1
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Takezawa Y, Kudo N, Fuse N, Shionoya M. DNA three-way junction structures with amino acid side chains prepared via post-synthetic amide condensation. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2024:1-14. [PMID: 38359331 DOI: 10.1080/15257770.2024.2314645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 01/30/2024] [Indexed: 02/17/2024]
Abstract
DNA three-way junction (3WJ) structures with three amino acid side chains in the core have been synthesized via post-synthetic DNA modification. Amide condensation reactions of oligonucleotides containing 2'-aminouridine with activated esters yielded DNA strands modified with His, Cys and Asp side chains to form modified 3WJs. Even a 3WJ with three negatively charged Asp side chains formed stably at room temperature. Furthermore, DNA hybridization alone placed two (His and Asp) and three (His, Cys, and Asp) side chains within the 3WJs, indicating that the DNA 3WJs are a useful platform for spatial arrangement of amino acid side chains.
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Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Naofumi Kudo
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Nobuyuki Fuse
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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2
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Zarandi MA, Pathak P, Beltrami N, Walker JN, Zhang F, Brodbelt JS, Schmehl R, Jayawickramarajah J. Heteromeric guanosine (G)-quadruplex derived antenna modules with directional energy transfer. NANOSCALE 2023; 15:19069-19073. [PMID: 37990645 DOI: 10.1039/d3nr04086k] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
A heteromeric guanosine (G)-quadruplex centered self-assembly approach is developed to prepare compact light-harvesting antenna modules featuring multiple donor dyes and a single toehold region. Due to the mix-and-match nature of our approach, the number and placement of donor dyes can be readily fine-tuned via quadruplex assembly. Moreover, hybridization of the toehold with an acceptor containing sequence results in directional energy transfer ensembles with effective absorption coefficients in the 105 M-1 cm-1 range. These compact antennas exhibit system efficiencies that are comparable to much larger and elaborate DNA architectures containing numerous DNA strands.
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Affiliation(s)
| | - Pravin Pathak
- Department of Chemistry, Tulane University, New Orleans, LA, 70118, USA.
| | - Noah Beltrami
- Department of Chemistry, Tulane University, New Orleans, LA, 70118, USA.
| | - Jada N Walker
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Fengqi Zhang
- Department of Chemistry, Tulane University, New Orleans, LA, 70118, USA.
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Russell Schmehl
- Department of Chemistry, Tulane University, New Orleans, LA, 70118, USA.
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3
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Nakamura M, Yoshioka H, Takada T. Conformational Switching of Pyrenes Associated on Hairpin Loop Region by DNA B‐Z Transition. ChemistrySelect 2022. [DOI: 10.1002/slct.202200696] [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
| | - Hibiki Yoshioka
- 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
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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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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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6
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Bindu Ramesan A, Vittala SK, Joseph J. DNA condensation and formation of ultrathin nanosheets via DNA assisted self-assembly of an amphiphilic fullerene derivative. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2022; 226:112352. [PMID: 34798504 DOI: 10.1016/j.jphotobiol.2021.112352] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 12/17/2022]
Abstract
DNA nanotechnology propose various assembly strategies to develop novel functional nanostructures utilizing unique interactions of DNA with small molecules, nanoparticles, polymers, and other biomolecules. Although, well defined nanostructures of DNA and amphiphilic small molecules were achieved through hybridization of covalently modified DNA, attaining precise organization of functional moieties through non-covalent interactions remain as a challenging task. Herein, we report mutually assisted assembly of an amphiphilic fullerene derivative and various DNA structures through non-covalent interactions, which leads to initial DNA condensation and subsequent assembly yielding ordered fullerene-DNA nanosheets. The molecular design of the cationic, amphiphilic fullerene derivative (FPy) ensures molecular solubility in the 10% DMSO-PBS buffer system and facile interactions with DNA through groove binding and electrostatic interactions of fullerene moiety and positively charged pyridinium moiety, respectively. The formation of FPy/DNA nanostructures were thoroughly investigated in the presence of λ-DNA, pBR322 plasmid DNA, and single and double stranded 20-mer oligonucleotides using UV-visible spectroscopy, AFM and TEM analysis. λ-DNA and pBR322 plasmid DNA readily condense in presence of FPy leading to micrometer sized few layer nanosheets with significant crystallinity due to ordered arrangement of fullerenes. Similarly, single and double stranded 20-mer oligonucleotides also interact efficiently with FPy and form highly crystalline nanosheets, signifying the role of electrostatic interaction and subsequent charge neutralization in the condensation triggered assembly. However, there is significant differences in the crystallinity and ordered arrangements of fullerenes between these two cases, where longer DNA form condensed structures and less ordered nanosheets while short oligonucleotides lead to more ordered and highly crystalline nanosheets, which could be attributed to the differential DNA condensation. Finally, we have demonstrated the addressability of the assembly using a cyanine modified single strand DNA, which also forms highly crystalline nanosheets and exhibit efficient quenching of the cyanine fluorescence upon self-assembly. These results open up new prospects in the development of functional DNA nanostructures through non-covalent interactions and hence have potential applications in the context of DNA nanotechnology.
