1
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Thiede J, Schneeberger T, Iacovache I, Langenegger SM, Zuber B, Häner R. Supramolecular assembly of phenanthrene-DNA conjugates into light-harvesting nanospheres. NEW J CHEM 2024; 48:15731-15734. [PMID: 39234596 PMCID: PMC11367589 DOI: 10.1039/d4nj02411g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 08/23/2024] [Indexed: 09/06/2024]
Abstract
The self-assembly of highly functionalized phenanthrene-DNA conjugates into supramolecular nanostructures is presented. DNA oligomers modified with phenanthrene residues at the 3'-end and internal positions self-assemble into spherical nanostructures. The nanospheres exhibit light-harvesting properties. Upon irradiation of phenanthrene, the excitation energy is transferred along phenanthrene units, resulting in phenanthrene-pyrene exciplex formation.
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Affiliation(s)
- Jan Thiede
- Department of Chemistry, Biochemistry, and Pharmaceutical Sciences, University of Bern Freiestrasse 3 CH-3012 Bern Switzerland https://www.haener.dcbp.unibe.ch
| | - Thomas Schneeberger
- Department of Chemistry, Biochemistry, and Pharmaceutical Sciences, University of Bern Freiestrasse 3 CH-3012 Bern Switzerland https://www.haener.dcbp.unibe.ch
| | - Ioan Iacovache
- Institute of Anatomy, University of Bern Baltzerstrasse 2 CH-3012 Bern Switzerland
| | - Simon M Langenegger
- Department of Chemistry, Biochemistry, and Pharmaceutical Sciences, University of Bern Freiestrasse 3 CH-3012 Bern Switzerland https://www.haener.dcbp.unibe.ch
| | - Benoît Zuber
- Institute of Anatomy, University of Bern Baltzerstrasse 2 CH-3012 Bern Switzerland
| | - Robert Häner
- Department of Chemistry, Biochemistry, and Pharmaceutical Sciences, University of Bern Freiestrasse 3 CH-3012 Bern Switzerland https://www.haener.dcbp.unibe.ch
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2
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Yang CF, Udumulla T, Sha R, Canary JW. Control of Solid-Supported Intra- vs Interstrand Stille Coupling Reactions for Synthesis of DNA-Oligophenylene Conjugates. Bioconjug Chem 2024; 35:1166-1171. [PMID: 39046902 PMCID: PMC11342295 DOI: 10.1021/acs.bioconjchem.4c00310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 07/27/2024]
Abstract
Programmed DNA structures and assemblies are readily accessible, but site-specific functionalization is critical to realize applications in various fields such as nanoelectronics, nanomaterials and biomedicine. Besides pre- and post-DNA synthesis conjugation strategies, on-solid support reactions offer advantages in certain circumstances. We describe on-solid support internucleotide coupling reactions, often considered undesirable, and a workaround strategy to overcome them. Palladium coupling reactions enabled on-solid support intra- and interstrand coupling between single-stranded DNAs (ss-DNAs). Dilution with a capping agent suppressed interstrand coupling, maximizing intrastrand coupling. Alternatively, interstrand coupling actually proved advantageous to provide dimeric organic/DNA conjugates that could be conveniently separated from higher oligomers, and was more favorable with longer terphenyl coupling partners.
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Affiliation(s)
- Chu-Fan Yang
- Department of Chemistry, New
York University, New York, New York 10003, United States
| | - Thanuka Udumulla
- Department of Chemistry, New
York University, New York, New York 10003, United States
| | - Ruojie Sha
- Department of Chemistry, New
York University, New York, New York 10003, United States
| | - James W. Canary
- Department of Chemistry, New
York University, New York, New York 10003, United States
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3
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Li C, Xie X, Li M, Wang H, Cheng X, Zhang J, Li Q, Li J, Zuo X, Fan C, Shen J. Ultrafast Super-Resolution Imaging Exploiting Spontaneous Blinking of Static Excimer Aggregates. J Am Chem Soc 2024; 146:18948-18957. [PMID: 38959409 DOI: 10.1021/jacs.4c01084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Single-molecule localization methods have been popularly exploited to obtain super-resolved images of biological structures. However, the low blinking frequency of randomly switching emission states of individual fluorophores greatly limits the imaging speed of single-molecule localization microscopy (SMLM). Here we present an ultrafast SMLM technique exploiting spontaneous fluorescence blinking of cyanine dye aggregates confined to DNA framework nanostructures. The DNA template guides the formation of static excimer aggregates as a "light-harvesting nanoantenna", whereas intermolecular excitation energy transfer (EET) between static excimers causes collective ultrafast fluorescence blinking of fluorophore aggregates. This DNA framework-based strategy enables the imaging of DNA nanostructures with 12.5-fold improvement in speed compared to conventional SMLM. Further, we demonstrate the use of this strategy to track the movement of super-resolved DNA nanostructures for over 20 min in a microfluidic system. Thus, this ultrafast SMLM holds great potential for revealing the dynamic processes of biomacromolecules in living cells.
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Affiliation(s)
- Cong Li
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaodong Xie
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mingqiang Li
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Haozhi Wang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xinyi Cheng
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jichao Zhang
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 239 Zhangheng Road, Shanghai 201204, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiang Li
- Institute of Materiobiology, Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jianlei Shen
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
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4
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Piteša T, Polonius S, González L, Mai S. Excitonic Configuration Interaction: Going Beyond the Frenkel Exciton Model. J Chem Theory Comput 2024; 20:5609-5634. [PMID: 38885637 PMCID: PMC11238547 DOI: 10.1021/acs.jctc.4c00157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/08/2024] [Accepted: 05/15/2024] [Indexed: 06/20/2024]
Abstract
We present the excitonic configuration interaction (ECI) method─a fragment-based analogue of the CI method for electronic structure calculations of multichromophoric systems. It can also be viewed as a generalization of the exciton approach, with the following properties: (i) It constructs the effective Hamiltonian exclusively from monomer calculations. (ii) It employs the strong orthogonality assumption and is exact within McWeeny's group function theory, thus requiring only one-electron density matrices of the monomer states. (iii) It is agnostic of the monomer electronic structure method, allowing us to use/combine different methods. (iv) It includes an embedding point charge scheme (called excitonic Hartree-Fock, EHF) to improve the accuracy of the monomer states, but such that the effective full-system Hamiltonian is not explicitly dependent on the embedding. (v) It is systematically improvable, by expanding the set of monomer states and by including configurations where two or more monomers are excited (defining the ECIS, ECISD, etc., methods). The performance of ECI is assessed by computing the absorption spectrum of two exemplary multichromophoric systems, using CIS as the monomer electronic structure method. The accuracy of ECI significantly depends on the chosen embedding charges and the ECI expansion. The most accurate assessed combinations─ECIS or ECISD with EHF embedding─yield spectra that agree qualitatively and quantitatively with full-system direct calculations, with deviations of the excitation energies below 0.1 eV. We also show that ECISD based on CIS monomer calculations can predict states where two monomers are excited simultaneously (e.g., triplet-triplet double-local excitations) that are inaccessible in a full-system CIS calculation.
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Affiliation(s)
- Tomislav Piteša
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
| | - Severin Polonius
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
- Vienna
Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna 1090, Austria
| | - Leticia González
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
- Vienna
Research Platform Accelerating Photoreaction Discovery, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
| | - Sebastian Mai
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
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5
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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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6
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Kowalski K. Synthesis and chemical transformations of glycol nucleic acid (GNA) nucleosides. Bioorg Chem 2023; 141:106921. [PMID: 37871392 DOI: 10.1016/j.bioorg.2023.106921] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/09/2023] [Accepted: 10/16/2023] [Indexed: 10/25/2023]
Abstract
Xeno nucleic acids (XNA) are an increasingly important class of hypermodified nucleic acids with great potential in bioorganic chemistry and synthetic biology. Glycol nucleic acid (GNA) is constructed from a three-carbon 1,2-propanediol (propylene glycol) backbone attached to a nucleobase entity, representing the simplest known XNA. This review is intended to present GNA nucleosides from a synthetic chemistry perspective-a perspective that serves as a starting point for biological studies. Therefore this account focuses on synthetic methods for GNA nucleoside synthesis, as well as their postsynthetic chemical transformations. The properties and biological activity of GNA constituents are also highlighted. A literature survey shows four major approaches toward GNA nucleoside scaffold synthesis. These approaches pertain to glycidol ring-opening, Mitsunobu, SN2, and dihydroxylation reactions. The general arsenal of reactions used in GNA chemistry is versatile and encompasses the Sonogashira reaction, Michael addition, silyl-Hilbert-Johnson reaction, halogenation, alkylation, cyclization, Rh-catalyzed N-allylation, Sharpless catalytic dihydroxylation, and Yb(OTf)3-catalyzed etherification. Additionally, various phosphorylation reactions have enabled the synthesis of diverse types of GNA nucleotides, dinucleoside phosphates, phosphordiamidites, and oligos. Furthermore, recent advances in GNA chemistry have resulted in the synthesis of previously unknown redox-active (ferrocenyl) and luminescent (pyrenyl and phenanthrenyl) GNA nucleosides, which are also covered in this review.
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Affiliation(s)
- Konrad Kowalski
- University of Lodz, Faculty of Chemistry, Department of Organic Chemistry, Tamka 12, PL-91403 Lodz, Poland.
