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Matić J, Piotrowski P, Vrban L, Kobetić R, Vianello R, Jurić I, Fabijanić I, Pernar Kovač M, Brozovic A, Piantanida I, Schmuck C, Radić Stojković M. Distinctive Nucleic Acid Recognition by Lysine-Embedded Phenanthridine Peptides. Int J Mol Sci 2024; 25:4866. [PMID: 38732083 PMCID: PMC11084427 DOI: 10.3390/ijms25094866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/25/2024] [Accepted: 04/27/2024] [Indexed: 05/13/2024] Open
Abstract
Three new phenanthridine peptide derivatives (19, 22, and 23) were synthesized to explore their potential as spectrophotometric probes for DNA and RNA. UV/Vis and circular dichroism (CD) spectra, mass spectroscopy, and computational analysis confirmed the presence of intramolecular interactions in all three compounds. Computational analysis revealed that compounds alternate between bent and open conformations, highlighting the latter's crucial influence on successful polynucleotide recognition. Substituting one glycine with lysine in two regioisomers (22, 23) resulted in stronger binding interactions with DNA and RNA than for a compound containing two glycines (19), thus emphasizing the importance of lysine. The regioisomer with lysine closer to the phenanthridine ring (23) exhibited a dual and selective fluorimetric response with non-alternating AT and ATT polynucleotides and induction of triplex formation from the AT duplex. The best binding constant (K) with a value of 2.5 × 107 M-1 was obtained for the interaction with AT and ATT polynucleotides. Furthermore, apart from distinguishing between different types of ds-DNA and ds-RNA, the same compound could recognize GC-rich DNA through distinct induced CD signals.
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Affiliation(s)
- Josipa Matić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
| | - Patryciusz Piotrowski
- Institute for Organic Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany; (P.P.)
| | - Lucija Vrban
- Laboratory for the Computational Design and Synthesis of Functional Materials, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (L.V.); (R.V.)
| | - Renata Kobetić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
| | - Robert Vianello
- Laboratory for the Computational Design and Synthesis of Functional Materials, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (L.V.); (R.V.)
| | - Ivona Jurić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
| | - Ivana Fabijanić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
| | - Margareta Pernar Kovač
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (M.P.K.); (A.B.)
| | - Anamaria Brozovic
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (M.P.K.); (A.B.)
| | - Ivo Piantanida
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
| | - Carsten Schmuck
- Institute for Organic Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany; (P.P.)
| | - Marijana Radić Stojković
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
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2
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Pramanik S, Chithra S, Rai S, Agrawal S, Shil D, Mukherjee S. Fluorescence Resonance Energy Transfer in a Supramolecular Assembly of Luminescent Silver Nanoclusters and a Cucurbit[8]uril-Based Host-Guest System. J Phys Chem B 2023. [PMID: 37470765 DOI: 10.1021/acs.jpcb.3c01914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
The understanding of interactions between organic chromophores and biocompatible luminescent noble metal nanoclusters (NCs) leading to an energy transfer process that has applications in light-harvesting materials is still in its nascent stage. This work describes a photoluminescent supramolecular assembly, made in two stages, employing an energy transfer process between silver (Ag) NCs as the donor and a host-guest system as the acceptor that can find potential applications in diverse fields. Initially, we explored the host-guest chemistry between a cationic guest ethidium bromide and cucurbit[8]uril host to modulate the fluorescence property of the acceptor. The host-guest interactions were characterized by using UV-vis absorption, steady-state and time-resolved spectroscopy, molecular docking, proton 1H nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry, and isothermal calorimetry studies. Next, we prepared a series of blue-emitting AgNCs using different templates such as proteins and peptides. We have found that these AgNCs can be employed as a donor in the energy transfer process upon mixing with the above acceptor for emission color tuning. Our in-depth studies also revealed that surface ligands could play a key role in modulating the energy transfer efficiency. Overall, by employing a noncovalent strategy, we have tried to develop Förster resonance energy transfer (FRET) pairs using blue-emitting NCs and a host-guest complex that could find potential applications in constructing advanced sustainable light-harvesting, white light-emitting, and anti-counterfeiting materials.