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Affiliation(s)
- Anjali Bindu Ramesan
- Photosciences and Photonics Section, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695 019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sandeepa Kulala Vittala
- Photosciences and Photonics Section, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695 019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Joshy Joseph
- Photosciences and Photonics Section, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695 019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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7
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Burns JR. Introducing Bacteria and Synthetic Biomolecules along Engineered DNA Fibers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2100136. [PMID: 33960622 DOI: 10.1002/smll.202100136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 03/12/2021] [Indexed: 06/12/2023]
Abstract
Deoxyribonucleic acid (DNA) nanotechnology enables user-defined structures to be built with unrivalled control. The approach is currently restricted across the nanoscale, yet the ability to generate macroscopic DNA structures has enormous potential with applications spanning material, physical, and biological science. To address this need, I employed DNA nanotechnology and developed a new macromolecular nanoarchitectonic assembly method to produce DNA fibers with customizable properties. The process involves coalescing DNA nanotubes under high salt conditions to yield filament superstructures. Using this strategy, fibers over 100 microns long, with stiffnesses 10 times greater than cytoskeletal actin filaments can be fabricated. The DNA framework enables fibers to be functionalized with advanced synthetic molecules, including, aptamers, origami, nanoparticles, and vesicles. In addition, the fibers can act as bacterial extracellular scaffolds and adhere Escherichia coli cells in a controllable fashion. These results showcase the opportunities offered from DNA nanotechnology across the macroscopic scale. The new biophysical approach should find widespread use, from the generation of hybrid-fabric materials, smart analytical devices in biomedicine, and platforms to study cell-cell interactions.
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Affiliation(s)
- Jonathan R Burns
- Department of Chemistry, Institute of Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK
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8
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Interactions of porphyrins with DNA: A review focusing recent advances in chemical modifications on porphyrins as artificial nucleases. J Inorg Biochem 2021; 219:111434. [PMID: 33819802 DOI: 10.1016/j.jinorgbio.2021.111434] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/18/2021] [Accepted: 03/18/2021] [Indexed: 12/14/2022]
Abstract
The advance of porphyrins as artificial nucleases along the years have developed a class of compounds having potential therapeutic applications. Being an extrovert of chemistry, a variety of chemical modifications have been done on porphyrin macrocycle in order to improve the spectroscopic properties and to adapt as artificial receptors that can recognize molecules. The last twenty years has witnessed broad research in the arena of porphyrin- DNA interactions and their evolution from simple to more complex entities. In this review, we summarize the recent advances in the porphyrin-based structural modifications, with a specific emphasis on various effects of porphyrin on DNA cleavage potency. We particularly detailed the nuclease activity of cationic and anionic porphyrins, porphyrin dimers and conjugates as well as heme proteins till the third generation porphyrins as artificial nucleases.
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9
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Röthlisberger P, Levi-Acobas F, Leumann CJ, Hollenstein M. Enzymatic synthesis of biphenyl-DNA oligonucleotides. Bioorg Med Chem 2020; 28:115487. [PMID: 32284226 DOI: 10.1016/j.bmc.2020.115487] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/27/2020] [Accepted: 04/01/2020] [Indexed: 12/25/2022]
Abstract
The incorporation of nucleotides equipped with C-glycosidic aromatic nucleobases into DNA and RNA is an alluring strategy for a number of practical applications including fluorescent labelling of oligonucleotides, expansion of the genetic alphabet for the generation of aptamers and semi-synthetic organisms, or the modulation of excess electron transfer within DNA. However, the generation of C-nucleoside containing oligonucleotides relies mainly on solid-phase synthesis which is quite labor intensive and restricted to short sequences. Here, we explore the possibility of constructing biphenyl-modified DNA sequences using enzymatic synthesis. The presence of multiple biphenyl-units or biphenyl residues modified with electron donors and acceptors permits the incorporation of a single dBphMP nucleotide. Moreover, templates with multiple abasic sites enable the incorporation of up to two dBphMP nucleotides, while TdT-mediated tailing reactions produce single-stranded DNA oligonucleotides with four biphenyl residues appended at the 3'-end.