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7
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Mathur D, Díaz SA, Hildebrandt N, Pensack RD, Yurke B, Biaggne A, Li L, Melinger JS, Ancona MG, Knowlton WB, Medintz IL. Pursuing excitonic energy transfer with programmable DNA-based optical breadboards. Chem Soc Rev 2023; 52:7848-7948. [PMID: 37872857 PMCID: PMC10642627 DOI: 10.1039/d0cs00936a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Indexed: 10/25/2023]
Abstract
DNA nanotechnology has now enabled the self-assembly of almost any prescribed 3-dimensional nanoscale structure in large numbers and with high fidelity. These structures are also amenable to site-specific modification with a variety of small molecules ranging from drugs to reporter dyes. Beyond obvious application in biotechnology, such DNA structures are being pursued as programmable nanoscale optical breadboards where multiple different/identical fluorophores can be positioned with sub-nanometer resolution in a manner designed to allow them to engage in multistep excitonic energy-transfer (ET) via Förster resonance energy transfer (FRET) or other related processes. Not only is the ability to create such complex optical structures unique, more importantly, the ability to rapidly redesign and prototype almost all structural and optical analogues in a massively parallel format allows for deep insight into the underlying photophysical processes. Dynamic DNA structures further provide the unparalleled capability to reconfigure a DNA scaffold on the fly in situ and thus switch between ET pathways within a given assembly, actively change its properties, and even repeatedly toggle between two states such as on/off. Here, we review progress in developing these composite materials for potential applications that include artificial light harvesting, smart sensors, nanoactuators, optical barcoding, bioprobes, cryptography, computing, charge conversion, and theranostics to even new forms of optical data storage. Along with an introduction into the DNA scaffolding itself, the diverse fluorophores utilized in these structures, their incorporation chemistry, and the photophysical processes they are designed to exploit, we highlight the evolution of DNA architectures implemented in the pursuit of increased transfer efficiency and the key lessons about ET learned from each iteration. We also focus on recent and growing efforts to exploit DNA as a scaffold for assembling molecular dye aggregates that host delocalized excitons as a test bed for creating excitonic circuits and accessing other quantum-like optical phenomena. We conclude with an outlook on what is still required to transition these materials from a research pursuit to application specific prototypes and beyond.
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Affiliation(s)
- Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland OH 44106, USA
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, USA.
| | - Niko Hildebrandt
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
- Department of Engineering Physics, McMaster University, Hamilton, L8S 4L7, Canada
| | - Ryan D Pensack
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Bernard Yurke
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Austin Biaggne
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Lan Li
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
- Center for Advanced Energy Studies, Idaho Falls, ID 83401, USA
| | - Joseph S Melinger
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Mario G Ancona
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA
- Department of Electrical and Computer Engineering, Florida State University, Tallahassee, FL 32310, USA
| | - William B Knowlton
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, USA.
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8
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Oschwald J, Reger D, Frühwald S, Warmbrunn V, Görling A, Jux N, Drewello T. Experimental and Theoretical Structure Elucidation of the [2 : 1] Complex Ion of Carbo[n]helicene with n=6, 7 and 8 and Ag . Chemphyschem 2023; 24:e202300496. [PMID: 37578805 DOI: 10.1002/cphc.202300496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 08/15/2023]
Abstract
Gas-phase complexes of [n]helicenes with n=6, 7 and 8 and the silver(I) cation are generated utilizing electrospray ionization mass spectrometry (ESI-MS). Besides the well-established [1 : 1] helicene/Ag+ -complex in which the helicene provides a tweezer-like surrounding for the Ag+ , there is also a [2 : 1] complex formed. Density functional theory (DFT) calculations in conjunction with energy-resolved collision-induced dissociation (ER-CID) experiments reveal that the second helicene attaches via π-π stacking to the first helicene, which is part of the pre-formed [1 : 1] tweezer complex with Ag+ . For polycyclic aromatic hydrocarbons (PAHs) of planar structure, the [2 : 1] complex with silver(I) is typically structured as an Ag+ -bound dimer in which the Ag+ would bind to both PAHs as the central metal ion (PAH-Ag+ -PAH). For helicenes, the Ag+ -bound dimer is of similar thermochemical stability as the π-π stacked dimer, however, it is kinetically inaccessible. Coronene (Cor) is investigated in comparison to the helicenes as an essentially planar PAH. In analogy to the π-π stacked dimer of the helicenes, the Cor-Ag+ -Cor-Cor complex is also observed. Competition experiments using [n]helicene mixtures reveal that the tweezer complexes of Ag+ are preferably formed with the larger helicenes, with n=6 being entirely ignored as the host for Ag+ in the presence of n=7 or 8.
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Affiliation(s)
- Johannes Oschwald
- Physical Chemistry I, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstraße 3, 91058, Erlangen, Germany
| | - David Reger
- Organic Chemistry II, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
- Current affiliation: Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, London, W12 0BZ, United Kingdom
| | - Stefan Frühwald
- Theoretical Chemistry, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstraße 3, 91058, Erlangen, Germany
| | - Vera Warmbrunn
- Physical Chemistry I, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstraße 3, 91058, Erlangen, Germany
| | - Andreas Görling
- Theoretical Chemistry, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstraße 3, 91058, Erlangen, Germany
| | - Norbert Jux
- Organic Chemistry II, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Thomas Drewello
- Physical Chemistry I, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstraße 3, 91058, Erlangen, Germany
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9
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Lai JH, Keum JW, Lee HG, Molaei M, Blair EJ, Li S, Soliman JW, Raol VK, Barker CL, Fodor SPA, Fan HC, Shum EY. New realm of precision multiplexing enabled by massively-parallel single molecule UltraPCR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.09.561546. [PMID: 37873291 PMCID: PMC10592712 DOI: 10.1101/2023.10.09.561546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
PCR has been a reliable and inexpensive method for nucleic acid detection in the past several decades. In particular, multiplex PCR is a powerful tool to analyze many biomarkers in the same reaction, thus maximizing detection sensitivity and reducing sample usage. However, balancing the amplification kinetics between amplicons and distinguishing them can be challenging, diminishing the broad adoption of high order multiplex PCR panels. Here, we present a new paradigm in PCR amplification and multiplexed detection using UltraPCR. UltraPCR utilizes a simple centrifugation workflow to split a PCR reaction into ∼34 million partitions, forming an optically clear pellet of spatially separated reaction compartments in a PCR tube. After in situ thermocycling, light sheet scanning is used to produce a 3D reconstruction of the fluorescent positive compartments within the pellet. At typical sample DNA concentrations, the magnitude of partitions offered by UltraPCR dictate that the vast majority of target molecules occupy a compartment uniquely. This single molecule realm allows for isolated amplification events, thereby eliminating competition between different targets and generating unambiguous optical signals for detection. Using a 4-color optical setup, we demonstrate that we can incorporate 10 different fluorescent dyes in the same UltraPCR reaction. We further push multiplexing to an unprecedented level by combinatorial labeling with fluorescent dyes - referred to as "comboplex" technology. Using the same 4-color optical setup, we developed a 22-target comboplex panel that can detect all targets simultaneously at high precision. Collectively, UltraPCR has the potential to push PCR applications beyond what is currently available, enabling a new class of precision genomics assays.
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10
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Neitz H, Höbartner C. A tolane-modified 5-ethynyluridine as a universal and fluorogenic photochemical DNA crosslinker. Chem Commun (Camb) 2023; 59:12003-12006. [PMID: 37727895 DOI: 10.1039/d3cc03796g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
We report the fluorescent nucleoside ToldU and its application as a photoresponsive crosslinker in three different DNA architectures with enhanced fluorescence emission of the crosslinked products. The fluorogenic ToldU crosslinking reaction enables the assembly of DNA polymers in a hybridization chain reaction for the concentration-dependent detection of a specific DNA sequence.
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Affiliation(s)
- Hermann Neitz
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.
| | - Claudia Höbartner
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.
- Center for Nanosystems Chemistry (CNC), University of Würzburg, Theodor-Boveri-Weg, 97074 Würzburg, Germany
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11
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Maity D, Bhaumik SK, Banerjee S. Contrasting luminescence in heparin and DNA-templated co-assemblies of dimeric cyanostilbenes: efficient energy transfer in heparin-based co-assemblies. Phys Chem Chem Phys 2023; 25:12810-12819. [PMID: 37129214 DOI: 10.1039/d3cp00709j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Dimeric cationic cyanostilbenes with peripheral alkyl chains demonstrated aggregation in aqueous media depending on the length of the hydrophobic segment and produced luminescent spherical nano-assemblies in the case of long alkyl chain derivatives. In the presence of heparin, a bio-polyanion that is routinely used as an anticoagulant, the self-assembled structures obtained from the amphiphilic dimers showed the formation of higher-order structures whereas the non-assembling dimers exhibited heparin-induced supramolecular structure formation. In both cases, a significant enhancement in the emission was observed. This led to the detection of heparin in aqueous buffer, serum and plasma with a "turn-on" fluorescence response. Interestingly, these derivatives also exhibited luminescence variation in the presence of ctDNA. However, the response towards DNA was opposite to that observed in the case of heparin i.e., "turn-off'' fluorescence response. Notably, depending on the length of the alkyl segment, divergent DNA binding modes of these derivatives were observed. Due to their enhanced luminescence, the heparin-based co-assemblies were further explored as artificial light-harvesting systems exhibiting an efficient energy transfer process to embedded acceptor dyes with a high antenna effect.