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Affiliation(s)
- Srikrishna Pramanik
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, Madhya Pradesh, India
| | - Sree Chithra
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, Madhya Pradesh, India
| | - Saurabh Rai
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, Madhya Pradesh, India
| | - Sameeksha Agrawal
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, Madhya Pradesh, India
| | - Debanggana Shil
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, Madhya Pradesh, India
| | - Saptarshi Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, Madhya Pradesh, India
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3
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Meier G, Thavarasah S, Ehrenbolger K, Hutter CAJ, Hürlimann LM, Barandun J, Seeger MA. Deep mutational scan of a drug efflux pump reveals its structure-function landscape. Nat Chem Biol 2023; 19:440-450. [PMID: 36443574 PMCID: PMC7615509 DOI: 10.1038/s41589-022-01205-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 10/10/2022] [Indexed: 11/30/2022]
Abstract
Drug efflux is a common resistance mechanism found in bacteria and cancer cells, but studies providing comprehensive functional insights are scarce. In this study, we performed deep mutational scanning (DMS) on the bacterial ABC transporter EfrCD to determine the drug efflux activity profile of more than 1,430 single variants. These systematic measurements revealed that the introduction of negative charges at different locations within the large substrate binding pocket results in strongly increased efflux activity toward positively charged ethidium, whereas additional aromatic residues did not display the same effect. Data analysis in the context of an inward-facing cryogenic electron microscopy structure of EfrCD uncovered a high-affinity binding site, which releases bound drugs through a peristaltic transport mechanism as the transporter transits to its outward-facing conformation. Finally, we identified substitutions resulting in rapid Hoechst influx without affecting the efflux activity for ethidium and daunorubicin. Hence, single mutations can convert EfrCD into a drug-specific ABC importer.
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Affiliation(s)
- Gianmarco Meier
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Sujani Thavarasah
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Kai Ehrenbolger
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
- Science for Life Laboratory, Umeå University, Umeå, Sweden
| | - Cedric A J Hutter
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Linkster Therapeutics AG, Zurich, Switzerland
| | - Lea M Hürlimann
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Linkster Therapeutics AG, Zurich, Switzerland
| | - Jonas Barandun
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
- Science for Life Laboratory, Umeå University, Umeå, Sweden
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
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4
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Excitation of phenanthridines in aqueous solution: Comparative theoretical analysis. J Photochem Photobiol A Chem 2023. [DOI: 10.1016/j.jphotochem.2022.114256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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Zhang A, Kondhare D, Leonard P, Seela F. Anomeric DNA Strand Displacement with α-D Oligonucleotides as Invaders and Ethidium Bromide as Fluorescence Sensor for Duplexes with α/β-, β/β- and α/α-D Configuration. Chemistry 2022; 28:e202201294. [PMID: 35652726 PMCID: PMC9543212 DOI: 10.1002/chem.202201294] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Indexed: 12/15/2022]
Abstract
DNA strand displacement is a technique to exchange one strand of a double stranded DNA by another strand (invader). It is an isothermal, enzyme free method driven by single stranded overhangs (toeholds) and is employed in DNA amplification, mismatch detection and nanotechnology. We discovered that anomeric (α/β) DNA can be used for heterochiral strand displacement. Homochiral DNA in β-D configuration was transformed to heterochiral DNA in α-D/β-D configuration and further to homochiral DNA with both strands in α-D configuration. Single stranded α-D DNA acts as invader. Herein, new anomeric displacement systems with and without toeholds were designed. Due to their resistance against enzymatic degradation, the systems are applicable to living cells. The light-up intercalator ethidium bromide is used as fluorescence sensor to follow the progress of displacement. Anomeric DNA displacement shows benefits over canonical DNA in view of toehold free displacement and simple detection by ethidium bromide.
