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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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2
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Kaerkitcha N, Sagawa T. Amplified polarization properties of electrospun nanofibers containing fluorescent dyes and helical polymer. Photochem Photobiol Sci 2018; 17:342-351. [DOI: 10.1039/c7pp00413c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Well-aligned nanofibers containing cationic fluorescent dyes and anionic chiral polymers prepared via electrospinning exhibit an enhanced circular dichroism, which is mainly caused by linear dichroism and linear birefringence.
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Affiliation(s)
- N. Kaerkitcha
- Graduate School of Energy Science
- Kyoto University
- Kyoto 606-8501
- Japan
| | - T. Sagawa
- Graduate School of Energy Science
- Kyoto University
- Kyoto 606-8501
- Japan
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3
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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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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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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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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 DOI: 10.1021/acs.jpca.6b10939] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [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 Straße 11, 81377 Munich, Germany
| | - Elisa A Hemmig
- Cavendish Laboratory, University of Cambridge , JJ Thomson Avenue, 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 Straße 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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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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9
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Nguyen T, Håkansson P, Edge R, Collison D, Goodman BA, Burns JR, Stulz E. EPR based distance measurement in Cu-porphyrin–DNA. NEW J CHEM 2014. [DOI: 10.1039/c4nj00673a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Measurement of EPR spectra of Cu-porphyrin–DNA reveals intermolecular interactions between the DNA strands with average distances of 6.5–8.9 Å.
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Affiliation(s)
- ThaoNguyen Nguyen
- School of Chemistry and Instituted of Life Sciences
- University of Southampton
- Southampton, UK
| | - Pär Håkansson
- School of Chemistry and Instituted of Life Sciences
- University of Southampton
- Southampton, UK
| | - Ruth Edge
- School of Chemistry and Photon Science Institute
- The University of Manchester
- Manchester, UK
| | - David Collison
- School of Chemistry and Photon Science Institute
- The University of Manchester
- Manchester, UK
| | - Bernard A. Goodman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources
- Guangxi University
- Nanning 530005, China
| | - Jonathan R. Burns
- School of Chemistry and Instituted of Life Sciences
- University of Southampton
- Southampton, UK
| | - Eugen Stulz
- School of Chemistry and Instituted of Life Sciences
- University of Southampton
- Southampton, UK
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10
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Markova LI, Malinovskii VL, Patsenker LD, Häner R. J- vs. H-type assembly: pentamethine cyanine (Cy5) as a near-IR chiroptical reporter. Chem Commun (Camb) 2013; 49:5298-300. [PMID: 23636273 DOI: 10.1039/c3cc42103a] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The DNA-enabled dimerization of pentamethine cyanine (Cy5) dyes was studied by optical methods. The value of cyanine as a chiroptical reporter using a monomer-to-dimer switch is demonstrated. The specific shape of the CD signal and its high intensity are a result of J-type assembly.
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Affiliation(s)
- Larysa I Markova
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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11
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Yamada Y, Mihara N, Shibano S, Sugimoto K, Tanaka K. Triply Stacked Heterogeneous Array of Porphyrins and Phthalocyanine through Stepwise Formation of a Fourfold Rotaxane and an Ionic Complex. J Am Chem Soc 2013; 135:11505-8. [DOI: 10.1021/ja405963t] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Yasuyuki Yamada
- Department of Chemistry, Graduate
School of Science, Nagoya University, Furo-cho,
Chikusa-ku, Nagoya 464-8602, Japan
- Research Center for Materials
Science, Nagoya University, Furo-cho, Chikusa-ku,
Nagoya 464-8602, Japan
| | - Nozomi Mihara
- Department of Chemistry, Graduate
School of Science, Nagoya University, Furo-cho,
Chikusa-ku, Nagoya 464-8602, Japan
| | - Shinya Shibano
- Department of Chemistry, Graduate
School of Science, Nagoya University, Furo-cho,
Chikusa-ku, Nagoya 464-8602, Japan
| | - Kunihisa Sugimoto
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho,
Sayo-gun, Hyogo 679-5198, Japan
| | - Kentaro Tanaka
- Department of Chemistry, Graduate
School of Science, Nagoya University, Furo-cho,
Chikusa-ku, Nagoya 464-8602, Japan
- CREST, Japan Science and Technology Agency, Honcho 4-1-8, Kawaguchi 332-0012,
Japan