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Affiliation(s)
- Dhananjoy Maity
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, Nadia, India.
| | - Shubhra Kanti Bhaumik
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, Nadia, India.
| | - Supratim Banerjee
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, Nadia, India.
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12
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Neitz H, Bessi I, Kuper J, Kisker C, Höbartner C. Programmable DNA Interstrand Crosslinking by Alkene-Alkyne [2 + 2] Photocycloaddition. J Am Chem Soc 2023; 145:9428-9433. [PMID: 37071840 DOI: 10.1021/jacs.3c01611] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Covalent crosslinking of DNA strands provides a useful tool for medical, biochemical, and DNA nanotechnology applications. Here we present a light-induced interstrand DNA crosslinking reaction using the modified nucleoside 5-phenylethynyl-2'-deoxyuridine (PhedU). The crosslinking ability of PhedU was programmed by base pairing and by metal ion interaction at the Watson-Crick base pairing site. Rotation to intrahelical positions was favored by hydrophobic stacking and enabled an unexpected photochemical alkene-alkyne [2 + 2] cycloaddition within the DNA duplex, resulting in efficient formation of a PhedU dimer after short irradiation times of a few seconds. A PhedU-dimer-containing DNA was shown to efficiently bind a helicase complex, but the covalent crosslink completely prevented DNA unwinding, suggesting possible applications in biochemistry or structural biology.
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Affiliation(s)
- Hermann Neitz
- Institute of Organic Chemistry, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Irene Bessi
- Institute of Organic Chemistry, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Jochen Kuper
- Rudolf-Virchow-Zentrum - Center for Integrative and Translational Bioimaging, Universität Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany
| | - Caroline Kisker
- Rudolf-Virchow-Zentrum - Center for Integrative and Translational Bioimaging, Universität Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany
| | - Claudia Höbartner
- Institute of Organic Chemistry, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
- Center for Nanosystems Chemistry (CNC), Universität Würzburg, 97074 Würzburg, Germany
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13
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Toldo JM, do Casal MT, Ventura E, do Monte SA, Barbatti M. Surface hopping modeling of charge and energy transfer in active environments. Phys Chem Chem Phys 2023; 25:8293-8316. [PMID: 36916738 PMCID: PMC10034598 DOI: 10.1039/d3cp00247k] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/01/2023] [Indexed: 03/05/2023]
Abstract
An active environment is any atomic or molecular system changing a chromophore's nonadiabatic dynamics compared to the isolated molecule. The action of the environment on the chromophore occurs by changing the potential energy landscape and triggering new energy and charge flows unavailable in the vacuum. Surface hopping is a mixed quantum-classical approach whose extreme flexibility has made it the primary platform for implementing novel methodologies to investigate the nonadiabatic dynamics of a chromophore in active environments. This Perspective paper surveys the latest developments in the field, focusing on charge and energy transfer processes.
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Affiliation(s)
| | | | - Elizete Ventura
- Departamento de Química, CCEN, Universidade Federal da Paraíba, 58059-900, João Pessoa, Brazil.
| | - Silmar A do Monte
- Departamento de Química, CCEN, Universidade Federal da Paraíba, 58059-900, João Pessoa, Brazil.
| | - Mario Barbatti
- Aix-Marseille University, CNRS, ICR, Marseille, France.
- Institut Universitaire de France, 75231, Paris, France
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14
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Lang F, Rönicke F, Wagenknecht HA. Aminophthalimide as a mimetic of purines and a fluorescent RNA base surrogate for RNA imaging. Org Biomol Chem 2023; 21:3079-3082. [PMID: 36943317 DOI: 10.1039/d3ob00302g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Aminophthalimide and N,N-dimethylaminophthalimide are used as fluorescent mimetics of purines due to their similar size and their possibility for hydrogen bonding. Their C-nucleotides were synthetically incorporated into RNA by means of phosphoramidite chemistry, behave as nonspecific fluorescent base analogs with flexible hydrogen bonding capabilities, and show solvatochromic fluorescence that is suitable for RNA imaging in live cells.
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Affiliation(s)
- Fabian Lang
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
| | - Franziska Rönicke
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
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15
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Takahashi S, Oshige M, Katsura S, Nagahara Y. A new fluorescence labeling method for molecular analysis of double-stranded DNA. Anal Biochem 2023; 662:115000. [PMID: 36470466 DOI: 10.1016/j.ab.2022.115000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/08/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
In this study, a double-stranded DNA (dsDNA) fluorescent labeling method was developed using the fusion proteins of fluorescent protein (FP), and 7 kDa DNA-binding family members including Sso7d from Sulfolobus solfataricus, Aho7c from Acidianus hospitalis, ATSV7 from Acidianus tailed spindle virus and Sto7 from Sulfolobus tokodaii. Using this fluorescent DNA labeling method, we succeeded in single-molecule imaging of bacteriophage λDNA molecules stretched on glass surfaces. The fluorescence of the λDNA with FP fusion proteins decayed 2.4- to 6.4-fold slower than that of the typical intercalating method with SYTOX Green (SxG). In addition, the dynamic behaviors of FP-fused Aho7c-λDNA were relaxed and stretched with and without buffer flow, respectively, in microflow channels and were similar to that with typical intercalating dye, such as YOYO-1 and SxG. this fluorescent DNA labeling method. This fluorescent DNA labeling method can solve the problem of rapid fluorescence decay due to the intercalating dyes and therefore can be expected as an alternative to compound-based fluorescent dye. Thus, this study establishes FP fusion proteins as useful fluorescent DNA probes at the single-molecule level.
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Affiliation(s)
- Shunsuke Takahashi
- Division of Life Science and Engineering, School of Science and Engineering, Tokyo Denki University, Ishizaka, Hatoyama-cho, Hiki-gun, Saitama, 350-0394, Japan.
| | - Masahiko Oshige
- Department of Environmental Engineering Science, Graduate School of Science and Technology, Gunma University, Kiryu, Gunma, 376-8515, Japan; Gunma University Center for Food Science and Wellness (GUCFW), Aramaki, Gunma, 371-8510, Japan
| | - Shinji Katsura
- Department of Environmental Engineering Science, Graduate School of Science and Technology, Gunma University, Kiryu, Gunma, 376-8515, Japan; Gunma University Center for Food Science and Wellness (GUCFW), Aramaki, Gunma, 371-8510, Japan
| | - Yukitoshi Nagahara
- Division of Life Science and Engineering, School of Science and Engineering, Tokyo Denki University, Ishizaka, Hatoyama-cho, Hiki-gun, Saitama, 350-0394, Japan
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16
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Kurahayashi K, Hanaya K, Sugai T, Hirai G, Higashibayashi S. Copper-Catalyzed Stereoselective Borylation and Palladium-Catalyzed Stereospecific Cross-Coupling to Give Aryl C-Glycosides. Chemistry 2023; 29:e202203376. [PMID: 36344464 DOI: 10.1002/chem.202203376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/06/2022] [Accepted: 11/07/2022] [Indexed: 11/09/2022]
Abstract
Metabolically stable C-glycosides are an essential family of compounds in bioactive natural products, therapeutic agents, and biological probes. For their application, development of synthetic methods by connecting glycosides and aglycons with strict stereocontrol at the anomeric carbon, as well as with high functional-group compatibility and environmental compatibility is a pivotal issue. Although Suzuki-Miyaura-type C(sp3 )-C(sp2 ) cross-coupling using glycosyl boronates is a potential candidate for the construction of C-glycosides, neither the cross-coupling itself nor the facile synthesis of the coupling precursor, glycosyl boronates, have been achieved to date. Herein, it was succeeded to develop a copper-catalyzed stereoselective one-step borylation of glycosyl bromides to glycosyl boronates and palladium-catalyzed stereospecific cross-coupling of β-glycosyl borates with aryl bromides to give aryl β-C-glycosides, in which the β-configuration of the anomeric carbon of the glycosyl trifluoroborates is stereoretentively transferred to that of the resulting aryl C-glycosides.
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Affiliation(s)
- Kazuki Kurahayashi
- Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo, 105-8512, Japan
| | - Kengo Hanaya
- Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo, 105-8512, Japan
| | - Takeshi Sugai
- Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo, 105-8512, Japan
| | - Go Hirai
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-ku, Fukuoka, 812-8582, Japan
| | - Shuhei Higashibayashi
- Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo, 105-8512, Japan
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17
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Chowdhury M, Hudson RHE. Exploring Nucleobase Modifications in Oligonucleotide Analogues for Use as Environmentally Responsive Fluorophores and Beyond. CHEM REC 2023; 23:e202200218. [PMID: 36344432 DOI: 10.1002/tcr.202200218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/07/2022] [Indexed: 11/09/2022]
Abstract
Over the past two decades, it has become abundantly clear that nucleic acid biochemistry, especially with respect to RNA, is more convoluted and complex than previously appreciated. Indeed, the application and exploitation of nucleic acids beyond their predestined role as the medium for storage and transmission of genetic information to the treatment and study of diseases has been achieved. In other areas of endeavor, utilization of nucleic acids as a probe molecule requires that they possess a reporter group. The reporter group of choice is often a luminophore because fluorescence spectroscopy has emerged as an indispensable tool to probe the structural and functional properties of modified nucleic acids. The scope of this review spans research done in the Hudson lab at The University of Western Ontario and is focused on modified pyrimidine nucleobases and their applications as environmentally sensitive fluorophores, base discriminating fluorophores, and in service of antisense applications as well as tantalizing new results as G-quadruplex destabilizing agents. While this review is a focused personal account, particularly influential work of colleagues in the chemistry community will be highlighted. The intention is not to make a comprehensive review, citations to the existing excellent reviews are given, any omission of the wonderful and impactful work being done by others globally is not intentional. Thus, this review will briefly introduce the context of our work, summarize what has been accomplished and finish with the prospects of future developments.