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Affiliation(s)
- Aigui Zhang
- Laboratory of Bioorganic Chemistry and Chemical Biology Center for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
| | - Dasharath Kondhare
- Laboratory of Bioorganic Chemistry and Chemical Biology Center for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology Center for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology Center for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
- Laboratorium für Organische und Bioorganische ChemieInstitut für Chemie neuer MaterialienUniversität OsnabrückBarbarastrasse 749069OsnabrückGermany
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6
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Kshirsagar N, Sonawane R, Pathan S, Kamble G, Pal Singh G. A Review on Synthetic Approaches of Phenanthridine. LETT ORG CHEM 2022. [DOI: 10.2174/1570178618666210218211424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract:
The phenanthridine family is widely found in medicinal chemistry and material science because
of the biological activity and its presence in a variety of significant natural products and synthetic
dye stuffs. The phenanthridine has many clinical applications, for e.g., being used as an anticancer agent,
possessing antibacterial, antiprotozoal, pharmaceutical, and optoelectronic properties. Many methods
have been reported for the synthesis of phenanthridine and phenanthridine alkaloids, such as Pd catalyzed
C-C bond formation, a reaction involving C-H activation, radical, microwave-assisted, transition
metal-catalyzed, one-pot cascade, benzyne mediated, photochemical, hypervalent iodine promoted methods,
etc. Here, we have summarized the literature data from 2014 to the present concerning novel or
improved synthetic approaches.
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Affiliation(s)
| | | | - Sultan Pathan
- Department of Chemistry, Bhupal Nobles
University, Udaipur, Rajasthan, India
| | - Ganesh Kamble
- Department of Chemistry, Osaka University, ISIR 8-1 Mihogaoka, Ibaraki,
Osaka 567-0047, Japan
| | - Girdhar Pal Singh
- Department of Chemistry, Bhupal Nobles
University, Udaipur, Rajasthan, India
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7
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Raturi S, Nair AV, Shinoda K, Singh H, Bai B, Murakami S, Fujitani H, van Veen HW. Engineered MATE multidrug transporters reveal two functionally distinct ion-coupling pathways in NorM from Vibrio cholerae. Commun Biol 2021; 4:558. [PMID: 33976372 PMCID: PMC8113278 DOI: 10.1038/s42003-021-02081-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 04/01/2021] [Indexed: 11/09/2022] Open
Abstract
Multidrug and toxic compound extrusion (MATE) transport proteins confer multidrug resistance on pathogenic microorganisms and affect pharmacokinetics in mammals. Our understanding of how MATE transporters work, has mostly relied on protein structures and MD simulations. However, the energetics of drug transport has not been studied in detail. Many MATE transporters utilise the electrochemical H+ or Na+ gradient to drive substrate efflux, but NorM-VC from Vibrio cholerae can utilise both forms of metabolic energy. To dissect the localisation and organisation of H+ and Na+ translocation pathways in NorM-VC we engineered chimaeric proteins in which the N-lobe of H+-coupled NorM-PS from Pseudomonas stutzeri is fused to the C-lobe of NorM-VC, and vice versa. Our findings in drug binding and transport experiments with chimaeric, mutant and wildtype transporters highlight the versatile nature of energy coupling in NorM-VC, which enables adaptation to fluctuating salinity levels in the natural habitat of V. cholerae.
