing also clarifies that the main ion-conducting path runs through the membrane-spanning channel lumen as opposed to any proposed gap between the outer pore wall and the lipid bilayer. At higher voltages, the channel shows a main low-conductance state probably caused by electric-field-induced changes of the DNA pore in its conformation or orientation. This voltage-dependent switching between the open and closed states is observed with planar lipid bilayers as well as bilayers mounted on glass nanopipettes. These findings settle a discrepancy between two previously published conductances. By systematically exploring a large space of parameters and answering key questions, our report supports the development of DNA nanopores for nanobiotechnology.
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Affiliation(s)
| | - Kerstin Göpfrich
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Jonathan R. Burns
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
| | - Niels Fertig
- Nanion Technologies GmbH, D-80636 Munich, Germany
| | - Ulrich F. Keyser
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
- Address correspondence to ;
| | - Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
- Address correspondence to ;
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44
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Shi W, Jia Y, Xu S, Li Z, Fu Y, Wei M, Shi S. A chiroptical switch based on DNA/layered double hydroxide ultrathin films. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:12916-12922. [PMID: 25285378 DOI: 10.1021/la502968z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A highly oriented film was fabricated by layer-by-layer self-assembly of DNA and MgAl-layered double hydroxide nanosheets, and its application in chiroptical switch was demonstrated via intercalation and deintercalation of an achiral molecule into the DNA cavity. DNA molecules are prone to forming an ordered and dispersive state in the interlayer region of rigid layered double hydroxide (LDH) nanosheets as confirmed by scanning electron microscopy and atomic force microscopy. The induced chiroptical ultrathin film (UTF) is achieved via the intercalation of an achiral chromophore [5,10,15,20-tetrakis(4-N-methylpyridyl)porphine tetra(p-toluenesulfonate) (TMPyP)] into the spiral cavity of DNA stabilized in the LDH matrix [denoted as TMPyP-(DNA/LDH)20]. Fluorescence and circular dichroism spectroscopy are utilized to testify the intercalation of TMPyP into (DNA/LDH)20 UTF that involves two steps: the electrostatic binding of TMPyP onto the surface of (DNA/LDH)20 followed by intercalation into base pairs of DNA. In addition, the TMPyP-(DNA/LDH)20 UTF exhibits good reversibility and repeatability in induced optical chirality, based on the intercalation and deintercalation of TMPyP by alternate exposure to HCl and NH3/H2O vapor, which can be potentially used as a chiroptical switch in data storage.
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Affiliation(s)
- Wenying Shi
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology , Beijing 100029, P. R. China
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45
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Vybornyi M, Nussbaumer AL, Langenegger SM, Häner R. Assembling multiporphyrin stacks inside the DNA double helix. Bioconjug Chem 2014; 25:1785-93. [PMID: 25186936 DOI: 10.1021/bc500297e] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Double stranded DNA hybrids containing up to four consecutive, face-to-face stacked porphyrins are described. Non-nucleosidic, 5,15-bisphenyl-substituted porphyrin building blocks were incorporated into complementary oligonucleotide strands. Upon hybridization multiple porphyrins are well accommodated inside the DNA scaffold without disturbing the overall B-DNA structure. The formation of double strands containing up to four free base porphyrins is enabled without compromising duplex stability. UV/vis, fluorescence, and CD spectroscopy demonstrate the formation of porphyrins H-aggregates inside the DNA double helix and provide evidence for the existence of strong excitonic coupling between interstrand stacked porphyrins. H-aggregation results in considerable fluorescence quenching. Most intense CD effects are observed in stacks containing four porphyrins. The findings demonstrate the value of DNA for the controlled formation of molecularly defined porphyrin aggregates.
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Affiliation(s)
- Mykhailo Vybornyi
- Department of Chemistry and Biochemistry, University of Bern , Freiestrasse 3, CH-3012 Bern, Switzerland
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46
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Interaction of meso-tetrakis(N-methylpyridinyl)porphyrin with single strand DNAs – poly(dA), poly(dT), poly(dG) and poly(dC): A photophysical study. J CHEM SCI 2014. [DOI: 10.1007/s12039-014-0639-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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47
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Yamada Y, Kubota T, Nishio M, Tanaka K. Sequential and spatial organization of metal complexes inside a peptide duplex. J Am Chem Soc 2014; 136:6505-9. [PMID: 24735178 DOI: 10.1021/ja502898t] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
To generate integrated organized molecular properties, multiple molecular components are required to be assembled into the molecular system with sequential and spatial accuracy in accordance with the design of the molecular assembly. Herein, we present a novel programmable synthesis of a cofacially stacked porphyrin array via repetitive construction of a peptide duplex. We designed and synthesized a novel porphyrin having two artificial amino acid moieties at the trans meso-positions. The amino acid moieties can be connected with another porphyrin unit by repetitive doubly coupling reactions to afford the peptide duplex bridged by the porphyrins. In the duplex, the porphyrin units are stacked cofacially, and the efficient electronic communication among the arrayed porphyrin units was characterized by split redox waves in the cyclic voltammograms. We also demonstrated the three different square-planar metal ions, namely Cu(2+), Ni(2+), and Pd(2+), were arranged inside the ladder-type porphyrin array in a programmable fashion.
