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Gao C, Mohamed HI, Deng J, Umer M, Anwar N, Chen J, Wu Q, Wang Z, He Y. Effects of Molecular Crowding on the Structure, Stability, and Interaction with Ligands of G-quadruplexes. ACS OMEGA 2023; 8:14342-14348. [PMID: 37125118 PMCID: PMC10134454 DOI: 10.1021/acsomega.3c01169] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/03/2023] [Indexed: 05/03/2023]
Abstract
G-quadruplexes (G4s) are widely found in cells and have significant biological functions, which makes them a target for screening antitumor and antiviral drugs. Most of the previous research on G4s has been conducted mainly in diluted solutions. However, cells are filled with organelles and many biomolecules, resulting in a constant state of a crowded molecular environment. The conformation and stability of some G4s were found to change significantly in the molecularly crowded environment, and interactions with ligands were disturbed to some extent. The structure of the G4s and their biological functions are correlated, and the effect of the molecularly crowded environment on G4 conformational transitions and interactions with ligands should be considered in drug design targeting G4s. This review discusses the changes in the conformation and stability of G4s in a physiological environment. Moreover, the mechanism of action of the molecularly crowded environment affecting the G4 has been further reviewed based on previous studies. Furthermore, current challenges and future research directions are put forward. This review has implications for the design of drugs targeting G4s.
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Affiliation(s)
- Chao Gao
- National
R&D Center for Se-rich Agricultural Products Processing, Hubei
Engineering Research Center for Deep Processing of Green Se-rich Agricultural
Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Hany I. Mohamed
- Chemistry
Department, Faculty of Science, Benha University, Benha 13518, Egypt
| | - Jieya Deng
- National
R&D Center for Se-rich Agricultural Products Processing, Hubei
Engineering Research Center for Deep Processing of Green Se-rich Agricultural
Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Muhammad Umer
- Institute
for Forest Resources and Environment of Guizhou and Forestry College,
Research Center of Forest Ecology, Guizhou
University, Guiyang 550025, China
| | - Naureen Anwar
- Department
of Zoology, University of Narowal, Narowal, Punjab 51600, Pakistan
| | - Jixin Chen
- National
R&D Center for Se-rich Agricultural Products Processing, Hubei
Engineering Research Center for Deep Processing of Green Se-rich Agricultural
Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Qiao Wu
- Wuhan
Botanical Garden, Chinese Academy of Science, Wuhan 430074, China
| | - Zhangqian Wang
- National
R&D Center for Se-rich Agricultural Products Processing, Hubei
Engineering Research Center for Deep Processing of Green Se-rich Agricultural
Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Yi He
- National
R&D Center for Se-rich Agricultural Products Processing, Hubei
Engineering Research Center for Deep Processing of Green Se-rich Agricultural
Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
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Gao C, Deng J, Anwar N, Umer M, Chen J, Wu Q, Dong X, Xu H, He Y, Wang Z. Molecular crowding promotes the aggregation of parallel structured G-quadruplexes. Int J Biol Macromol 2023; 240:124442. [PMID: 37062387 DOI: 10.1016/j.ijbiomac.2023.124442] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 04/09/2023] [Accepted: 04/10/2023] [Indexed: 04/18/2023]
Abstract
G-quadruplexes are widely distributed in cells and are usually essential in mediating biological processes. The intracellular environment is often in a state of molecular crowding, and the current research considerably focuses on the effect of molecular crowding on the conformation of telomeric G-quadruplexes. However, G-quadruplex-forming oligonucleotides are primarily located in the promoter region of the proto-oncogene and on mRNA inside the cell and are reported to fold into parallel structures. Thus, studying the interaction mechanism between ligands and parallel structured G-quadruplexes under crowding conditions is crucial for the design of drugs targeting G-quadruplexes. In our study, molecular crowding was simulated through polyethylene glycol with an average molecular weight of 200 (PEG200) to investigate the parallel structure of the canonical G-quadruplexes c-KIT1, c-MYC, and 32KRAS and their interactions with ligands. Circular dichroism (CD) spectral scanning, fluorescence resonance energy transfer (FRET), and native polyacrylamide gel electrophoresis (PAGE) analysis revealed that molecular crowding failed to induce oligonucleotides to form parallel G-quadruplex structures in the explored model sequences while induced telomeric G-rich sequences to form antiparallel G-quadruplexes in solution without K+. Molecular crowding did not induce changes in their parallel structures but promoted the formation of G-quadruplex aggregates. Moreover, to some extent, molecular crowding also induced a looser structure of the monomer G-quadruplexes. Further studies showed that molecular crowding did not alter the binding stoichiometry of the ligand 3,11-difluoro-6,8,13-trimethyl-8H-quino [4,3,2-kl] acridinium methosulfate (RHPS4) to c-KIT1, while it inhibited its interaction with parallel structured G-quadruplexes. This work provides new insights into developing anticancer drugs targeting parallel structured G-quadruplexes.