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Affiliation(s)
- Sagar Raturi
- Department of Pharmacology, University of Cambridge, Cambridge, UK
- University College Dublin Clinical Research Centre, St. Vincent's University Hospital, Dublin, Ireland
| | - Asha V Nair
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Keiko Shinoda
- Microbial Membrane Transport Engineering, Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Himansha Singh
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Boyan Bai
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Satoshi Murakami
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama, Japan
| | - Hideaki Fujitani
- Laboratories for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Meguro-ku, Tokyo, Japan
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8
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Lončar B, Perin N, Mioč M, Boček I, Grgić L, Kralj M, Tomić S, Stojković MR, Hranjec M. Novel amino substituted tetracyclic imidazo[4,5-b]pyridine derivatives: Design, synthesis, antiproliferative activity and DNA/RNA binding study. Eur J Med Chem 2021; 217:113342. [PMID: 33751978 DOI: 10.1016/j.ejmech.2021.113342] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 02/06/2023]
Abstract
A novel series of tetracyclic imidazo[4,5-b]pyridine derivatives was designed and synthesized as potential antiproliferative agents. Their antiproliferative activity against human cancer cells was influenced by the introduction of chosen amino side chains on the different positions on the tetracyclic skeleton and particularly, by the position of N atom in the pyridine nuclei. Thus, the majority of compounds showed improved activity in comparison to standard drug etoposide. Several compounds showed pronounced cytostatic effect in the submicromolar range, especially on HCT116 and MCF-7 cancer cells. The obtained results have confirmed the significant impact of the position of N nitrogen in the pyridine ring on the enhancement of antiproliferative activity, especially for derivatives bearing amino side chains on position 2. Thus, regioisomers 6, 7 and 9 showed noticeable enhancement of activity in comparison to their counterparts 10, 11 and 13 with IC50 values in a nanomolar range of concentration (0.3-0.9 μM). Interactions with DNA (including G-quadruplex structure) and RNA were influenced by the position of amino side chains on the tetracyclic core of imidazo[4,5-b]pyridine derivatives and the ligand charge. Moderate to high binding affinities (logKs = 5-7) obtained for selected imidazo[4,5-b]pyridine derivatives suggest that DNA/RNA are potential cell targets.
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Affiliation(s)
- Borka Lončar
- Pliva d.o.o., odjel TAPI I&R, Unapređenje tehnoloških procesa i Podrška proizvodnji, Croatia
| | - Nataša Perin
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, HR-10000, Zagreb, Croatia
| | - Marija Mioč
- Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia
| | - Ida Boček
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, HR-10000, Zagreb, Croatia
| | - Lea Grgić
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Bijenička cesta 54, 10 000, Zagreb, Croatia
| | - Marijeta Kralj
- Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia
| | - Sanja Tomić
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Bijenička cesta 54, 10 000, Zagreb, Croatia
| | - Marijana Radić Stojković
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Bijenička cesta 54, 10 000, Zagreb, Croatia.
| | - Marijana Hranjec
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, HR-10000, Zagreb, Croatia.
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Tumir LM, Zonjić I, Žuna K, Brkanac SR, Jukić M, Huđek A, Durgo K, Crnolatac I, Glavaš-Obrovac L, Cardullo N, Pulvirenti L, Muccilli V, Tringali C, Stojković MR. Synthesis, DNA/RNA-interaction and biological activity of benzo[k,l]xanthene lignans. Bioorg Chem 2020; 104:104190. [PMID: 32919130 DOI: 10.1016/j.bioorg.2020.104190] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/30/2020] [Accepted: 08/05/2020] [Indexed: 12/20/2022]
Abstract
Interactions of two newly synthesized and six previously reported benzoxanthene lignans (BXLs), analogues of rare natural products, with DNA/RNA, G-quadruplex and HSA were evaluated by a set of spectrophotometric methods. Presence/absence of methoxy and hydroxy groups on the benzoxanthene core and minor modifications at C-1/C-2 side pendants - presence/absence of phenyl ring and presence/absence of methoxy and hydroxy groups on phenyl ring - influenced the fluorescence changes and the binding strength to double-stranded (ds-) and G-quadruplex structures. In general, compounds without phenyl ring showed stronger fluorescence changes upon binding than phenyl-substituted BXLs. On the other hand, BXLs with an unsubstituted phenyl ring showed the best stabilization effects of G-quadruplex. Circular dichroism spectroscopy results suggest mixed binding mode, groove binding and partial intercalation, to ds-DNA/RNA and end-stacking to top or bottom G-tetrads as the main binding modes of BXLs to those targets. All compounds exhibited micromolar binding affinities toward HSA and an increased protein thermal stability. Moderate to strong antiradical scavenging activity was observed for all BXLs with hydroxy groups at C-6, C-9 and C-10 positions of the benzoxanthene core, except for derivative bearing methoxy groups at these positions. BXLs with unsubstituted or low-substituted phenyl ring and one derivative without phenyl ring showed strong growth inhibition of Gram-positive Staphylococcus aureus. All compounds showed moderate to strong tumor cell growth-inhibitory activity and cytotoxicity.