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MoradpourHafshejani S, Hedley JH, Haigh AO, Pike AR, Tuite EM. Synthesis and binding of proflavine diazides as functional intercalators for directed assembly on DNA. RSC Adv 2013. [DOI: 10.1039/c3ra43090a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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13
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Albinsson B, Hannestad JK, Börjesson K. Functionalized DNA nanostructures for light harvesting and charge separation. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2012.02.024] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Affiliation(s)
- Yin Nah Teo
- Department of Chemistry, Stanford University, California 94305, United States
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Börjesson K, Woller JG, Parsa E, Mårtensson J, Albinsson B. A bioinspired self assembled dimeric porphyrin pocket that binds electron accepting ligands. Chem Commun (Camb) 2012; 48:1793-5. [PMID: 22215229 DOI: 10.1039/c2cc17434k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A binding pocket consisting of two zinc porphyrins self assembled by Watson-Crick base pairing is presented. The porphyrin binding pocket is located in the confined environment of a lipid membrane whereas the DNA is located in the water phase. Bidentate electron accepting ligands are shown to coordinate in-between the two porphyrins.
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Affiliation(s)
- Karl Börjesson
- Department of Chemical and Biological Engineering, Chalmers University of Technology, 41296, Göteborg, Sweden
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Kashida H, Asanuma H. Preparation of supramolecular chromophoric assemblies using a DNA duplex. Phys Chem Chem Phys 2012; 14:7196-204. [DOI: 10.1039/c2cp40520b] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Zelenka K, Trnka T, Tišlerová I, Monti D, Cinti S, Naitana ML, Schiaffino L, Venanzi M, Laguzzi G, Luvidi L, Mancini G, Nováková Z, Šimák O, Wimmer Z, Drašar P. Spectroscopic, Morphological, and Mechanistic Investigation of the Solvent-Promoted Aggregation of Porphyrins Modified in meso-Positions by Glucosylated Steroids. Chemistry 2011; 17:13743-53. [DOI: 10.1002/chem.201101163] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Indexed: 01/21/2023]
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Burns JR, Zekonyte J, Siligardi G, Hussain R, Stulz E. Directed formation of DNA nanoarrays through orthogonal self-assembly. Molecules 2011; 16:4912-22. [PMID: 21677604 PMCID: PMC6264196 DOI: 10.3390/molecules16064912] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 05/31/2011] [Accepted: 06/10/2011] [Indexed: 01/12/2023] Open
Abstract
We describe the synthesis of terpyridine modified DNA strands which selectively form DNA nanotubes through orthogonal hydrogen bonding and metal complexation interactions. The short DNA strands are designed to self-assemble into long duplexes through a sticky-end approach. Addition of weakly binding metals such as Zn(II) and Ni(II) induces the formation of tubular arrays consisting of DNA bundles which are 50-200 nm wide and 2-50 nm high. TEM shows additional long distance ordering of the terpy-DNA complexes into fibers.
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Affiliation(s)
- Jonathan R. Burns
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Jurgita Zekonyte
- National Centre for Advanced Tribology, School of Engineering Sciences, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - Giuliano Siligardi
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Rohanah Hussain
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Eugen Stulz
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
- Author to whom correspondence should be addressed; ; Tel +44-2380-599369
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Stephenson AWI, Partridge AC, Filichev VV. Synthesis of β-pyrrolic-modified porphyrins and their incorporation into DNA. Chemistry 2011; 17:6227-38. [PMID: 21503985 DOI: 10.1002/chem.201003200] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 02/01/2011] [Indexed: 12/20/2022]
Abstract
A synthetic methodology for the synthesis of various β-pyrrolic-functionalised porphyrins and their covalent attachment to 2'-deoxyuridine and DNA is described. Palladium(0)-catalysed Sonogashira and copper(I)-catalysed Huisgen 1,3-dipolar cycloaddition reactions were used to insert porphyrins into the structure of 2'-deoxyuridine and DNA. Insertion of a porphyrin into the middle of single-stranded CT oligonucleotides possessing a 5'-terminal run of four cytosines was shown to trigger the formation of pH- and temperature-dependent i-motif structures. Porphyrin insertion also led to the aggregation of single-stranded purine-pyrimidine sequences, which could be dissociated by heating at 90 °C for 5 min. Parallel triplexes and anti-parallel duplexes were formed in the presence of the appropriate complementary strand(s). Depending on the modification, porphyrins were placed in the major and minor grooves of duplexes and were used as bulged intercalating insertions in duplexes and triplexes. In general, the thermal stabilisation of parallel triplexes possessing porphyrin-modified triplex-forming oligonucleotide (TFO) strands was observed, whereas anti-parallel duplexes were destabilised. These results are compared and discussed on the basis of the results of molecular modelling calculations.
