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P Neme N, Jansen TLC, Havenith RWA. Cyclopentene ring effects in cyanine dyes: a handle to fine-tune photophysical properties. Phys Chem Chem Phys 2024; 26:6235-6241. [PMID: 38305348 PMCID: PMC10866127 DOI: 10.1039/d3cp05219b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/11/2024] [Indexed: 02/03/2024]
Abstract
The aim of this study is to investigate the photophysical properties of a cyanine dye analogue by performing first-principles calculations based on density functional theory (DFT) and time dependent-DFT. Cationic cyanine dyes are the subject of great importance due to their versatile applications and the tunability of their photophysical properties, such as by modifying their end groups and chain length. An example of this is the vinylene shift, which is experimentally known for these molecules, and it consists of a bathochromic (red) shift of approximately 100 nm of the 0-0 vibronic transition when a vinyl group is added to the polymethine chain. Our study shows that when the saturated moiety C2H4 of the cyclopentene ring is added to the chain, it interacts with the conjugated π-system, resulting in a smaller HOMO-LUMO gap. Here, we demonstrate the origin of this interaction and how it can be used to fine tune the absorption energies of this class of dyes.
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Affiliation(s)
- Natália P Neme
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands.
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Thomas L C Jansen
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands.
| | - Remco W A Havenith
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands.
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
- Department of Chemistry, Ghent University, Gent B-9000, Belgium
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2
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Kurutos A, Minkovska S, Nedialkov PT, Fedorov YV. Facile and environmentally benign synthetic approach to the selective mono‐chlorination and mono‐bromination of benzo[
d
]oxazol‐2(
3H
)‐ones. J Heterocycl Chem 2022. [DOI: 10.1002/jhet.4522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Atanas Kurutos
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences Sofia Bulgaria
| | - Stela Minkovska
- Institute of Catalysis, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bldg. 11, Sofia Bulgaria
| | - Paraskev T. Nedialkov
- Department of Pharmacognosy, Faculty of Pharmacy Medical University of Sofia 2 Dunav str., Sofia Bulgaria
| | - Yury V. Fedorov
- A. N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences 119991, Vavilova str., 28, Moscow Russia
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3
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Kurutos A, Citterio D. Synthesis and spectral properties of near-infrared cyanine dyes showing enhanced Stokes shift: A paradigm of ICT dipolar state polymethine chromophoric systems. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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4
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Electronic transport behavior of 2-amino-4,5-bis(2,5-dimethylthiophen-3-yl)furan-3-carbonitrile (a diarylethene) as optical molecular switch: a first-principles approach. Theor Chem Acc 2021. [DOI: 10.1007/s00214-021-02837-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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5
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Kurutos A, Nikodinovic-Runic J, Veselinovic A, Veselinović JB, Kamounah FS, Ilic-Tomic T. RNA-targeting low-molecular-weight fluorophores for nucleoli staining: synthesis, in silico modelling and cellular imaging. NEW J CHEM 2021. [DOI: 10.1039/d1nj01659h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Herein we present our work on the synthesis, investigation of the photophysical properties, interactions with nucleic acids, molecular docking, and imaging application of three carbocyanine dyes.