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Affiliation(s)
- Mria Chowdhury
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, N6A 5B7
| | - Robert H E Hudson
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, N6A 5B7
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18
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Schöllkopf S, Knoll A, Homer A, Seitz O. Double FIT hybridization probes – towards enhancing brightness, turn-on and specificity of RNA detection. Chem Sci 2023; 14:4166-4173. [PMID: 37063796 PMCID: PMC10094420 DOI: 10.1039/d3sc00363a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/22/2023] [Indexed: 03/31/2023] Open
Abstract
Efficient fluorogenic hybridization probes combine high brightness and specificity of fluorescence signaling with large turn-on of fluorescence.
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Affiliation(s)
- Sophie Schöllkopf
- Institut für Chemie, Humboldt-Universität zu Berlin 12489 Berlin Germany
| | - Andrea Knoll
- Institut für Chemie, Humboldt-Universität zu Berlin 12489 Berlin Germany
| | - Amal Homer
- Institut für Chemie, Humboldt-Universität zu Berlin 12489 Berlin Germany
| | - Oliver Seitz
- Institut für Chemie, Humboldt-Universität zu Berlin 12489 Berlin Germany
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19
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Fernandes R, Chowdhary S, Mikula N, Saleh N, Kanevche K, Berlepsch HV, Hosogi N, Heberle J, Weber M, Böttcher C, Koksch B. Cyanine Dye Coupling Mediates Self-assembly of a pH Sensitive Peptide into Novel 3D Architectures. Angew Chem Int Ed Engl 2022; 61:e202208647. [PMID: 36161448 PMCID: PMC9828782 DOI: 10.1002/anie.202208647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Indexed: 01/12/2023]
Abstract
Synthetic multichromophore systems are of great importance in artificial light harvesting devices, organic optoelectronics, tumor imaging and therapy. Here, we introduce a promising strategy for the construction of self-assembled peptide templated dye stacks based on coupling of a de novo designed pH sensitive peptide with a cyanine dye Cy5 at its N-terminus. Microscopic techniques, in particular cryogenic TEM (cryo-TEM) and cryo-electron tomography technique (cryo-ET), reveal two types of highly ordered three-dimensional assembly structures on the micrometer scale. Unbranched compact layered rods are observed at pH 7.4 and two-dimensional membrane-like assemblies at pH 3.4, both species displaying spectral features of H-aggregates. Molecular dynamics simulations reveal that the coupling of Cy5 moieties promotes the formation of both ultrastructures, whereas the protonation states of acidic and basic amino acid side chains dictates their ultimate three-dimensional organization.
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Affiliation(s)
- Rita Fernandes
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2014195BerlinGermany
| | - Suvrat Chowdhary
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2014195BerlinGermany
| | - Natalia Mikula
- Mathematics for Life and Materials SciencesZuse Institute BerlinTakustraße 714195BerlinGermany
| | - Noureldin Saleh
- Mathematics for Life and Materials SciencesZuse Institute BerlinTakustraße 714195BerlinGermany
| | - Katerina Kanevche
- Department of PhysicsExperimental Molecular BiophysicsFreie Universität BerlinArnimallee 1414195BerlinGermany
| | - Hans v. Berlepsch
- Research Center for Electron Microscopy and Core Facility BioSupraMolFreie Universität BerlinFabeckstraße 36a14195BerlinGermany
| | | | - Joachim Heberle
- Department of PhysicsExperimental Molecular BiophysicsFreie Universität BerlinArnimallee 1414195BerlinGermany
| | - Marcus Weber
- Mathematics for Life and Materials SciencesZuse Institute BerlinTakustraße 714195BerlinGermany
| | - Christoph Böttcher
- Research Center for Electron Microscopy and Core Facility BioSupraMolFreie Universität BerlinFabeckstraße 36a14195BerlinGermany
| | - Beate Koksch
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2014195BerlinGermany
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20
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Yuan Y, Li H, Yang H, Han C, Hu H, Govorov AO, Yan H, Lan X. Unraveling the Complex Chirality Evolution in DNA‐Assembled High‐Order, Hybrid Chiroplasmonic Superstructures from Multi‐Scale Chirality Mechanisms. Angew Chem Int Ed Engl 2022; 61:e202210730. [DOI: 10.1002/anie.202210730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Yongqing Yuan
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials Center for Advanced Low-dimension Materials College of Materials Science and Engineering Donghua University Shanghai 201620 China
| | - Huacheng Li
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials Center for Advanced Low-dimension Materials College of Materials Science and Engineering Donghua University Shanghai 201620 China
| | - Hao Yang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials Center for Advanced Low-dimension Materials College of Materials Science and Engineering Donghua University Shanghai 201620 China
| | - Cong Han
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials Center for Advanced Low-dimension Materials College of Materials Science and Engineering Donghua University Shanghai 201620 China
| | - Huatian Hu
- Hubei Key Laboratory of Optical Information and Pattern Recognition Wuhan Institute of Technology Wuhan Hubei 430205 China
| | - Alexander O. Govorov
- Department of Physics and Astronomy and the Nanoscale & Quantum Phenomena Institute Ohio University Athens OH 45701 USA
| | - Hao Yan
- Center for Molecular Design and Biomimetics The Biodesign Institute, School of Molecular Sciences Arizona State University Tempe AZ 85287 USA
| | - Xiang Lan
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials Center for Advanced Low-dimension Materials College of Materials Science and Engineering Donghua University Shanghai 201620 China
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21
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Yuan Y, Li H, Yang H, Han C, Hu H, Govorov AO, Yan H, Lan X. Unraveling the Complex Chirality Evolution in DNA‐Assembled High‐Order, Hybrid Chiroplasmonic Superstructures from Multi‐Scale Chirality Mechanisms. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202210730] [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)
- Yongqing Yuan
- Donghua University - Songjiang Campus: Donghua University Center for Advanced Low-dimension Materials CHINA
| | - Huacheng Li
- Donghua University - Songjiang Campus: Donghua University Center for Advanced Low-dimension Materials CHINA
| | - Hao Yang
- Donghua University - Songjiang Campus: Donghua University Center for Advanced Low-dimension Materials CHINA
| | - Cong Han
- Donghua University - Songjiang Campus: Donghua University Center for Advanced Low-dimension Materials CHINA
| | - Huatian Hu
- Wuhan Institute of Technology Hubei Key Laboratory of Optical Information and Pattern Recognition CHINA
| | - Alexander O. Govorov
- Ohio University Department of Physics and Astronomy and the Nanoscale & Quantum Phenomena Institute UNITED STATES
| | - Hao Yan
- Arizona State University The Biodesign Institute UNITED STATES
| | - Xiang Lan
- Donghua University - Songjiang Campus: Donghua University Center for Advanced Low-Dimension Materials No.2999 North Renmin Str, Songjiang Dist 201620 Shanghai CHINA
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22
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Zhao L, Ahmed F, Xiong H. An excimer ‘ON OFF’ switch based on telomeric G-quadruplex and rGO for trace thrombin detection. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.02.048] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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23
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Zhou X, Lin S, Yan H. Interfacing DNA nanotechnology and biomimetic photonic complexes: advances and prospects in energy and biomedicine. J Nanobiotechnology 2022; 20:257. [PMID: 35658974 PMCID: PMC9164479 DOI: 10.1186/s12951-022-01449-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/05/2022] [Indexed: 11/16/2022] Open
Abstract
Self-assembled photonic systems with well-organized spatial arrangement and engineered optical properties can be used as efficient energy materials and as effective biomedical agents. The lessons learned from natural light-harvesting antennas have inspired the design and synthesis of a series of biomimetic photonic complexes, including those containing strongly coupled dye aggregates with dense molecular packing and unique spectroscopic features. These photoactive components provide excellent features that could be coupled to multiple applications including light-harvesting, energy transfer, biosensing, bioimaging, and cancer therapy. Meanwhile, nanoscale DNA assemblies have been employed as programmable and addressable templates to guide the formation of DNA-directed multi-pigment complexes, which can be used to enhance the complexity and precision of artificial photonic systems and show the potential for energy and biomedical applications. This review focuses on the interface of DNA nanotechnology and biomimetic photonic systems. We summarized the recent progress in the design, synthesis, and applications of bioinspired photonic systems, highlighted the advantages of the utilization of DNA nanostructures, and discussed the challenges and opportunities they provide.
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Affiliation(s)
- Xu Zhou
- Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
| | - Su Lin
- Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Hao Yan
- Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA. .,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.