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Affiliation(s)
- Lidija-Marija Tumir
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Iva Zonjić
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Kristina Žuna
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierrotijeva 6, 10000 Zagreb, Croatia
| | - Sandra Radić Brkanac
- University of Zagreb, Faculty of Science, Department of Biology, Rooseveltov trg 6/III, HR-10 000 Zagreb, Croatia
| | - Marijana Jukić
- Department of Medicinal Chemistry, Biochemistry and Laboratory Medicine, Faculty of Medicine Osijek, Josip Juraj Strossmayer University of Osijek, Huttlerova 4, HR-31000 Osijek, Croatia
| | - Ana Huđek
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierrotijeva 6, 10000 Zagreb, Croatia
| | - Ksenija Durgo
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierrotijeva 6, 10000 Zagreb, Croatia
| | - Ivo Crnolatac
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Ljubica Glavaš-Obrovac
- Department of Medicinal Chemistry, Biochemistry and Laboratory Medicine, Faculty of Medicine Osijek, Josip Juraj Strossmayer University of Osijek, Huttlerova 4, HR-31000 Osijek, Croatia
| | - Nunzio Cardullo
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, I-95125 Catania, Italy
| | - Luana Pulvirenti
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, I-95125 Catania, Italy
| | - Vera Muccilli
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, I-95125 Catania, Italy
| | - Corrado Tringali
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, I-95125 Catania, Italy
| | - Marijana Radić Stojković
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Bijenička cesta 54, 10000 Zagreb, Croatia.
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10
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Alnajrani MN, Alsager OA. Decomposition of DNA staining agent ethidium bromide by gamma irradiation: Conditions, kinetics, by-products, biological activity, and removal from wastewater. JOURNAL OF HAZARDOUS MATERIALS 2020; 389:122142. [PMID: 32004843 DOI: 10.1016/j.jhazmat.2020.122142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/14/2020] [Accepted: 01/18/2020] [Indexed: 06/10/2023]
Abstract
Ethidium Bromide (Eth-Br) is an intercalating agent commonly used in medical and biological laboratories as a DNA staining dye. Despite its popular use, aqueous solutions containing Eth-Br showed high toxicity, mutagenic capacity, and deactivate DNA transcription. In this study, the removal of Eth-Br from aqueous solutions by gamma irradiation has been fully investigated. Gamma irradiation was capable of achieving a near complete removal of Eth-Br in neutral and non-buffered aqueous solutions at an absorbed dose of 15 kGy. Various experimental conditions were studied and showed that the removal efficiency is not diminished. The addition of hydrogen peroxide (2 %) to the irradiated solutions reduced the D50 and D90 by 50 %. Modeling Eth-Br decomposition showed that the reaction followed pseudo first-order kinetics and reaches at least 90 % removal under all experimental conditions. TOC and HPLC measurements confirmed that Eth-Br is fully mineralized when the absorbed dose reaches 15 kGy. The biological activity of Eth-Br after irradiation treatment was investigated with synthetic DNA and natural DNA. The biological activity of Eth-Br was deactivated at an absorbed dose as low as 5 kGy. Toxicity measurement with E-coli bacteria also confirmed that the absorbed dose of 5 kGy was sufficient to remove Eth-Br toxicity.