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Affiliation(s)
- Atanas Kurutos
- Institute of Organic Chemistry with Centre of Phytochemistry
- Bulgarian Academy of Sciences
- 1113 Sofia
- Bulgaria
| | | | | | - Jovana B. Veselinović
- Institute of Molecular Genetics and Genetic Engineering
- University of Belgrade
- 11000 Belgrade
- Serbia
| | - Fadhil S. Kamounah
- Department of Chemistry
- University of Copenhagen
- DK-2100 Copenhagen
- Denmark
| | - Tatjana Ilic-Tomic
- Institute of Molecular Genetics and Genetic Engineering
- University of Belgrade
- 11000 Belgrade
- Serbia
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6
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Šmidlehner T, Bonnet H, Chierici S, Piantanida I. Fluorescently-labelled amyloid paired helical filaments (PHF) in monitoring its fibrillation kinetics. Bioorg Chem 2020; 104:104196. [DOI: 10.1016/j.bioorg.2020.104196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/13/2020] [Accepted: 08/15/2020] [Indexed: 10/23/2022]
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7
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Šmidlehner T, Košćak M, Božinović K, Majhen D, Schmuck C, Piantanida I. Fluorimetric and CD Recognition between Various ds-DNA/RNA Depends on a Cyanine Connectivity in Cyanine-guanidiniocarbonyl-pyrrole Conjugate. Molecules 2020; 25:molecules25194470. [PMID: 33003366 PMCID: PMC7583847 DOI: 10.3390/molecules25194470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 09/25/2020] [Accepted: 09/27/2020] [Indexed: 11/16/2022] Open
Abstract
Two novel isosteric conjugates of guanidiniocarbonyl-pyrrole and 6-bromo-TO (thiazole orange) were prepared, differing only in linker connectivity to cyanine (benzothiazole nitrogen vs. quinoline nitrogen). The quinoline analog was significantly more susceptible to aggregation in an aqueous medium, which resulted in induced circular dichroism (ICD; λ = 450-550 nm) recognition between A-T(U) and G-C basepair containing polynucleotides. The benzothiazole-isostere showed pronounced (four-fold) fluorimetric selectivity toward ds-RNA in comparison to any ds-DNA, at variance to its quinoline-analogue fluorescence being weakly selective to GC-DNA. Preliminary screening on human tumor and normal lung cell lines showed that both dyes very efficiently enter living cells and accumulate in mitochondria, causing moderate cytotoxic effects, and thus could be considered as lead compounds toward novel theragnostic mitochondrial dyes.
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Affiliation(s)
- Tamara Šmidlehner
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (T.Š.); (M.K.)
| | - Marta Košćak
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (T.Š.); (M.K.)
| | - Ksenija Božinović
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (K.B.); (D.M.)
| | - Dragomira Majhen
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (K.B.); (D.M.)
| | - Carsten Schmuck
- Institute of Organic Chemistry, University of Duisburg-Essen, 45141 Essen, Germany;
| | - Ivo Piantanida
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (T.Š.); (M.K.)
- Correspondence: ; Tel.: +385-1-4571-326
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8
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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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9
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10
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11
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Šmidlehner T, Rožman A, Piantanida I. Advances in Cyanine - Amino Acid Conjugates and Peptides for Sensing of DNA, RNA and Protein Structures. Curr Protein Pept Sci 2019; 20:1040-1045. [PMID: 31092178 DOI: 10.2174/1389203720666190513084102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 01/23/2019] [Accepted: 04/06/2019] [Indexed: 12/27/2022]
Abstract
Small molecule spectrophotometric probes for DNA/RNA and proteins are of the utmost importance for diagnostics in biochemical and biomedical research. Both, naturally occurring and synthetic probes, often include peptide sequence responsible for the selectivity toward the particular target; however, commercially available dyes are restricted to single point attachment to the peptide (having one reactive group). Here presented are our recent advances in the development of novel amino acidfluorophore probes, with the unique characteristic of free N- and C-terminus available for incorporation at any peptide backbone position. Intriguingly, already monomeric amino acid-fluorophores showed recognition among various DNA/RNA, whereby steric impact and contribution of halogens is systematically studied. Moreover, some dyes revealed intracellular mitochondria specificity. Further, several hetero-dimeric chromophore systems were prepared, demonstrating that synergistic effect can lead to simultaneous DNA, RNA and protein fluorimetric recognition, combined with enzyme inhibition. Also, homodimeric cyanines equipped with chlorine revealed intriguing DNA/RNA selectivity in respect to well-known parent TOTO and YOYO dyes.
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Affiliation(s)
- Tamara Šmidlehner
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry. Ruder Boskovic Institute, Zagreb, Croatia
| | - Andrea Rožman
- Pliva Croatia Ltd, Research and Development, Zagreb, Croatia
| | - Ivo Piantanida
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry. Ruder Boskovic Institute, Zagreb, Croatia
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12
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Luo SH, Yang K, Lin JY, Gao JJ, Wu XY, Wang ZY. Synthesis of amino acid derivatives of 5-alkoxy-3,4-dihalo-2(5H)-furanones and their preliminary bioactivity investigation as linkers. Org Biomol Chem 2019; 17:5138-5147. [PMID: 31073571 DOI: 10.1039/c9ob00736a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A series of amino acid derivatives are successfully synthesized via a metal-free C-N coupling reaction of 5-alkoxy-3,4-dihalo-2(5H)-furanones and amino acids. Their structures are well characterized with 1H NMR, 13C NMR, ESI-MS and elemental analysis. As potential linkers of the 2(5H)-furanone unit with other drug moieties containing a hydroxyl or amino group, the effect of amino acids is investigated by comparison with other 2(5H)-furanone compounds by constructing C-O/C-S bonds. The preliminary results of the biological activity assay by the MTT method on a series of cancer cell lines in vitro reveal that the introduction of amino acids basically has no toxic effect. This can lead to these 2(5H)-furanone derivatives being further well-linked with other bioactive moieties with amino or hydroxy groups as expected. Thus, the biological activity assay gives a direction for the design of bioactive 2(5H)-furanones based on these amino acid linkers.