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Affiliation(s)
- Chao Gao
- National R&D Center for Se-rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Jieya Deng
- National R&D Center for Se-rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Naureen Anwar
- Department of Zoology, University of Narowal, Narowal, Punjab 51600, Pakistan
| | - Muhammad Umer
- Institute for Forest Resources and Environment of Guizhou and Forestry College, Research Center of Forest Ecology, Guizhou University, Guiyang 550025, China
| | - Jixin Chen
- National R&D Center for Se-rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Qiao Wu
- Wuhan Botanical Garden, Chinese Academy of Science, Wuhan 40074, China
| | - Xingxing Dong
- National R&D Center for Se-rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Hua Xu
- National R&D Center for Se-rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Yi He
- National R&D Center for Se-rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China.
| | - Zhangqian Wang
- National R&D Center for Se-rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China; State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China.
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Pandya N, Singh M, Rani R, Kumar V, Kumar A. G-quadruplex-mediated specific recognition, stabilization and transcriptional repression of bcl-2 by small molecule. Arch Biochem Biophys 2023; 734:109483. [PMID: 36513132 DOI: 10.1016/j.abb.2022.109483] [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: 08/03/2022] [Revised: 11/22/2022] [Accepted: 11/25/2022] [Indexed: 12/14/2022]
Abstract
The presence of the G-quadruplex (G4) structure in the promoter region of the human bcl-2 oncogenes makes it a promising target for developing anti-cancer therapeutics. Bcl-2 inhibits apoptosis, and its frequent overexpression in cancer cells contributes to tumor initiation, progression, and resistance to therapy. Small molecules that can specifically bind to bcl-2 G4 with high affinity and selectivity are remaining elusive. Here, we report that small molecule 1,3-bis-) furane-2yl-methylidene-amino) guanidine (BiGh) binds to bcl-2 G4 DNA structure with very high affinity and selectivity over other genomic G4 DNA structures and duplex DNA. BiGh stabilizes folded parallel conformation of bcl-2 G4 via non-covalent and electrostatic interactions and increases the thermal stabilization up to 15 °C. The ligand significantly suppresses the bcl-2 transcription in HeLa cells by a G4-dependent mechanism and induces cell cycle arrest which promotes apoptosis. The in silico ADME profiling confirms the potential 'drug-likeness' of BiGh. Our results showed that BiGh stabilizes the bcl-2 G-quadruplex motif, downregulates the bcl-2 gene transcription as well as translation process in cervical cancer cells, and exhibits potential anti-cancer activity. This work provides a potential platform for the development of lead compound(s) as G4 stabilizers with drug-like properties of BiGh for cancer therapeutics.
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Affiliation(s)
- Nirali Pandya
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, Madhya Pradesh, 453552, India
| | - Mamta Singh
- Amity Institute of Biotechnology, Amity University Noida, Uttar Pradesh, 201303, India
| | - Reshma Rani
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Noida, Uttar Pradesh, 201303, India
| | - Vinit Kumar
- Amity Institute of Biotechnology, Amity University Noida, Uttar Pradesh, 201303, India
| | - Amit Kumar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, Madhya Pradesh, 453552, India.
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Wang Z, Deng J, Umer M, Anwar N, Wang Y, Dong X, Xu H, He Y, Gao C. RHPS4 shifted the conformation ensemble equilibrium of Tel24 by preferentially stabilizing the (3 + 1) hybrid-2 conformation. RSC Adv 2022; 12:26011-26015. [PMID: 36199604 PMCID: PMC9469490 DOI: 10.1039/d2ra03959a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/04/2022] [Indexed: 11/21/2022] Open
Abstract
Telomeric G-quadruplexes have been a promising target for developing antitumor drugs with fewer side effects. The intracellular environment is usually in a state of molecular crowding. Studying the interaction mechanism among ligands and telomeric G-quadruplexes under crowded conditions is important for designing drugs that target telomeric G-quadruplexes. In the present study, the telomeric G-quadruplex Tel24 (TTAGGG)4 was found to fold into a conformational ensemble of parallel and (3 + 1) hybrid-2 conformations in solution with molecular crowding conditions created by PEG200. G-quadruplex-ligand 3,11-difluoro-6,8,13-trimethyl-8H-quino[4,3,2-kl] acridinium methosulfate (RHPS4) preferentially stabilized the (3 + 1) hybrid-2 conformation and shifted the conformational ensemble equilibrium of Tel24 towards the hybrid conformation. We also found that the (3 + 1) hybrid-2 conformation of Tel24 was more likely to form as compared to the parallel conformation in the conformational ensemble of Tel24. Overall, this study provides new insights into the conformation of telomere G-quadruplexes and their interactions with ligands in a physiological environment. Tel24 G-quadruplex can form a conformational ensemble consisting of parallel and (3 + 1) hybrid-2 conformations. RHPS4 preferentially stabilized the hybrid-2 conformation and shifted the conformational ensemble equilibrium.![]()
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Affiliation(s)
- Zhangqian Wang
- National R&D Center for Se-rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Jieya Deng
- National R&D Center for Se-rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Muhammad Umer
- Institute for Forest Resources and Environment of Guizhou and Forestry College, Research Center of Forest Ecology, Guizhou University, Guiyang, 550025, China