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24
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Petty JT, Lewis D, Carnahan S, Kim D, Couch C. Tug-of-War between DNA Chelation and Silver Agglomeration in DNA-Silver Cluster Chromophores. J Phys Chem B 2022; 126:3822-3830. [PMID: 35594191 DOI: 10.1021/acs.jpcb.2c01054] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Supramolecular chromophores form when a DNA traps silvers that then coalesce into clusters with discrete, molecular electronic states. However, DNA strands are polymeric ligands that disperse silvers and thus curb agglomeration. We study this competition using two chromophores that share three common components: a dimeric DNA scaffold, Ag+-nucleobase base pairs, and Ag0 chromophores. The DNA host C4-A2-iC4T mimics structural elements in a DNA-cluster crystal structure using a phosphodiester backbone with combined 5' → 3' and 3' → 5' (indicated by "i") directions. The backbone directions must alternate to form the two silver clusters, and this interdependence supports a silver-linked structure. This template creates two chromophores with distinct sizes, charges, and hence spectra: (C4-A2-iC4T)2/Ag117+ with λabs/λem = 430/520 nm and (C4-A2-iC4T)2/Ag148+ with λabs/λem = 510/630 nm. The Ag+ and Ag0 constituents in these partially oxidized clusters are linked with structural elements in C4-A2-iC4T. Ag+ alone binds sparsely but strongly to form C4-A2-iC4T/3-4 Ag+ and (C4-A2-iC4T)2/7-8 Ag+ complexes, and these stoichiometries suggest that Ag+ cross-links pairs of cytosines to form a hairpin with a metallo-C4/iC4 duplex and an adenine loop. The Ag0 are chemically orthogonal because they can be oxidatively etched without disrupting the underlying Ag+-DNA matrix, and their reactivity is attributed to their valence electrons and weaker chelation by the adenines. These studies suggest that Ag+ disperses with the cytosines to create an adenine binding pocket for the Ag0 cluster chromophores.
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Affiliation(s)
- Jeffrey T Petty
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - David Lewis
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Savannah Carnahan
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Dahye Kim
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Caroline Couch
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
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25
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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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26
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Cui H, Fang J, Sun M, Liu Z, Li Z, Liu K, Liu M. Color-changing Fluorescent DNA Probe Containing Solvatochromic Dansyl-nucleoside Surrogate for Sensing Local Variation of DNA Duplex. Bioorg Med Chem Lett 2022; 59:128551. [DOI: 10.1016/j.bmcl.2022.128551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/06/2022] [Accepted: 01/12/2022] [Indexed: 11/27/2022]
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27
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Mentzel P, Holzapfel M, Schmiedel A, Krummenacher I, Braunschweig H, Wodyński A, Kaupp M, Würthner F, Lambert C. Excited states and spin–orbit coupling in chalcogen substituted perylene diimides and their radical anions. Phys Chem Chem Phys 2022; 24:26254-26268. [DOI: 10.1039/d2cp02723b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A novel series of chalcogen bay-substituted perylene diimides show increasing SOC, which was investigated in detail via (time-resolved) optical spectroscopy, (spectro)electrochemistry, EPR spectroscopy and TD-DFT calculations.
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Affiliation(s)
- Paul Mentzel
- Institut für Organische Chemie, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Marco Holzapfel
- Institut für Organische Chemie, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Alexander Schmiedel
- Institut für Organische Chemie, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Ivo Krummenacher
- Institut für Anorganische Chemie, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
- Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Holger Braunschweig
- Institut für Anorganische Chemie, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
- Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Artur Wodyński
- Technische Universität Berlin, Institut für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Martin Kaupp
- Technische Universität Berlin, Institut für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Frank Würthner
- Institut für Organische Chemie, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
- Center for Nanosystems Chemistry, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Christoph Lambert
- Institut für Organische Chemie, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
- Center for Nanosystems Chemistry, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
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28
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Roy S, Mass OA, Kellis DL, Wilson CK, Hall JA, Yurke B, Knowlton WB. Exciton Delocalization and Scaffold Stability in Bridged Nucleotide-Substituted, DNA Duplex-Templated Cyanine Aggregates. J Phys Chem B 2021; 125:13670-13684. [PMID: 34894675 PMCID: PMC8713290 DOI: 10.1021/acs.jpcb.1c07602] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/04/2021] [Indexed: 11/28/2022]
Abstract
Molecular excitons play a foundational role in chromophore aggregates found in light-harvesting systems and offer potential applications in engineered excitonic systems. Controlled aggregation of chromophores to promote exciton delocalization has been achieved by covalently tethering chromophores to deoxyribonucleic acid (DNA) scaffolds. Although many studies have documented changes in the optical properties of chromophores upon aggregation using DNA scaffolds, more limited work has investigated how structural modifications of DNA via bridged nucleotides and chromophore covalent attachment impact scaffold stability as well as the configuration and optical behavior of attached aggregates. Here we investigated the impact of two types of bridged nucleotides, LNA and BNA, as a structural modification of duplex DNA-templated cyanine (Cy5) aggregates. The bridged nucleotides were incorporated in the domain of one to four Cy5 chromophores attached between adjacent bases of a DNA duplex. We found that bridged nucleotides increase the stability of DNA scaffolds carrying Cy5 aggregates in comparison with natural nucleotides in analogous constructs. Exciton coupling strength and delocalization in Cy5 aggregates were evaluated via steady-state absorption, circular dichroism, and theoretical modeling. Replacing natural nucleotides with bridged nucleotides resulted in a noticeable increase in the coupling strength (≥10 meV) between chromophores and increased H-like stacking behavior (i.e., more face-to-face stacking). Our results suggest that bridged nucleotides may be useful for increasing scaffold stability and coupling between DNA templated chromophores.
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Affiliation(s)
- Simon
K. Roy
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Olga A. Mass
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Donald L. Kellis
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Christopher K. Wilson
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - John A. Hall
- Division
of Research and Economic Development, Boise
State University, Boise, Idaho 83725, United States
| | - Bernard Yurke
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
- Department
of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - William B. Knowlton
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
- Department
of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
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29
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Takaishi K, Murakami S, Iwachido K, Ema T. Chiral exciplex dyes showing circularly polarized luminescence: extension of the excimer chirality rule. Chem Sci 2021; 12:14570-14576. [PMID: 34881009 PMCID: PMC8580037 DOI: 10.1039/d1sc04403f] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/18/2021] [Indexed: 11/21/2022] Open
Abstract
A series of axially chiral binaphthyls and quaternaphthyls possessing two kinds of aromatic fluorophores, such as pyrenyl, perylenyl, and 4-(dimethylamino)phenyl groups, arranged alternately were synthesized by a divergent method. In the excited state, the fluorophores selectively formed a unidirectionally twisted exciplex (excited heterodimer) by a cumulative steric effect and exhibited circularly polarized luminescence (CPL). They are the first examples of a monomolecular exciplex CPL dye. This versatile method for producing exciplex CPL dyes also improved fluorescence intensity, and the CPL properties were not very sensitive to the solvent or to the temperature owing to the conformationally rigid exciplex. This systematic study allowed us to confirm that the excimer chirality rule can be applied to the exciplex dyes: left- and right-handed exciplexes with a twist angle of less than 90° exhibit (-)- and (+)-CPL, respectively.
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Affiliation(s)
- Kazuto Takaishi
- Division of Applied Chemistry, Graduate School of Natural Science and Technology, Okayama University Tsushima Okayama 700-8530 Japan
| | - Sho Murakami
- Division of Applied Chemistry, Graduate School of Natural Science and Technology, Okayama University Tsushima Okayama 700-8530 Japan
| | - Kazuhiro Iwachido
- Division of Applied Chemistry, Graduate School of Natural Science and Technology, Okayama University Tsushima Okayama 700-8530 Japan
| | - Tadashi Ema
- Division of Applied Chemistry, Graduate School of Natural Science and Technology, Okayama University Tsushima Okayama 700-8530 Japan
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30
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Peterková K, Durník I, Marek R, Plavec J, Podbevšek P. c-kit2 G-quadruplex stabilized via a covalent probe: exploring G-quartet asymmetry. Nucleic Acids Res 2021; 49:8947-8960. [PMID: 34365512 PMCID: PMC8421218 DOI: 10.1093/nar/gkab659] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/12/2021] [Accepted: 07/22/2021] [Indexed: 11/23/2022] Open
Abstract
Several sequences forming G-quadruplex are highly conserved in regulatory regions of genomes of different organisms and affect various biological processes like gene expression. Diverse G-quadruplex properties can be modulated via their interaction with small polyaromatic molecules such as pyrene. To investigate how pyrene interacts with G-rich DNAs, we incorporated deoxyuridine nucleotide(s) with a covalently attached pyrene moiety (Upy) into a model system that forms parallel G-quadruplex structures. We individually substituted terminal positions and positions in the pentaloop of the c-kit2 sequence originating from the KIT proto-oncogene with Upy and performed a detailed NMR structural study accompanied with molecular dynamic simulations. Our results showed that incorporation into the pentaloop leads to structural polymorphism and in some cases also thermal destabilization. In contrast, terminal positions were found to cause a substantial thermodynamic stabilization while preserving topology of the parent c-kit2 G-quadruplex. Thermodynamic stabilization results from π–π stacking between the polyaromatic core of the pyrene moiety and guanine nucleotides of outer G-quartets. Thanks to the prevalent overall conformation, our structures mimic the G-quadruplex found in human KIT proto-oncogene and could potentially have antiproliferative effects on cancer cells.