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Affiliation(s)
- Shi-He Luo
- School of Chemistry and Environment, South China Normal University, Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, Guangzhou 510006, P. R. China. and School of Chemistry and Chemical Engineering, Key Laboratory of Functional Molecular Engineering of Guangdong Province, South China University of Technology, Guangzhou 510641, P. R. China
| | - Kai Yang
- School of Chemistry and Environment, South China Normal University, Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, Guangzhou 510006, P. R. China. and College of Pharmacy, Gannan Medical University, Ganzhou, Jiangxi province 341000, P. R. China.
| | - Jian-Yun Lin
- School of Chemistry and Environment, South China Normal University, Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, Guangzhou 510006, P. R. China.
| | - Juan-Juan Gao
- College of Sports and Rehabilitation, Gannan Medical University, Ganzhou, Jiangxi province 341000, P. R. China
| | - Xin-Yan Wu
- School of Chemistry and Environment, South China Normal University, Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, Guangzhou 510006, P. R. China.
| | - Zhao-Yang Wang
- School of Chemistry and Environment, South China Normal University, Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, Guangzhou 510006, P. R. China. and School of Chemistry and Chemical Engineering, Key Laboratory of Functional Molecular Engineering of Guangdong Province, South China University of Technology, Guangzhou 510641, P. R. China
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13
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Ban Ž, Žinić B, Matković M, Tomašić Paić A, Crnolatac I, Piantanida I. Pyrrolocytosine–pyrene conjugates as fluorescent and CD probes for the fine sensing of ds-polynucleotide secondary structure and specific recognition of poly G. NEW J CHEM 2019. [DOI: 10.1039/c8nj05286g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Multipurpose dual method (fluorescence and CD) probes differentiate between various ds-RNA/RNA structures and specifically recognise Watson–Crick pairing complementary poly G.
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Affiliation(s)
- Željka Ban
- Laboratory for Biomolecular Interactions and Spectroscopy
- Division of Organic Chemistry & Biochemistry
- Ruđer Bošković Institute
- HR 10002 Zagreb
- Croatia
| | - Biserka Žinić
- Laboratory for Biomolecular Interactions and Spectroscopy
- Division of Organic Chemistry & Biochemistry
- Ruđer Bošković Institute
- HR 10002 Zagreb
- Croatia
| | - Marija Matković
- Laboratory for Biomolecular Interactions and Spectroscopy
- Division of Organic Chemistry & Biochemistry
- Ruđer Bošković Institute
- HR 10002 Zagreb
- Croatia
| | - Ana Tomašić Paić
- Laboratory for Biomolecular Interactions and Spectroscopy
- Division of Organic Chemistry & Biochemistry
- Ruđer Bošković Institute
- HR 10002 Zagreb
- Croatia
| | - Ivo Crnolatac
- Laboratory for Biomolecular Interactions and Spectroscopy
- Division of Organic Chemistry & Biochemistry
- Ruđer Bošković Institute
- HR 10002 Zagreb
- Croatia
| | - Ivo Piantanida
- Laboratory for Biomolecular Interactions and Spectroscopy
- Division of Organic Chemistry & Biochemistry
- Ruđer Bošković Institute
- HR 10002 Zagreb
- Croatia
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14
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Fluorescent cyanine-guanidiniocarbonyl-pyrrole conjugate with pH-dependent DNA/RNA recognition and DPP III fluorescent labelling and inhibition properties. MONATSHEFTE FUR CHEMIE 2018. [DOI: 10.1007/s00706-018-2192-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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