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Affiliation(s)
- Adam W I Stephenson
- College of Sciences, Institute of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand
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Zhou H, Johnson AT, Wiest O, Zhang L. Incorporation of porphyrin acetylides into duplexes of the simplified nucleic acid GNA. Org Biomol Chem 2011; 9:2840-9. [PMID: 21365112 DOI: 10.1039/c0ob00439a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A porphyrin-acetylide-modified GNA (glycol nucleic acid) phosphoramidite building block was synthesized in an economical fashion starting from (S)-glycidyl-4,4'- dimethoxytrityl ether in just 4 steps with an overall yield of 48%. The porphyrin acetylide nucleotide was incorporated into GNA duplexes opposite ethylene glycol abasic sites and the duplexes were analyzed by UV-melting, UV-vis, fluorescence spectroscopy, and circular dichroism. The modified GNA duplexes display lower thermal stabilities, however, the stabilities of the duplexes can be modulated by the incorporation of Zn(2+) (further destabilization) or Ni(2+) (stabilization relative to the uncomplexed porphyrin). Uncomplexed as well as Ni(2+)-coordinated porphyrins intercalate into the GNA duplex whereas Zn(2+)-coordinated porphyrins are most likely located outside the base stack. Adjacent porphyrins in opposite strands of GNA duplexes show an electronic interaction with each other which might be exploited in the future for the design of photoelectrical devices.
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Affiliation(s)
- Hui Zhou
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße, D-35032, Marburg, Germany
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21
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Galindo MA, Hannant J, Harrington RW, Clegg W, Horrocks BR, Pike AR, Houlton A. Pyrrolyl-, 2-(2-thienyl)pyrrolyl- and 2,5-bis(2-thienyl)pyrrolyl-nucleosides: synthesis, molecular and electronic structure, and redox behaviour of C5-thymidine derivatives. Org Biomol Chem 2011; 9:1555-64. [PMID: 21240418 DOI: 10.1039/c0ob00466a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A series of modified nucleosides based on thymidine have been prepared by Pd-catalysed cross-coupling between N-alkyl-alkynyl functionalised pyrrolyl- (py), 2-(2-thienyl)pyrrolyl- (tp) or 2,5-bis(2-thienyl)pyrrolyl (tpt) groups with 5-iodo-2'-deoxyuridine. The length of the alkyl chain linking the nucleoside and pyrrolyl-containing unit, N(CH(2))(n)C[triple bond, length as m-dash]C-nucleoside (where n = 1-3) was also varied. The compounds have been characterised by (1)H NMR, ES-MS, UV-vis, cyclic voltammetry (CV) and, in some cases, single-crystal X-ray diffraction. Cyclic voltammetry studies demonstrated that all the py-, tp- and tpt-alkynyl derivatives 1-7 can be electrochemically polymerised to form conductive materials. It was found that increasing the N-alkyl chain length in these cases resulted in only minor changes in the oxidation potential. The same behaviour was observed for the tp- and tpt-modified nucleosides 9-12; however, the py-derivative, 8, produced a poorly conducting material. DFT calculations on the one-electron oxidised cation of the modified nucleosides bearing tp or tpt showed that spin density is located on the pyrrolyl and thienyl units in all cases and that the coplanarity of adjacent rings increases upon oxidation. In contrast, in the corresponding pyrrolyl cases the spin density is distributed over the whole molecule, suggesting that polymerisation does not occur solely at the pyrrolyl-Cα position and the conjugation is interrupted.