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Affiliation(s)
- Kateřina Peterková
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czechia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Ivo Durník
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czechia.,CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
| | - Radek Marek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czechia.,CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia.,Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Trg OF 13, SI-1000 Ljubljana, Slovenia
| | - Peter Podbevšek
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
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31
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Takada T, Nishida K, Honda Y, Nakano A, Nakamura M, Fan S, Kawai K, Fujitsuka M, Yamana K. Stacked Thiazole Orange Dyes in DNA Capable of Switching Emissive Behavior in Response to Structural Transitions. Chembiochem 2021; 22:2729-2735. [PMID: 34191388 DOI: 10.1002/cbic.202100309] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Indexed: 12/20/2022]
Abstract
Functional nucleic acids with the capability of generating fluorescence in response to hybridization events, microenvironment or structural changes are valuable as structural probes and chemical sensors. We now demonstrate the enzyme-assisted preparation of nucleic acids possessing multiple thiazole orange (TO) dyes and their fluorescent behavior, that show a spectral change from the typical monomer emission to the excimer-type red-shifted emission. We found that the fluorescent response and emission wavelength of the TO dyes were dependent on both the state of the DNA structure (single- or double-stranded DNA) and the arrangement of the TO dyes. We showed that the fluorescent behavior of the TO dyes can be applied for the detection of RNA molecules, suggesting that our approach for preparing the fluorescent nucleic acids functionalized with multiple TO dyes could be useful to design a fluorescence bioimaging and detection technique of biomolecules.
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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
| | - Koma Nishida
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo, 671-2280, Japan
| | - Yurika Honda
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo, 671-2280, Japan
| | - Aoi Nakano
- 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
| | - Shuya Fan
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Mamoru Fujitsuka
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Kazushige Yamana
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo, 671-2280, Japan
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32
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Dziuba D, Didier P, Ciaco S, Barth A, Seidel CAM, Mély Y. Fundamental photophysics of isomorphic and expanded fluorescent nucleoside analogues. Chem Soc Rev 2021; 50:7062-7107. [PMID: 33956014 DOI: 10.1039/d1cs00194a] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are structurally diverse mimics of the natural essentially non-fluorescent nucleosides which have found numerous applications in probing the structure and dynamics of nucleic acids as well as their interactions with various biomolecules. In order to minimize disturbance in the labelled nucleic acid sequences, the FNA chromophoric groups should resemble the natural nucleobases in size and hydrogen-bonding patterns. Isomorphic and expanded FNAs are the two groups that best meet the criteria of non-perturbing fluorescent labels for DNA and RNA. Significant progress has been made over the past decades in understanding the fundamental photophysics that governs the spectroscopic and environmentally sensitive properties of these FNAs. Herein, we review recent advances in the spectroscopic and computational studies of selected isomorphic and expanded FNAs. We also show how this information can be used as a rational basis to design new FNAs, select appropriate sequences for optimal spectroscopic response and interpret fluorescence data in FNA applications.
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Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Stefano Ciaco
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France. and Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Anders Barth
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Claus A M Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
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33
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Madhu M, Ramakrishnan R, Vijay V, Hariharan M. Free Charge Carriers in Homo-Sorted π-Stacks of Donor-Acceptor Conjugates. Chem Rev 2021; 121:8234-8284. [PMID: 34133137 DOI: 10.1021/acs.chemrev.1c00078] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Inspired by the high photoconversion efficiency observed in natural light-harvesting systems, the hierarchical organization of molecular building blocks has gained impetus in the past few decades. Particularly, the molecular arrangement and packing in the active layer of organic solar cells (OSCs) have garnered significant attention due to the decisive role of the nature of donor/acceptor (D/A) heterojunctions in charge carrier generation and ultimately the power conversion efficiency. This review focuses on the recent developments in emergent optoelectronic properties exhibited by self-sorted donor-on-donor/acceptor-on-acceptor arrangement of covalently linked D-A systems, highlighting the ultrafast excited state dynamics of charge transfer and transport. Segregated organization of donors and acceptors promotes the delocalization of photoinduced charges among the stacks, engendering an enhanced charge separation lifetime and percolation pathways with ambipolar conductivity and charge carrier yield. Covalently linking donors and acceptors ensure a sufficient D-A interface and interchromophoric electronic coupling as required for faster charge separation while providing better control over their supramolecular assemblies. The design strategies to attain D-A conjugate assemblies with optimal charge carrier generation efficiency, the scope of their application compared to state-of-the-art OSCs, current challenges, and future opportunities are discussed in the review. An integrated overview of rational design approaches derived from the comprehension of underlying photoinduced processes can pave the way toward superior optoelectronic devices and bring in new possibilities to the avenue of functional supramolecular architectures.
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Affiliation(s)
- Meera Madhu
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Vithura, Thiruvananthapuram, Kerala, India 695551
| | - Remya Ramakrishnan
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Vithura, Thiruvananthapuram, Kerala, India 695551
| | - Vishnu Vijay
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Vithura, Thiruvananthapuram, Kerala, India 695551
| | - Mahesh Hariharan
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, Vithura, Thiruvananthapuram, Kerala, India 695551
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34
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Mohd Yusof Chan NN, Idris A, Zainal Abidin ZH, Tajuddin HA, Abdullah Z. White light employing luminescent engineered large (mega) Stokes shift molecules: a review. RSC Adv 2021; 11:13409-13445. [PMID: 35423891 PMCID: PMC8697633 DOI: 10.1039/d1ra00129a] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 05/14/2021] [Accepted: 03/03/2021] [Indexed: 12/14/2022] Open
Abstract
Large (mega) Stokes shift molecules have shown great potential in white light emission for optoelectronic applications, such as flat panel display technology, light-emitting diodes, photosensitizers, molecular probes, cellular and bioimaging, and other applications. This review aims to summarize recent developments of white light generation that incorporate a large Stokes shift component, key approaches to designing large Stokes shift molecules, perspectives on future opportunities, and remaining challenges confronting this emerging research field. After a brief introduction of feasible pathways in generating white light, exemplifications of large Stokes shift molecules as white light candidates from organic and inorganic-based materials are illustrated. Various possible ways to design such molecules have been revealed by integrating the photophysical mechanisms that are essential to produce red-shifted emission upon photoexcitation, such as excited state intramolecular proton transfer (ESIPT), intramolecular charge transfer (ICT), excited state geometrical relaxation or structural deformation, aggregation-induced emission (AIE) alongside the different formations of aggregates, interplay between monomer and excimer emission, host-guest interaction, and lastly metal to ligand charge transfer (MLCT) via harvesting triplet state. Furthermore, previously reported fluorescent materials are described and categorized based on luminescence behaviors on account of the Stokes shifts value. This review will serve as a rationalized introduction and reference for researchers who are interested in exploring large or mega Stokes shift molecules, and will motivate new strategies along with instigation of persistent efforts in this prominent subject area with great avenues.
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Affiliation(s)
- Nadia Nabihah Mohd Yusof Chan
- Department of Chemistry, Faculty of Science, University of Malaya 50603 Kuala Lumpur Malaysia
- Centre for Ionics University of Malaya, Department of Physics, Faculty of Science, University of Malaya 50603 Kuala Lumpur Malaysia
| | - Azila Idris
- Department of Chemistry, Faculty of Science, University of Malaya 50603 Kuala Lumpur Malaysia
| | - Zul Hazrin Zainal Abidin
- Centre for Ionics University of Malaya, Department of Physics, Faculty of Science, University of Malaya 50603 Kuala Lumpur Malaysia
| | - Hairul Anuar Tajuddin
- Department of Chemistry, Faculty of Science, University of Malaya 50603 Kuala Lumpur Malaysia
| | - Zanariah Abdullah
- Department of Chemistry, Faculty of Science, University of Malaya 50603 Kuala Lumpur Malaysia
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35
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Bhaumik SK, Banerjee S. Highly sensitive and ratiometric luminescence sensing of heparin through templated cyanostilbene assemblies. Analyst 2021; 146:2194-2202. [PMID: 33587729 DOI: 10.1039/d0an01808b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The assembly of organic dyes on bio-molecular templates is an attractive strategy for the creation of bio-materials with intriguing optical properties. This principle is exploited here for the detection of polyanion heparin, a known anticoagulant, by employing di-cationic cyanostilbene derivatives with inherent aggregation induced emission (AIE) features. The cyanostilbene derivatives exhibited weak cyan-blue monomeric emissions in solutions but upon electrostatic co-assembly with heparin, formed highly luminescent clusters on the polyanion surface. The cyanostilbene chromophores in the clusters exhibited greenish-yellow excimer emissions with remarkably longer life-times (up to 70-fold) and higher quantum yields (up to 85-fold) compared to their aqueous solutions. This led to heparin detection in aqueous buffer in low nanomolar concentrations. Additionally, and more importantly, a ratiometric detection of heparin was achieved in highly competitive media such as 50% human serum and 60% human plasma in medically relevant concentrations.
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Affiliation(s)
- Shubhra Kanti Bhaumik
- The Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, Nadia, India.