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Affiliation(s)
- Pascal Röthlisberger
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR 3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France; Institut Pasteur, Department of Genome and Genetics, Paris, France
| | - Fabienne Levi-Acobas
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR 3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France; Institut Pasteur, Department of Genome and Genetics, Paris, France
| | - Christian J Leumann
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Marcel Hollenstein
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR 3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France; Institut Pasteur, Department of Genome and Genetics, Paris, France.
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10
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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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11
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Nakamura M, Takada T, Yamana K. Controlling Pyrene Association in DNA Duplexes by B‐ to Z‐DNA Transitions. Chembiochem 2019; 20:2949-2954. [DOI: 10.1002/cbic.201900350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Mitsunobu Nakamura
- Department of Applied ChemistryUniversity of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
| | - Tadao Takada
- Department of Applied ChemistryUniversity of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
| | - Kazushige Yamana
- Department of Applied ChemistryUniversity of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
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12
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Nakamura M, Matsui Y, Takada T, Yamana K. Chromophore Arrays Constructed in the Major Groove of DNA Duplexes Using a Post-Synthetic Strategy. ChemistrySelect 2019. [DOI: 10.1002/slct.201803464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Mitsunobu Nakamura
- Department of Applied Chemistry; University of Hyogo; 2167 Shosha, Himeji Hyogo 671-2280 Japan
| | - Yuki Matsui
- 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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13
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Linares F, García-Fernández E, López-Garzón FJ, Domingo-García M, Orte A, Rodríguez-Diéguez A, Galindo MA. Multifunctional behavior of molecules comprising stacked cytosine-Ag I-cytosine base pairs; towards conducting and photoluminescence silver-DNA nanowires. Chem Sci 2019; 10:1126-1137. [PMID: 30774910 PMCID: PMC6346629 DOI: 10.1039/c8sc04036b] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 11/04/2018] [Indexed: 12/20/2022] Open
Abstract
DNA molecules containing a 1D silver array may be applied for nanotechnology applications, but first their conducting and photoluminescence behavior must be enhanced. Here we have synthesized and characterized three new helical compounds based on stacked silver-mediated cytosine base pairs [Ag(mC)2]X (mC = N1-methylcytosine; X = NO3 (1), BF4 (2) and ClO4 (3)), that contain uninterrupted polymeric AgI chains that run through the center of the helixes, comparable to related silver-DNA structures. The exposure of nanostructures of [Ag(mC)2]BF4 (2) to cold hydrogen plasma stimulates the reduction of the prearranged AgI polymeric chains to metallic silver along the material. This solvent-free reduction strategy leads to the compound [AgI(mC)2]X@Ag0 (2H) that contains uniformly well-distributed silver metallic nanostructures that are responsible for the new conducting and photoluminescence properties of the material. The presence of silver nanostructures alongside compound 2H has been evaluated by means of X-ray photoelectron spectroscopy (XPS), UV-vis spectroscopy, and X-ray powder diffraction (XRPD). The conducting and photoactive properties of 2H were studied by electrostatic force microscopy (EFM) and conducting-AFM (c-AFM), and photoluminescence microscopy (PL), respectively. The results demonstrate that the presence of well-organized metallic silver nanoentities on the material is responsible for the novel conductivity and photoactive properties of the material. This methodology can be employed for the generation of multifunctional silver-DNA related materials with tailored properties.