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Affiliation(s)
- Miguel A Galindo
- Chemical Nanoscience Laboratory, School of Chemistry, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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22
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Stephenson AWI, Bomholt N, Partridge AC, Filichev VV. Significantly enhanced DNA thermal stability resulting from porphyrin H-aggregate formation in the minor groove of the duplex. Chembiochem 2011; 11:1833-9. [PMID: 20677201 DOI: 10.1002/cbic.201000326] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Adam W I Stephenson
- College of Sciences, Institute of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand
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23
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Biner SM, Kummer D, Malinovskii VL, Häner R. Signal control by self-assembly of fluorophores in a molecular beacon—a model study. Org Biomol Chem 2011; 9:2628-33. [DOI: 10.1039/c0ob01132k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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24
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Brewer A, Siligardi G, Neylon C, Stulz E. Introducing structural flexibility into porphyrin-DNA zipper arrays. Org Biomol Chem 2010; 9:777-82. [PMID: 21103551 DOI: 10.1039/c0ob00535e] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A more flexible nucleotide building block for the synthesis of new DNA based porphyrin-zipper arrays is described. Changing the rigid acetylene linker between the porphyrin substituent and the 2'-deoxyuridine to a more flexible propargyl amide containing linkage leads in part to an increased duplex stability. The CD spectra reveal different electronic interactions between the porphyrins depending on the type of linker used. Molecular modelling suggests large variation of the relative orientation of the porphyrins within the major groove of the DNA. The porphyrins can be metallated post-synthetically with different metals as shown with zinc, cobalt and copper. The spectroscopic features do not alter drastically upon metallation apart from the CD spectra, and the stability of the metal complex is highly dependent on the nature of the metal. As shown by CD spectroscopy, the zinc porphyrin is rapidly demetallated at high temperatures. Globular structure determination using SAXS indicates that a molecular assembly comprised of a two to four helical bundle dominates in solution at higher concentrations (≥50 μM) which is not observed by spectroscopy at lower concentrations (≤1 μM).
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Affiliation(s)
- Ashley Brewer
- School of Chemistry, University of Southampton, Highfield, Southampton, UK SO17 1BJ
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25
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Börjesson K, Wiberg J, El-Sagheer AH, Ljungdahl T, Mårtensson J, Brown T, Nordén B, Albinsson B. Functionalized nanostructures: redox-active porphyrin anchors for supramolecular DNA assemblies. ACS NANO 2010; 4:5037-5046. [PMID: 20809571 DOI: 10.1021/nn100667b] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
We have synthesized and studied a supramolecular system comprising a 39-mer DNA with porphyrin-modified thymidine nucleosides anchored to the surface of large unilamellar vesicles (liposomes). Liposome porphyrin binding characteristics, such as orientation, strength, homogeneity, and binding site size, was determined, suggesting that the porphyrin is well suited as a photophysical and redox-active lipid anchor, in comparison to the inert cholesterol anchor commonly used today. Furthermore, the binding characteristics and hybridization capabilities were studied as a function of anchor size and number of anchoring points, properties that are of importance for our future plans to use the addressability of these redox-active nodes in larger DNA-based nanoconstructs. Electron transfer from photoexcited porphyrin to a lipophilic benzoquinone residing in the lipid membrane was characterized by steady-state and time-resolved fluorescence and verified by femtosecond transient absorption.