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36
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37
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Kim S, Ahn DS, Ahn M, Wee KR, Choi J, Ihee H. Charge transfer induced by electronic state mixing in a symmetric X-Y-X-type multi-chromophore system. Phys Chem Chem Phys 2020; 22:28440-28447. [PMID: 33305764 DOI: 10.1039/d0cp05132b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Charge transfer (CT) from electron donor (D) to acceptor (A) plays an important role in photoelectric or electrochemical devices and is a useful concept for a molecule with D and A well distinguishable. Here, we report our finding that even in a molecule with D and A not resolvable, CT can be induced by electronic state mixing (ESM) in a symmetric multi-chromophore system (MCS), namely 1,4-di(1-pyrenyl)benzene (Py-Benz-Py). Unlike Py and Py-Benz, Py-Benz-Py exhibits unique photophysical properties attributable to the reduction of the energy gap between two electronic states induced by ESM. The ESM for Py-Benz-Py is due to the extended π-conjugation owing to the further introduction of Py into Py-Benz, and consequently leads to the favorable intramolecular CT, followed by the planarization due to the twisting motion between Py and phenyl moieties. Time-resolved spectroscopic data demonstrate that the twisting process of the Py moiety in acetonitrile occurs with two unequal time constants, suggesting the localized CT state and the asynchronous twisting dynamics of two Py moieties unlike the delocalized CT state in nonpolar and low-polarity solvents leading to the synchronous twisting of two Py moieties. This means that the symmetry-breaking CT in MCSs can induce an asynchronous twisting motion. The results reported here support that a molecule without CT can be turned into another molecule with CT induced by ESM and demonstrate that the excited-state relaxation dynamics can be regulated through the ESM induced by introducing the substituents or changing the environmental factors such as solvent polarities.
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Affiliation(s)
- Siin Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
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38
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Oh I, Lee H, Kim TW, Kim CW, Jun S, Kim C, Choi EH, Rhee YM, Kim J, Jang W, Ihee H. Enhancement of Energy Transfer Efficiency with Structural Control of Multichromophore Light-Harvesting Assembly. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001623. [PMID: 33101863 PMCID: PMC7578888 DOI: 10.1002/advs.202001623] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 06/24/2020] [Indexed: 06/11/2023]
Abstract
Multichromophore systems (MCSs) are envisioned as building blocks of molecular optoelectronic devices. While it is important to understand the characteristics of energy transfer in MCSs, the effect of multiple donors on energy transfer has not been understood completely, mainly due to the lack of a platform to investigate such an effect systematically. Here, a systematic study on how the number of donors (n D) and interchromophore distances affect the efficiency of energy transfer (η FRET) is presented. Specifically, η FRET is calculated for a series of model MCSs using simulations, a series of multiporphyrin dendrimers with systematic variation of n D and interdonor distances is synthesized, and η FRETs of those dendrimers using transient absorption spectroscopy are measured. The simulations predict η FRET in the multiporphyrin dendrimers well. In particular, it is found that η FRET is enhanced by donor-to-donor energy transfer only when structural heterogeneity exists in an MCS, and the relationships between the η FRET enhancement and the structural parameters of the MCS are revealed.
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Affiliation(s)
- Inhwan Oh
- Department of ChemistryKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
- Center for Nanomaterials and Chemical ReactionsInstitute for Basic Science (IBS)Daejeon34141Republic of Korea
- KI for the BioCenturyKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
| | - Hosoowi Lee
- Department of ChemistryCollege of ScienceYonsei UniversitySeoul120‐749Republic of Korea
| | - Tae Wu Kim
- Department of ChemistryKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
- Center for Nanomaterials and Chemical ReactionsInstitute for Basic Science (IBS)Daejeon34141Republic of Korea
- KI for the BioCenturyKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
| | - Chang Woo Kim
- Department of ChemistryKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
| | - Sunhong Jun
- Center for Nanomaterials and Chemical ReactionsInstitute for Basic Science (IBS)Daejeon34141Republic of Korea
| | - Changwon Kim
- Department of ChemistryKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
- Center for Nanomaterials and Chemical ReactionsInstitute for Basic Science (IBS)Daejeon34141Republic of Korea
- KI for the BioCenturyKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
| | - Eun Hyuk Choi
- Department of ChemistryKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
- Center for Nanomaterials and Chemical ReactionsInstitute for Basic Science (IBS)Daejeon34141Republic of Korea
- KI for the BioCenturyKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
| | - Young Min Rhee
- Department of ChemistryKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
| | - Jeongho Kim
- Department of ChemistryInha UniversityIncheon22212Republic of Korea
| | - Woo‐Dong Jang
- Department of ChemistryCollege of ScienceYonsei UniversitySeoul120‐749Republic of Korea
| | - Hyotcherl Ihee
- Department of ChemistryKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
- Center for Nanomaterials and Chemical ReactionsInstitute for Basic Science (IBS)Daejeon34141Republic of Korea
- KI for the BioCenturyKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
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39
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Bürki N, Grossenbacher E, Cannizzo A, Feurer T, Langenegger SM, Häner R. DNA-organized artificial LHCs - testing the limits of chromophore segmentation. Org Biomol Chem 2020; 18:6818-6822. [PMID: 32936197 DOI: 10.1039/d0ob01531h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
DNA-organized multi-chromophoric systems containing phenanthrene and pyrene derivatives exhibit a highly efficient excitation energy transfer from phenanthrene (donor) to pyrene (acceptor). The energy transfer also occurs if the phenanthrene antenna is interrupted by intervening DNA base pairs. Artificial light-harvesting complexes composed of up to five phenanthrene-DNA alternations with fluorescence quantum yields as high as 68% are described.
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Affiliation(s)
- Nutcha Bürki
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
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40
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Jana P, Šupljika F, Schmuck C, Piantanida I. Naphthalene diimide bis-guanidinio-carbonyl-pyrrole as a pH-switchable threading DNA intercalator. Beilstein J Org Chem 2020; 16:2201-2211. [PMID: 32983268 PMCID: PMC7492691 DOI: 10.3762/bjoc.16.185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/26/2020] [Indexed: 12/16/2022] Open
Abstract
A novel naphthalene diimde analogue (NDI) equipped at the imide positions with two guanidinio-carbonyl-pyrrole (GCP) pendant arms interacted significantly stronger with ds-DNA at pH 5 than at pH 7, due to reversible protonation of the GCP arms. This was consequence of a pH-switchable threading intercalation into ds-DNAs only at pH 5, while at neutral conditions (pH 7) NDI-GCP2 switched to the DNA minor groove binding. Intriguingly, NDI-GCP2 was at both pH values studied bound to the ds-RNA major groove, still showing a higher affinity and thermal denaturation effect at pH 5 due to GCP protonation. At excess over the DNA/RNA conjugate NDI-GCP2 showed also aggregation along the ds-polynucleotide and AFM and DLS demonstrated that NDI-GCP2 has pronounced ds-DNA condensation ability.
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Affiliation(s)
- Poulami Jana
- Institute for Organic Chemistry, University of Duisburg-Essen, Universitässtrasse 7, 45141 Essen, Germany.,Integrated Science Education & Research Centre, Siksha-Bhavana, Visva-Bharati, Santiniketan-731235, India
| | - Filip Šupljika
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, P. O. Box 180, HR-10002 Zagreb, Croatia.,Laboratory for Physical Chemistry and Corrosion, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Croatia
| | - Carsten Schmuck
- Institute for Organic Chemistry, University of Duisburg-Essen, Universitässtrasse 7, 45141 Essen, Germany
| | - Ivo Piantanida
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, P. O. Box 180, HR-10002 Zagreb, Croatia
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41
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Weißenstein A, Vysotsky MO, Piantanida I, Würthner F. Naphthalene diimide–amino acid conjugates as novel fluorimetric and CD probes for differentiation between ds-DNA and ds-RNA. Beilstein J Org Chem 2020; 16:2032-2045. [PMID: 32874350 PMCID: PMC7445415 DOI: 10.3762/bjoc.16.170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/04/2020] [Indexed: 11/23/2022] Open
Abstract
Two novel unnatural amino acids, prepared by linking a dicationic purple-coloured and fluorescent naphthalene diimide (NDI) at core position to amino acid side chains of variable length, strongly interacted with ds-DNA/RNA by threading intercalation. Different from a reference NDI dye with identical visible range absorbance (520–540 nm) and Stokes shifts in emission (+60 nm, quantum yield > 0.2), only these amino acid–NDI conjugates showed selective fluorimetric response for GC-DNA in respect to AT(U)-polynucleotides. The DNA/RNA binding-induced circular dichroism (ICD) response of NDI at 450–550 nm strongly depended on the length and rigidity of the linker to the amino acid unit, which controls the orientation of the NDI unit inside within the intercalative binding site. The ICD selectivity also depends on the type of polynucleotide, thus the studied NDI dyes act as dual fluorimetric/ICD probes for sensing the difference between here used GC-DNA, AT-DNA and AU-RNA.