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Affiliation(s)
- Fátima Linares
- Unidad de Microscopía de Fuerza Atómica , Centro de Instrumentación Científica , Universidad de Granada , Paseo Prof. Juan Osorio s/n , 18003 , Granada , Spain .
| | - Emilio García-Fernández
- Departamento de Fisicoquímica , Facultad de Farmacia , Universidad de Granada , Campus Cartuja , 18071 , Granada , Spain
| | - F Javier López-Garzón
- Departamento de Química Inorgánica , Facultad de Ciencias , Universidad de Granada , Avd. Fuentenueva s/n , 18071 , Granada , Spain .
| | - María Domingo-García
- Departamento de Química Inorgánica , Facultad de Ciencias , Universidad de Granada , Avd. Fuentenueva s/n , 18071 , Granada , Spain .
| | - Angel Orte
- Departamento de Fisicoquímica , Facultad de Farmacia , Universidad de Granada , Campus Cartuja , 18071 , Granada , Spain
| | - Antonio Rodríguez-Diéguez
- Departamento de Química Inorgánica , Facultad de Ciencias , Universidad de Granada , Avd. Fuentenueva s/n , 18071 , Granada , Spain .
| | - Miguel A Galindo
- Departamento de Química Inorgánica , Facultad de Ciencias , Universidad de Granada , Avd. Fuentenueva s/n , 18071 , Granada , Spain .
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14
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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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15
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Lebedeva NS, Yurina ES, Gubarev YA, Syrbu SA. Interactions of tetracationic porphyrins with DNA and their effects on DNA cleavage. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 199:235-241. [PMID: 29625380 DOI: 10.1016/j.saa.2018.03.066] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 03/19/2018] [Accepted: 03/23/2018] [Indexed: 06/08/2023]
Abstract
The interaction of tetracationic porphyrins with DNA was studied using UV-Vis absorption, fluorescence spectroscopy and viscometry, and the particle sizes were determined. Аs cationic porphyrins, two isomer porphyrins, 3,3',3″,3‴-(5,10,15,20-Porphyrintetrayl)tetrakis(1-methylpyridinium) (TMPyP3) and 4,4',4″,4‴-(5,10,15,20-Porphyrintetrayl)tetrakis(1-methylpyridinium) (TMPyP4), were studied. They differ in the position of NCH3+ group in phenyl ring of the porphyrins and hence, in degree of freedom of rotation of the phenyl rings about the central macrocycle. It was found that intercalated complexes are formed at DNA/porphyrin molar ratios (R) of 2.2 and 3.9 for TMPyP3 и TMPyP4, respectively. Decreasing R up to 0.4 and 0.8 for TMPyP3 и TMPyP4, respectively, leads mainly to formation of outside complexes due to π-π stacking between the porphyrin chromophores interacting electrostatically with phosphate framework of DNA. Each type of the obtained complexes was characterized using Scatchard approach. It was ascertained that the affinity of TMPyP4 to DNA is stronger than TMPyP3, meanwhile the wedge effect of the latter is higher. The differences between the porphyrin isomers become more evident at irradiation of their complexes with DNA. It was established that irradiation of the intercalated complexes results in DNA fragmentation. In the case of TMPyP4, DNA fragments of different size are formed. The irradiation of the outside DNA/porphyrin complexes leads to cleavage of DNA (TMPyP3 and TMPyP4) and partial destruction of the complex due to photolysis of the porphyrin (TMPyP3).
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Affiliation(s)
- Natalya Sh Lebedeva
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya, 1, 153045 Ivanovo, Russia
| | - Elena S Yurina
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya, 1, 153045 Ivanovo, Russia
| | - Yury A Gubarev
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya, 1, 153045 Ivanovo, Russia.
| | - Sergey A Syrbu
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya, 1, 153045 Ivanovo, Russia
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16
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Lubbe AS, Szymanski W, Feringa BL. Recent developments in reversible photoregulation of oligonucleotide structure and function. Chem Soc Rev 2018; 46:1052-1079. [PMID: 28128377 DOI: 10.1039/c6cs00461j] [Citation(s) in RCA: 209] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
There is a growing interest in the photoregulation of biological functions, due to the high level of spatiotemporal precision achievable with light. Additionally, light is non-invasive and waste-free. In particular, the photoregulation of oligonucleotide structure and function is a rapidly developing study field with relevance to biological, physical and material sciences. Molecular photoswitches have been incorporated in oligonucleotides for 20 years, and the field has currently grown beyond fundamental studies on photochemistry of the switches and DNA duplex stability, and is moving towards applications in chemical biology, nanotechnology and material science. Moreover, the currently emerging field of photopharmacology indicates the relevance of photocontrol in future medicine. In recent years, a large number of publications has appeared on photoregulation of DNA and RNA structure and function. New strategies are evaluated and novel, exciting applications are shown. In this comprehensive review, the key strategies for photoswitch inclusion in oligonucleotides are presented and illustrated with recent examples. Additionally the applications that have emerged in recent years are discussed, including gene regulation, drug delivery and materials design. Finally, we identify the challenges that the field currently faces and look forward to future applications.