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Affiliation(s)
- Yasuyuki Yamada
- Department of Chemistry, Graduate School of Science and ‡Research Center for Materials Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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48
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Wellner C, Wagenknecht HA. Synthesis of DNA conjugates with metalated tetracationic porphyrins by postsynthetic cycloadditions. Org Lett 2014; 16:1692-5. [PMID: 24606171 DOI: 10.1021/ol500364j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Tetracationic porphyrins of the TMPP (meso-tetra-(4-N-methylpyridyl)porphyrin) type, metalated with Cu(II) or with Au(III), were conjugated covalently to oligonucleotides. The Cu(I)-catalyzed cycloaddition (between an azide and an ethynyl group) and the Diels-Alder cycloaddition (between a furan and a maleimide functionality) were successfully applied as two alternative postsynthetic methods to modify the 2'-position of an internal uridine. Melting temperatures and UV/vis absorption properties were compared. CD measurements indicated that the type of conjugation chemistry determines the grade of intercalation of the attached and positively charged porphyrins.
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Affiliation(s)
- Christian Wellner
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry , Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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49
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Pan K, Boulais E, Yang L, Bathe M. Structure-based model for light-harvesting properties of nucleic acid nanostructures. Nucleic Acids Res 2014; 42:2159-70. [PMID: 24311563 PMCID: PMC3936709 DOI: 10.1093/nar/gkt1269] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 11/01/2013] [Accepted: 11/14/2013] [Indexed: 12/11/2022] Open
Abstract
Programmed self-assembly of DNA enables the rational design of megadalton-scale macromolecular assemblies with sub-nanometer scale precision. These assemblies can be programmed to serve as structural scaffolds for secondary chromophore molecules with light-harvesting properties. Like in natural systems, the local and global spatial organization of these synthetic scaffolded chromophore systems plays a crucial role in their emergent excitonic and optical properties. Previously, we introduced a computational model to predict the large-scale 3D solution structure and flexibility of nucleic acid nanostructures programmed using the principle of scaffolded DNA origami. Here, we use Förster resonance energy transfer theory to simulate the temporal dynamics of dye excitation and energy transfer accounting both for overall DNA nanostructure architecture as well as atomic-level DNA and dye chemical structure and composition. Results are used to calculate emergent optical properties including effective absorption cross-section, absorption and emission spectra and total power transferred to a biomimetic reaction center in an existing seven-helix double stranded DNA-based antenna. This structure-based computational framework enables the efficient in silico evaluation of nucleic acid nanostructures for diverse light-harvesting and photonic applications.
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Affiliation(s)
- Keyao Pan
- Department of Biological Engineering, Laboratory for Computational Biology & Biophysics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Etienne Boulais
- Department of Biological Engineering, Laboratory for Computational Biology & Biophysics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lun Yang
- Department of Biological Engineering, Laboratory for Computational Biology & Biophysics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mark Bathe
- Department of Biological Engineering, Laboratory for Computational Biology & Biophysics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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50
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Grabowska I, Singleton DG, Stachyra A, Góra-Sochacka A, Sirko A, Zagórski-Ostoja W, Radecka H, Stulz E, Radecki J. A highly sensitive electrochemical genosensor based on Co-porphyrin-labelled DNA. Chem Commun (Camb) 2014; 50:4196-9. [DOI: 10.1039/c4cc00172a] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cobalt-porphyrin-modified DNA was used to design an electrochemical genosensor which is able to detect a minimum of 1000 DNA molecules.
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Affiliation(s)
- Iwona Grabowska
- Institute of Animal Reproduction and Food Research
- Polish Academy of Sciences
- 10-747 Olsztyn, Poland
| | - Daniel G. Singleton
- School of Chemistry and Institute for Life Sciences
- University of Southampton
- Southampton SO17 1BJ, UK
| | - Anna Stachyra
- Institute of Biochemistry and Biophysics
- Polish Academy of Sciences
- 02-106 Warsaw, Poland
| | - Anna Góra-Sochacka
- Institute of Biochemistry and Biophysics
- Polish Academy of Sciences
- 02-106 Warsaw, Poland
| | - Agnieszka Sirko
- Institute of Biochemistry and Biophysics
- Polish Academy of Sciences
- 02-106 Warsaw, Poland
| | | | - Hanna Radecka
- Institute of Animal Reproduction and Food Research
- Polish Academy of Sciences
- 10-747 Olsztyn, Poland
| | - Eugen Stulz
- School of Chemistry and Institute for Life Sciences
- University of Southampton
- Southampton SO17 1BJ, UK
| | - Jerzy Radecki
- Institute of Animal Reproduction and Food Research
- Polish Academy of Sciences
- 10-747 Olsztyn, Poland
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