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Affiliation(s)
- Annike Weißenstein
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Myroslav O Vysotsky
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Ivo Piantanida
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, PO Box 180, 10002 Zagreb, Croatia
| | - Frank Würthner
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
- Center for Nanosystems Chemistry (CNC), Universität Würzburg, Theodor-Boveri-Weg, 97074 Würzburg, Germany
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42
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Kashida H, Azuma H, Maruyama R, Araki Y, Wada T, Asanuma H. Efficient Light‐Harvesting Antennae Resulting from the Dense Organization of Dyes into DNA Junctions through
d
‐Threoninol. Angew Chem Int Ed Engl 2020; 59:11360-11363. [DOI: 10.1002/anie.202004221] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Indexed: 01/07/2023]
Affiliation(s)
- Hiromu Kashida
- Department of Biomolecular Engineering Graduate School of Engineering Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Hidenori Azuma
- Department of Biomolecular Engineering Graduate School of Engineering Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Ryoko Maruyama
- Department of Biomolecular Engineering Graduate School of Engineering Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Yasuyuki Araki
- Institute of Multidisciplinary Research for Advanced Materials Tohoku University 2-1-1, Katahira, Aoba-ku Sendai 980-8577 Japan
| | - Takehiko Wada
- Institute of Multidisciplinary Research for Advanced Materials Tohoku University 2-1-1, Katahira, Aoba-ku Sendai 980-8577 Japan
| | - Hiroyuki Asanuma
- Department of Biomolecular Engineering Graduate School of Engineering Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
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43
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Kashida H, Azuma H, Maruyama R, Araki Y, Wada T, Asanuma H. Efficient Light‐Harvesting Antennae Resulting from the Dense Organization of Dyes into DNA Junctions through
d
‐Threoninol. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Hiromu Kashida
- Department of Biomolecular Engineering Graduate School of Engineering Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Hidenori Azuma
- Department of Biomolecular Engineering Graduate School of Engineering Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Ryoko Maruyama
- Department of Biomolecular Engineering Graduate School of Engineering Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Yasuyuki Araki
- Institute of Multidisciplinary Research for Advanced Materials Tohoku University 2-1-1, Katahira, Aoba-ku Sendai 980-8577 Japan
| | - Takehiko Wada
- Institute of Multidisciplinary Research for Advanced Materials Tohoku University 2-1-1, Katahira, Aoba-ku Sendai 980-8577 Japan
| | - Hiroyuki Asanuma
- Department of Biomolecular Engineering Graduate School of Engineering Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
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Aparin IO, Sergeeva OV, Mishin AS, Khaydukov EV, Korshun VA, Zatsepin TS. Excimer-FRET Cascade in Dual DNA Probes: Open Access to Large Stokes Shift, Enhanced Acceptor Light up, and Robust RNA Sensing. Anal Chem 2020; 92:7028-7036. [DOI: 10.1021/acs.analchem.0c00270] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ilya O. Aparin
- Skolkovo Institute of Science and Technology, 143026 Skolkovo, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - Olga V. Sergeeva
- Skolkovo Institute of Science and Technology, 143026 Skolkovo, Russia
| | - Alexander S. Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - Evgeny V. Khaydukov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- Federal Scientific Research Centre “Crystallography and Photonics” RAS, 119333 Moscow, Russia
- Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Vladimir A. Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- Gause Institute of New Antibiotics, 119021 Moscow, Russia
- Department of Biology and Biotechnology, National Research University Higher School of Economics, 117312 Moscow, Russia
| | - Timofei S. Zatsepin
- Skolkovo Institute of Science and Technology, 143026 Skolkovo, Russia
- Department of Chemistry, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
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45
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Surin M, Ulrich S. From Interaction to Function in DNA-Templated Supramolecular Self-Assemblies. ChemistryOpen 2020; 9:480-498. [PMID: 32328404 PMCID: PMC7175023 DOI: 10.1002/open.202000013] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/24/2020] [Indexed: 12/13/2022] Open
Abstract
DNA-templated self-assembly represents a rich and growing subset of supramolecular chemistry where functional self-assemblies are programmed in a versatile manner using nucleic acids as readily-available and readily-tunable templates. In this review, we summarize the different DNA recognition modes and the basic supramolecular interactions at play in this context. We discuss the recent results that report the DNA-templated self-assembly of small molecules into complex yet precise nanoarrays, going from 1D to 3D architectures. Finally, we show their emerging functions as photonic/electronic nanowires, sensors, gene delivery vectors, and supramolecular catalysts, and their growing applications in a wide range of area from materials to biological sciences.
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Affiliation(s)
- Mathieu Surin
- Laboratory for Chemistry of Novel MaterialsCenter of Innovation and Research in Materials and Polymers (CIRMAP)University of Mons-UMONS7000MonsBelgium
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46
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Marx A, Betz K. The Structural Basis for Processing of Unnatural Base Pairs by DNA Polymerases. Chemistry 2020; 26:3446-3463. [PMID: 31544987 PMCID: PMC7155079 DOI: 10.1002/chem.201903525] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/17/2019] [Indexed: 12/16/2022]
Abstract
Unnatural base pairs (UBPs) greatly increase the diversity of DNA and RNA, furthering their broad range of molecular biological and biotechnological approaches. Different candidates have been developed whereby alternative hydrogen-bonding patterns and hydrophobic and packing interactions have turned out to be the most promising base-pairing concepts to date. The key in many applications is the highly efficient and selective acceptance of artificial base pairs by DNA polymerases, which enables amplification of the modified DNA. In this Review, computational as well as experimental studies that were performed to characterize the pairing behavior of UBPs in free duplex DNA or bound to the active site of KlenTaq DNA polymerase are highlighted. The structural studies, on the one hand, elucidate how base pairs lacking hydrogen bonds are accepted by these enzymes and, on the other hand, highlight the influence of one or several consecutive UBPs on the structure of a DNA double helix. Understanding these concepts facilitates optimization of future UBPs for the manifold fields of applications.
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Affiliation(s)
- Andreas Marx
- Department of ChemistryKonstanz Research School Chemical BiologyUniversity of KonstanzUniversitätsstrasse 1078464KonstanzGermany
| | - Karin Betz
- Department of ChemistryKonstanz Research School Chemical BiologyUniversity of KonstanzUniversitätsstrasse 1078464KonstanzGermany
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47
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Michel BY, Dziuba D, Benhida R, Demchenko AP, Burger A. Probing of Nucleic Acid Structures, Dynamics, and Interactions With Environment-Sensitive Fluorescent Labels. Front Chem 2020; 8:112. [PMID: 32181238 PMCID: PMC7059644 DOI: 10.3389/fchem.2020.00112] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 02/06/2020] [Indexed: 12/13/2022] Open
Abstract
Fluorescence labeling and probing are fundamental techniques for nucleic acid analysis and quantification. However, new fluorescent probes and approaches are urgently needed in order to accurately determine structural and conformational dynamics of DNA and RNA at the level of single nucleobases/base pairs, and to probe the interactions between nucleic acids with proteins. This review describes the means by which to achieve these goals using nucleobase replacement or modification with advanced fluorescent dyes that respond by the changing of their fluorescence parameters to their local environment (altered polarity, hydration, flipping dynamics, and formation/breaking of hydrogen bonds).
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Affiliation(s)
- Benoît Y. Michel
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
| | - Dmytro Dziuba
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Rachid Benhida
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
- Mohamed VI Polytechnic University, UM6P, Ben Guerir, Morocco
| | - Alexander P. Demchenko
- Laboratory of Nanobiotechnologies, Palladin Institute of Biochemistry, Kyiv, Ukraine
- Institute of Physical, Technical and Computer Science, Yuriy Fedkovych National University, Chernivtsi, Ukraine
| | - Alain Burger
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
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48
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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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49
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Ready Access to Molecular Rotors Based on Boron Dipyrromethene Dyes-Coumarin Dyads Featuring Broadband Absorption. MOLECULES (BASEL, SWITZERLAND) 2020; 25:molecules25040781. [PMID: 32059435 PMCID: PMC7070740 DOI: 10.3390/molecules25040781] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/06/2020] [Accepted: 02/08/2020] [Indexed: 01/01/2023]
Abstract
Herein we report on a straightforward access method for boron dipyrromethene dyes (BODIPYs)-coumarin hybrids linked through their respective 8- and 6- positions, with wide functionalization of the coumarin fragment, using salicylaldehyde as a versatile building block. The computationally-assisted photophysical study unveils broadband absorption upon proper functionalization of the coumarin, as well as the key role of the conformational freedom of the coumarin appended at the meso position of the BODIPY. Such free motion almost suppresses the fluorescence signal, but enables us to apply these dyads as molecular rotors to monitor the surrounding microviscosity.
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50
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Kulyk O, Rocard L, Maggini L, Bonifazi D. Synthetic strategies tailoring colours in multichromophoric organic nanostructures. Chem Soc Rev 2020; 49:8400-8424. [PMID: 33107504 DOI: 10.1039/c9cs00555b] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Mimicking nature to develop light-harvesting materials is a timely challenge. This tutorial review examines the chemical strategies to engineer and customise innovative multi-coloured architectures with specific light-absorbing and emitting properties.
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Affiliation(s)
- Olesia Kulyk
- School of Chemistry
- Cardiff University
- Main Building
- Park Place
- Cardiff
| | - Lou Rocard
- School of Chemistry
- Cardiff University
- Main Building
- Park Place
- Cardiff
| | - Laura Maggini
- Institute of Organic Chemistry
- Faculty of Chemistry, University of Vienna, Währinger Strasse 38
- Vienna
- Austria
| | - Davide Bonifazi
- School of Chemistry
- Cardiff University
- Main Building
- Park Place
- Cardiff
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