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Affiliation(s)
- Anouk S Lubbe
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
| | - Wiktor Szymanski
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands. and Department of Radiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands.
| | - Ben L Feringa
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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17
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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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18
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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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19
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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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20
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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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21
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Chatelain G, Clavé G, Saint-Pierre C, Gasparutto D, Campidelli S. Self-assembly of porphyrin–DNA hybrids into large flat nanostructures. Org Biomol Chem 2017; 15:6257-6263. [DOI: 10.1039/c7ob01267e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two complementary 21-mer oligonucleotide/porphyrin hybrids were synthesized and assembled into nanostructures.
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Affiliation(s)
| | - G. Clavé
- LICSEN
- NIMBE
- CEA
- CNRS
- Université Paris-Saclay
| | - C. Saint-Pierre
- Université Grenoble Alpes
- INAC-SyMMES/UMR 5819 CEA-CNRS-UGA
- CEA-Grenoble
- F-38000 Grenoble
- France
| | - D. Gasparutto
- Université Grenoble Alpes
- INAC-SyMMES/UMR 5819 CEA-CNRS-UGA
- CEA-Grenoble
- F-38000 Grenoble
- France
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22
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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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23
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Kim KT, Choi TS, Kim KY, Kim HI, Kim BH. Disassembly of Chromophore-Guided DNA Duplexes through Site-Selective Binding of Coralyne to Pyrene-Modified Adenine Bases. Chempluschem 2016; 81:590-593. [DOI: 10.1002/cplu.201600230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Ki Tae Kim
- Department of Chemistry; Division of Advanced Materials Science; Pohang University of Science and Technology; Pohang 37673 Republic of Korea
| | - Tae Su Choi
- Department of Chemistry; Division of Advanced Materials Science; Pohang University of Science and Technology; Pohang 37673 Republic of Korea
- Department of Chemistry; Korea University; Seoul 02841 Republic of Korea
| | - Ka Young Kim
- Department of Chemistry; Division of Advanced Materials Science; Pohang University of Science and Technology; Pohang 37673 Republic of Korea
| | - Hugh I. Kim
- Department of Chemistry; Division of Advanced Materials Science; Pohang University of Science and Technology; Pohang 37673 Republic of Korea
- Department of Chemistry; Korea University; Seoul 02841 Republic of Korea
| | - Byeang Hyean Kim
- Department of Chemistry; Division of Advanced Materials Science; Pohang University of Science and Technology; Pohang 37673 Republic of Korea
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24
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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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25
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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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26
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Accetta A, Petrovic AG, Marchelli R, Berova N, Corradini R. Structural Studies on Porphyrin-PNA Conjugates in Parallel PNA:PNA Duplexes: Effect of Stacking Interactions on Helicity. Chirality 2015; 27:864-74. [PMID: 26412743 DOI: 10.1002/chir.22521] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 08/04/2015] [Accepted: 08/06/2015] [Indexed: 02/01/2023]
Abstract
Parallel PNA:PNA duplexes were synthesized and conjugated with meso-tris(pyridyl)phenylporphyrin carboxylic acid at the N-terminus. The introduction of one porphyrin unit was shown to affect slightly the stability of the PNA:PNA parallel duplex, whereas the presence of two porphyrin units at the same end resulted in a dramatic increase of the melting temperature, accompanied by hysteresis between melting and cooling curves. The circular dichroism (CD) profile of the Soret band and fluorescence quenching strongly support the occurrence of a face-to-face interaction between the two porphyrin units. Introduction of a L-lysine residue at the C-terminal of one strand of the parallel duplex induced a left-handed helical structure in the PNA:PNA duplex if the latter contains only one or no porphyrin moiety. The left-handed helicity was revealed by nucleobase CD profile at 240-280 nm and by the induced-CD observed in the presence of the DiSC2 (5) cyanine dye at ~500-550 nm. Surprisingly, the presence of two porphyrin units led to the disappearance of the nucleobase CD signal and the absence of CD exciton coupling within the Soret band region. In addition, a dramatic decrease of induced CD of DiSC2 (5) was observed. These results are in agreement with a model where the porphyrin-porphyrin interactions cause partial loss of chirality of the PNA:PNA parallel duplex, forcing it to adopt a ladder-like conformation.