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Affiliation(s)
- Mohammed N Alnajrani
- National Center for Irradiation Technology, Nuclear Science Research Institute, King Abdulaziz City for Science and Technology, P.O. Box 6086, Riyadh, 11442, Saudi Arabia
| | - Omar A Alsager
- National Center for Irradiation Technology, Nuclear Science Research Institute, King Abdulaziz City for Science and Technology, P.O. Box 6086, Riyadh, 11442, Saudi Arabia.
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11
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Li Z, Chang PH, Jiang WT, Liu Y. Enhanced removal of ethidium bromide (EtBr) from aqueous solution using rectorite. JOURNAL OF HAZARDOUS MATERIALS 2020; 384:121254. [PMID: 31586911 DOI: 10.1016/j.jhazmat.2019.121254] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 09/03/2019] [Accepted: 09/17/2019] [Indexed: 05/07/2023]
Abstract
Ethidium bromide (EtBr) is an intercalating agent commonly used as nucleic acid fluorescent tag in various techniques of life science field. It is considered as a serious biohazard due to its mutagenicity and carcinogenicity. As such, developing high efficiency and low cost materials as cleanup kits is in urgent need although many methods have already been developed. In this study we take use of the affinity of organic cations for clay minerals of high cation exchange capacity (CEC) and large specific surface area (SSA) and tested the removal of EtBr using rectorite, a type of clay mineral made of 1:1 regularly mixed layers of illite and montmorillonite. Our results showed that the uptake of Et+ on rectorite could be as high as 400 mmol/kg and the removal of Et+ was extremely fast. Desorption of inorganic cation Ca2+ and sorption of counterion Br- revealed that cation exchange was the dominating mechanism of Et+ removal using rectorite. Thermal analyses revealed that the EtBr could be thermally destructed inside the interlayer of rectorite and the material could be thermally regenerated. Thus, clay minerals could have a great potential to be fabricated into cleanup kits for the removal of EtBr in case of spill.
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Affiliation(s)
- Zhaohui Li
- Beijing Key Laboratory of Materials Utilization of Nonmetallic Minerals and Solid Wastes, National Laboratory of Mineral Materials, School of Materials Science and Technology, China University of Geosciences, 29 Xueyuan Road, Beijing, 100083, China; Department of Earth Sciences, National Cheng Kung University, 1 University Road, Tainan 70101, Taiwan; Department of Geosciences, University of Wisconsin - Parkside, 900 Wood Road, Kenosha, WI 53144, USA.
| | - Po-Hsiang Chang
- Department of Earth Sciences, National Cheng Kung University, 1 University Road, Tainan 70101, Taiwan
| | - Wei-Teh Jiang
- Department of Earth Sciences, National Cheng Kung University, 1 University Road, Tainan 70101, Taiwan.
| | - Yujuan Liu
- Department of Chemistry, University of Wisconsin - Parkside, 900 Wood Road, Kenosha, WI 53144, USA
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12
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DNA/RNA recognition controlled by the glycine linker and the guanidine moiety of phenanthridine peptides. Int J Biol Macromol 2019; 134:422-434. [PMID: 31082420 DOI: 10.1016/j.ijbiomac.2019.05.063] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/09/2019] [Accepted: 05/09/2019] [Indexed: 12/27/2022]
Abstract
The binding of four phenanthridine-guanidine peptides to DNA/RNA was evaluated via spectrophotometric/microcalorimetric methods and computations. The minor structural modifications-the type of the guanidine group (pyrrole guanidine (GCP) and arginine) and the linker length (presence or absence of glycine)-greatly affected the conformation of compounds and consequently the binding to double- (ds-) and single-stranded (ss-) polynucleotides. GCP peptide with shorter linker was able to distinguish between RNA (A-helix) and DNA (B-helix) by different circular dichroism response at 295 nm and thus can be used as a chiral probe. Opposed to the dominant stretched conformation of GCP peptide with shorter linker, the more flexible and longer linker of its analogue enabled the molecule to adopt the intramolecularly stacked form which resulted in weaker yet selective binding to DNA. Beside efficient organization of ss-polynucleotide structures, GCP peptide with shorter linker bound stronger to ss-DNA/RNA compared to arginine peptides which emphasize the importance of GCP unit.