| | - Naureen Anwar
- Department of Zoology, University of Narowal, Narowal, Punjab, 51600, Pakistan
| | - Yidang Wang
- National R&D Center for Se-rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - XingXing Dong
- National R&D Center for Se-rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Hua Xu
- National R&D Center for Se-rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Yi He
- National R&D Center for Se-rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Chao Gao
- National R&D Center for Se-rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
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Substituent effects of cyclic naphthalene diimide on G-quadruplex binding and the inhibition of cancer cell growth. Bioorg Med Chem Lett 2021; 50:128323. [PMID: 34400300 DOI: 10.1016/j.bmcl.2021.128323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 08/04/2021] [Accepted: 08/09/2021] [Indexed: 11/21/2022]
Abstract
Interaction of cyclic naphthalene diimide derivatives (cNDIs), 1-4, with TA-core and c-myc as G-quartet (G4) DNA was studied under dilute or molecular crowding condition. Binding study for TA-core based on an isothermal titration calorimetry showed that 1-4 has 106 M-1 order of binding affinity with the following order: 1 > 4 > 2 > 3 under both conditions. Meting temperature (Tm) of TA-core obtained from the temperature dependence of circular dichroism spectra shows that TA-core was most stabilized by 4, which is in agreement with the result of PCR stop assay and the stabilization effect for 1-3 was correlated with their binding affinity under dilute condition. 3 showed specific growth inhibition of cancer cell line Ca9-22 at <0.03 μM of IC50, with no inhibitory effect against normal bone marrow cells. 3, which has highest value of ΔH/ΔG, shows the highest inhibition ability for Ca9-22, carrying a highest expression level of telomerase mRNA.
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Matsumoto S, Sugimoto N. New Insights into the Functions of Nucleic Acids Controlled by Cellular Microenvironments. Top Curr Chem (Cham) 2021; 379:17. [PMID: 33782792 DOI: 10.1007/s41061-021-00329-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 03/11/2021] [Indexed: 12/11/2022]
Abstract
The right-handed double-helical B-form structure (B-form duplex) has been widely recognized as the canonical structure of nucleic acids since it was first proposed by James Watson and Francis Crick in 1953. This B-form duplex model has a monochronic and static structure and codes genetic information within a sequence. Interestingly, DNA and RNA can form various non-canonical structures, such as hairpin loops, left-handed helices, triplexes, tetraplexes of G-quadruplex and i-motif, and branched junctions, in addition to the canonical structure. The formation of non-canonical structures depends not only on sequence but also on the surrounding environment. Importantly, these non-canonical structures may exhibit a wide variety of biological roles by changing their structures and stabilities in response to the surrounding environments, which undergo vast changes at specific locations and at specific times in cells. Here, we review recent progress regarding the interesting behaviors and functions of nucleic acids controlled by molecularly crowded cellular conditions. New insights gained from recent studies suggest that nucleic acids not only code genetic information in sequences but also have unknown functions regarding their structures and stabilities through drastic structural changes in cellular environments.
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Affiliation(s)
- Saki Matsumoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan. .,Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan.
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Platella C, Napolitano E, Riccardi C, Musumeci D, Montesarchio D. Disentangling the Structure-Activity Relationships of Naphthalene Diimides as Anticancer G-Quadruplex-Targeting Drugs. J Med Chem 2021; 64:3578-3603. [PMID: 33751881 PMCID: PMC8041303 DOI: 10.1021/acs.jmedchem.1c00125] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
In the context of
developing efficient anticancer therapies aimed
at eradicating any sort of tumors, G-quadruplexes represent excellent
targets. Small molecules able to interact with G-quadruplexes can
interfere with cell pathways specific of tumors and common to all
cancers. Naphthalene diimides
(NDIs) are among the most promising, putative anticancer G-quadruplex-targeting
drugs, due to their ability to simultaneously target multiple G-quadruplexes
and their strong, selective in vitro and in vivo anticancer activity.
Here, all the available biophysical, biological, and structural data
concerning NDIs targeting G-quadruplexes were systematically analyzed.
Structure–activity correlations were obtained by analyzing
biophysical data of their interactions with G-quadruplex targets and
control duplex structures, in parallel to biological data concerning
the antiproliferative activity of NDIs on cancer and normal cells.
In addition, NDI binding modes to G-quadruplexes were discussed in
consideration of the structures and properties of NDIs by in-depth
analysis of the available structural models of G-quadruplex/NDI complexes.
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Affiliation(s)
- Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy
| | - Ettore Napolitano
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy
| | - Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy.,Institute of Biostructures and Bioimages, CNR, via Mezzocannone 16, I-80134 Naples, Italy
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy
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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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