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Affiliation(s)
- Alessandro Accetta
- Department of Chemistry, University of Parma, Parma, Italy.,Department of Chemistry, Columbia University, New York, New York, USA
| | - Ana G Petrovic
- Department of Chemistry, Columbia University, New York, New York, USA.,Department of Life Sciences, New York Institute of Technology (NYIT), New York, New York, USA
| | | | - Nina Berova
- Department of Chemistry, Columbia University, New York, New York, USA
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27
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Nakamura M, Tsuto K, Jomura A, Takada T, Yamana K. Donor-Acceptor Heterojunction Configurations Based on DNA-Multichromophore Arrays. Chemistry 2015; 21:11788-92. [DOI: 10.1002/chem.201501955] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Indexed: 12/22/2022]
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28
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Ensslen P, Brandl F, Sezi S, Varghese R, Kutta RJ, Dick B, Wagenknecht HA. DNA-Based Oligochromophores as Light-Harvesting Systems. Chemistry 2015; 21:9349-54. [PMID: 26069203 DOI: 10.1002/chem.201501213] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Indexed: 12/20/2022]
Abstract
The chromophores ethynyl pyrene as blue, ethynyl perylene as green and ethynyl Nile red as red emitter were conjugated to the 5-position of 2'-deoxyuridine via an acetylene bridge. Using phosphoramidite chemistry on solid phase labelled DNA duplexes were prepared that bear single chromophore modifications, and binary and ternary combinations of these chromophore modifications. The steady-state and time-resolved fluorescence spectra of all three chromophores were studied in these modified DNA duplexes. An energy-transfer cascade occurs from ethynyl pyrene over ethynyl perylene to ethynyl Nile red and subsequently an electron-transfer cascade in the opposite direction (from ethynyl Nile red to ethynyl perylene or ethynyl pyrene, but not from ethynyl perylene to ethynyl pyrene). The electron-transfer processes finally provide charge separation. The efficiencies by these energy and electron-transfer processes can be tuned by the distances between the chromophores and the sequences. Most importantly, excitation at any wavelength between 350 and 700 nm finally leads to charge separated states which make these DNA samples promising candidates for light-harvesting systems.
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Affiliation(s)
- Philipp Ensslen
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe (Germany)
| | - Fabian Brandl
- Institute of Physical and Theoretical Chemistry, University of Regensburg, Universitätsstr. 31, 93053 Regensburg (Germany)
| | - Sabrina Sezi
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe (Germany)
| | - Reji Varghese
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe (Germany)
| | - Roger-Jan Kutta
- Institute of Physical and Theoretical Chemistry, University of Regensburg, Universitätsstr. 31, 93053 Regensburg (Germany)
| | - Bernhard Dick
- Institute of Physical and Theoretical Chemistry, University of Regensburg, Universitätsstr. 31, 93053 Regensburg (Germany)
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe (Germany).
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29
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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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30
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Avinash MB, Govindaraju T. Nanoarchitectonics of biomolecular assemblies for functional applications. NANOSCALE 2014; 6:13348-69. [PMID: 25287110 DOI: 10.1039/c4nr04340e] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The stringent processes of natural selection and evolution have enabled extraordinary structure-function properties of biomolecules. Specifically, the archetypal designs of biomolecules, such as amino acids, nucleobases, carbohydrates and lipids amongst others, encode unparalleled information, selectivity and specificity. The integration of biomolecules either with functional molecules or with an embodied functionality ensures an eclectic approach for novel and advanced nanotechnological applications ranging from electronics to biomedicine, besides bright prospects in systems chemistry and synthetic biology. Given this intriguing scenario, our feature article intends to shed light on the emerging field of functional biomolecular engineering.
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Affiliation(s)
- M B Avinash
- Bioorganic Chemistry Laboratory, New Chemistry Unit (NCU), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur P. O., Bangalore 560064, India.