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Affiliation(s)
- Karl Börjesson
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, S-41296 Gothenburg, Sweden
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26
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Bandy TJ, Brewer A, Burns JR, Marth G, Nguyen T, Stulz E. DNA as supramolecular scaffold for functional molecules: progress in DNA nanotechnology. Chem Soc Rev 2010; 40:138-48. [PMID: 20694258 DOI: 10.1039/b820255a] [Citation(s) in RCA: 197] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Oligonucleotides have recently gained increased attraction as a supramolecular scaffold for the design and synthesis of functional molecules on the nanometre scale. This tutorial review focuses on the recent progress in this highly active field of research with an emphasis on covalent modifications of DNA; non-covalent interactions of DNA with molecules such as groove binders or intercalators are not part of this review. Both terminal and internal modifications are covered, and the various points of attachment (nucleobase, sugar moiety or phosphodiester backbone) are compared. Using selected examples of the recent literature, the diversity of the functionalities that have been incorporated into DNA strands is discussed.
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Affiliation(s)
- Thomas J Bandy
- University of Southampton, School of Chemistry, Highfield, Southampton SO17 1BJ, UK
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27
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Abstract
Due to its self-assembling nature, DNA is undoubtedly an excellent molecule for the creation of various multidimensional nanostructures and the placement of functional molecules and materials. DNA molecules behave according to the programs of their sequences. Mixtures of numbers of DNA molecules can be placed precisely and organized into single structures to form nanoarchitectures. Once the appropriate sequences for the target nanostructure are established, the predesigned structure can be built up by self-assembly of the designed DNA strands. DNA nanotechnology has already reached the stage at which the organization of desired functional molecules and nanomaterials can be programmed on a defined DNA scaffold. In this review, we will focus on DNA nanotechnology and describe the potential of synthetic chemistry to contribute to the further development of DNA nanomaterials.
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Affiliation(s)
- Masayuki Endo
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
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28
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Affiliation(s)
- Thomas Rühl
- a School of Chemistry , University of Southampton , Highfield, Southampton, SO17 1EW, UK
| | - Eugen Stulz
- a School of Chemistry , University of Southampton , Highfield, Southampton, SO17 1EW, UK
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29
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Schwartz E, Le Gac S, Cornelissen JJLM, Nolte RJM, Rowan AE. Macromolecular multi-chromophoric scaffolding. Chem Soc Rev 2010; 39:1576-99. [DOI: 10.1039/b922160c] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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Malinovskii VL, Wenger D, Häner R. Nucleic acid-guided assembly of aromatic chromophores. Chem Soc Rev 2009; 39:410-22. [PMID: 20111767 DOI: 10.1039/b910030j] [Citation(s) in RCA: 225] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The rational formation of aromatic chromophore arrays is an intriguing challenge since ordered collectives of chromophores possess properties that are largely different from those of the individual molecules. Therefore, nucleic acids are increasingly used as scaffolds for the construction of multi-chromophore arrays. This tutorial review provides an introduction to the field of nucleic acid-guided chromophore assemblies for non-specialists and a reference point for those familiar with the area by highlighting the recent developments and describing some of the spectroscopic methods used for the study of oligonucleotide-chromophore conjugates.
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Affiliation(s)
- Vladimir L Malinovskii
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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31
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Monti D, De Rossi M, Sorrenti A, Laguzzi G, Gatto E, Stefanelli M, Venanzi M, Luvidi L, Mancini G, Paolesse R. Supramolecular Chirality in Solvent-Promoted Aggregation of Amphiphilic Porphyrin Derivatives: Kinetic Studies and Comparison between Solution Behavior and Solid-State Morphology by AFM Topography. Chemistry 2009; 16:860-70. [DOI: 10.1002/chem.200901964] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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32
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Wagenknecht HA. Helicale Anordnung von Porphyrinen entlang der DNA: auf dem Weg zu DNA-Nanoarchitekturen. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200900327] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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33
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Wagenknecht HA. Helical Arrangement of Porphyrins along DNA: Towards Photoactive DNA-Based Nanoarchitectures. Angew Chem Int Ed Engl 2009; 48:2838-41. [DOI: 10.1002/anie.200900327] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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34
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Nguyen T, Brewer A, Stulz E. Duplex Stabilization and Energy Transfer in Zipper Porphyrin-DNA. Angew Chem Int Ed Engl 2009; 48:1974-7. [DOI: 10.1002/anie.200805657] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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35
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Nguyen T, Brewer A, Stulz E. Duplex Stabilization and Energy Transfer in Zipper Porphyrin-DNA. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200805657] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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