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31
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Ensslen P, Fritz Y, Wagenknecht HA. Mixed non-covalent assemblies of ethynyl nile red and ethynyl pyrene along oligonucleotide templates. Org Biomol Chem 2014; 13:487-92. [PMID: 25374296 DOI: 10.1039/c4ob01860e] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Ethynyl pyrene and ethynyl nile red as modifications at the 5-position of 2'-deoxyuridines self-assemble non-covalently and specifically along oligo-2'-deoxyadenosines as templates. Oligo-2'-deoxyadenosines of the lengths (dA)10-(dA)20 are able to retain nearly exactly as many ethynyl nile red units in solution as binding sites are available on these templates. In contrast, in the presence of oligo-2'-thymidines the ethynyl nile red moieties are similarly insoluble to those in the absence of any oligonucleotide and yield an aggregate. The mixed assemblies of both chromophores are highly ordered, show left-handed chirality and yield dual fluorescence. The strong excitonic coupling indicates assemblies with a high degree of order. These results show that DNA represents an important supramolecular scaffold for the templated, helical and non-covalent arrangement not only for one type of chromophore but also for mixtures of two different chromophores.
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Affiliation(s)
- Philipp Ensslen
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
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32
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Burns JR, Al-Juffali N, Janes SM, Howorka S. Membrane-Spanning DNA Nanopores with Cytotoxic Effect. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405719] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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33
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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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34
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35
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Kumar P, Østergaard ME, Baral B, Anderson BA, Guenther DC, Kaura M, Raible DJ, Sharma PK, Hrdlicka PJ. Synthesis and biophysical properties of C5-functionalized LNA (locked nucleic acid). J Org Chem 2014; 79:5047-61. [PMID: 24825249 PMCID: PMC4049237 DOI: 10.1021/jo500614a] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Indexed: 01/07/2023]
Abstract
Oligonucleotides modified with conformationally restricted nucleotides such as locked nucleic acid (LNA) monomers are used extensively in molecular biology and medicinal chemistry to modulate gene expression at the RNA level. Major efforts have been devoted to the design of LNA derivatives that induce even higher binding affinity and specificity, greater enzymatic stability, and more desirable pharmacokinetic profiles. Most of this work has focused on modifications of LNA's oxymethylene bridge. Here, we describe an alternative approach for modulation of the properties of LNA: i.e., through functionalization of LNA nucleobases. Twelve structurally diverse C5-functionalized LNA uridine (U) phosphoramidites were synthesized and incorporated into oligodeoxyribonucleotides (ONs), which were then characterized with respect to thermal denaturation, enzymatic stability, and fluorescence properties. ONs modified with monomers that are conjugated to small alkynes display significantly improved target affinity, binding specificity, and protection against 3'-exonucleases relative to regular LNA. In contrast, ONs modified with monomers that are conjugated to bulky hydrophobic alkynes display lower target affinity yet much greater 3'-exonuclease resistance. ONs modified with C5-fluorophore-functionalized LNA-U monomers enable fluorescent discrimination of targets with single nucleotide polymorphisms (SNPs). In concert, these properties render C5-functionalized LNA as a promising class of building blocks for RNA-targeting applications and nucleic acid diagnostics.
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Affiliation(s)
- Pawan Kumar
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
- Department of Chemistry, Kurukshetra University, Kurukshetra 136119, India
| | - Michael E. Østergaard
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Bharat Baral
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Brooke A. Anderson
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Dale C. Guenther
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Mamta Kaura
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Daniel J. Raible
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Pawan K. Sharma
- Department of Chemistry, Kurukshetra University, Kurukshetra 136119, India
| | - Patrick J. Hrdlicka
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
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36
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Tsuto K, Nakamura M, Takada T, Yamana K. Diketopyrrolopyrrole J-Aggregates Formed by Self-Organization with DNA. Chem Asian J 2014; 9:1618-22. [DOI: 10.1002/asia.201402063] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Indexed: 01/08/2023]
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37
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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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38
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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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39
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Sargsyan G, Leonard BM, Kubelka J, Balaz M. Supramolecular ssDNA Templated Porphyrin and Metalloporphyrin Nanoassemblies with Tunable Helicity. Chemistry 2014; 20:1878-92. [DOI: 10.1002/chem.201304153] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Indexed: 01/01/2023]
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40
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Lou C, Dallmann A, Marafini P, Gao R, Brown T. Enhanced H-bonding and π-stacking in DNA: a potent duplex-stabilizing and mismatch sensing nucleobase analogue. Chem Sci 2014. [DOI: 10.1039/c4sc00948g] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Combining enhanced π-stacking, H-bonding and electrostatic attraction in a single C-monomer greatly increases DNA duplex stability and massively destabilises mismatches.
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Affiliation(s)
- Chenguang Lou
- School of Chemistry
- University of Southampton
- Highfield
- Southampton SO17 1BJ, UK
| | - Andre Dallmann
- Institute of Structural Biology
- Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Center for Integrated Protein Science Munich and Chair of Biomolecular NMR
- TU München
- 85747 Garching, Germany
| | - Pietro Marafini
- School of Chemistry
- University of Southampton
- Highfield
- Southampton SO17 1BJ, UK
- Department of Chemistry
| | - Rachel Gao
- School of Chemistry
- University of Southampton
- Highfield
- Southampton SO17 1BJ, UK
| | - Tom Brown
- School of Chemistry
- University of Southampton
- Highfield
- Southampton SO17 1BJ, UK
- Department of Chemistry
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41
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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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42
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Burns JR, Göpfrich K, Wood JW, Thacker VV, Stulz E, Keyser UF, Howorka S. Lipid-bilayer-spanning DNA nanopores with a bifunctional porphyrin anchor. Angew Chem Int Ed Engl 2013; 52:12069-72. [PMID: 24014236 PMCID: PMC4016739 DOI: 10.1002/anie.201305765] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Indexed: 12/15/2022]
Affiliation(s)
- Jonathan R Burns
- Department of Chemistry, University College London20 Gordon Street, London WC1H OAJ (UK)
| | - Kerstin Göpfrich
- Cavendish Laboratory, University of CambridgeCambridge CB3 0HE (UK)
| | - James W Wood
- School of Chemistry, University of SouthamptonSouthampton SO17 1BJ (UK)
| | - Vivek V Thacker
- Cavendish Laboratory, University of CambridgeCambridge CB3 0HE (UK)
| | - Eugen Stulz
- School of Chemistry, University of SouthamptonSouthampton SO17 1BJ (UK)
| | - Ulrich F Keyser
- Cavendish Laboratory, University of CambridgeCambridge CB3 0HE (UK)
| | - Stefan Howorka
- Department of Chemistry, University College London20 Gordon Street, London WC1H OAJ (UK)
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43
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Burns JR, Göpfrich K, Wood JW, Thacker VV, Stulz E, Keyser UF, Howorka S. Lipid-Bilayer-Spanning DNA Nanopores with a Bifunctional Porphyrin Anchor. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201305765] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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44
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Kaura M, Kumar P, Hrdlicka PJ. Synthesis and hybridization properties of oligonucleotides modified with 5-(1-aryl-1,2,3-triazol-4-yl)-2'-deoxyuridines. Org Biomol Chem 2013; 10:8575-8. [PMID: 23042241 DOI: 10.1039/c2ob26717a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Oligonucleotides modified with consecutive incorporations of 5-(1-aryl-1,2,3-triazol-4-yl)-2'-deoxyuridine monomers display strong thermal affinity and binding specificity toward RNA targets, due to formation of chromophore arrays in the major groove.
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Affiliation(s)
- Mamta Kaura
- Department of Chemistry, University of Idaho, PO Box 442343, Moscow, ID 83844-2343, USA
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45
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Chen W, Schuster GB. Precise Sequence Control in Linear and Cyclic Copolymers of 2,5-Bis(2-thienyl)pyrrole and Aniline by DNA-Programmed Assembly. J Am Chem Soc 2013; 135:4438-49. [DOI: 10.1021/ja312507z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Wen Chen
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332,
United States
| | - Gary B. Schuster
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332,
United States
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46
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Sezi S, Wagenknecht HA. DNA-templated formation of fluorescent self-assembly of ethynyl pyrenes. Chem Commun (Camb) 2013; 49:9257-9. [DOI: 10.1039/c3cc44733b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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47
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Sargsyan G, Schatz AA, Kubelka J, Balaz M. Formation and helicity control of ssDNA templated porphyrin nanoassemblies. Chem Commun (Camb) 2013; 49:1020-2. [DOI: 10.1039/c2cc38150h] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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48
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Chen W, Schuster GB. Structural stabilization of DNA-templated nanostructures: crosslinking with 2,5-bis(2-thienyl)pyrrole monomers. Org Biomol Chem 2013; 11:35-40. [DOI: 10.1039/c2ob26716k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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49
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Sancho Oltra N, Browne WR, Roelfes G. Hierarchical Self-Assembly of a Biomimetic Light-Harvesting Antenna Based on DNA G-Quadruplexes. Chemistry 2012; 19:2457-61. [DOI: 10.1002/chem.201202550] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 11/09/2012] [Indexed: 01/20/2023]
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50
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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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