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13
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Van Overtveldt M, Braem L, Struk S, Kaczmarek AM, Boyer FD, Van Deun R, Gevaert K, Goormachtig S, Heugebaert TSA, Stevens CV. Design and visualization of second-generation cyanoisoindole-based fluorescent strigolactone analogs. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:165-180. [PMID: 30552776 DOI: 10.1111/tpj.14197] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 11/22/2018] [Accepted: 12/04/2018] [Indexed: 06/09/2023]
Abstract
Strigolactones (SLs) are a family of terpenoid allelochemicals that were recognized as plant hormones only a decade ago. They influence a myriad of both above- and below-ground developmental processes, and are an important survival strategy for plants in nutrient-deprived soils. A rapidly emerging approach to gain knowledge on hormone signaling is the use of traceable analogs. A unique class of labeled SL analogs was constructed, in which the original tricyclic lactone moiety of natural SLs is replaced by a fluorescent cyanoisoindole ring system. Biological evaluation as parasitic seed germination stimulant and hypocotyl elongation repressor proved the potency of the cyanoisoindole strigolactone analogs (CISAs) to be comparable to the commonly accepted standard GR24. Additionally, via a SMXL6 protein degradation assay, we provided molecular evidence that the compounds elicit SL-like responses through the natural signaling cascade. All CISAs were shown to exhibit fluorescent properties, and the high quantum yield and Stokes shift of the pyrroloindole derivative CISA-7 also enabled in vivo visualization in plants. In contrast to the previously reported fluorescent analogs, CISA-7 displays a large similarity in shape and structure with natural SLs, which renders the analog a promising tracer to investigate the spatiotemporal distribution of SLs in plants and fungi.
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Affiliation(s)
- Melissa Van Overtveldt
- SynBioC Research Group, Department of Green Chemistry and Technology, Campus Coupure, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Lukas Braem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
- Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
- Center for Medical Biotechnology, VIB, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
| | - Sylwia Struk
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
| | - Anna M Kaczmarek
- Luminescent Lanthanide Lab, Department of Chemistry, Ghent University, Krijgslaan 281 - S3, 9000, Ghent, Belgium
| | - François-Didier Boyer
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles, France
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Univ. Paris-Sud, Université Paris-Saclay, 1 Avenue de la Terrasse, 91198, Gif-sur-Yvette, France
| | - Rik Van Deun
- Luminescent Lanthanide Lab, Department of Chemistry, Ghent University, Krijgslaan 281 - S3, 9000, Ghent, Belgium
| | - Kris Gevaert
- Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
- Center for Medical Biotechnology, VIB, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
| | - Thomas S A Heugebaert
- SynBioC Research Group, Department of Green Chemistry and Technology, Campus Coupure, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Christian V Stevens
- SynBioC Research Group, Department of Green Chemistry and Technology, Campus Coupure, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
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14
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Strmiskova M, Bilodeau DA, Chigrinova M, Pezacki JP. Phenanthridine-based nitrones as substrates for strain-promoted alkyne-nitrone cycloadditions. CAN J CHEM 2019. [DOI: 10.1139/cjc-2018-0253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Over the past decade, bioorthogonal chemistry that facilitates the efficient conjugation of biomolecules has expanded from the copper-catalyzed alkyne-azide cycloadditions to a multitude of diverse reactions, varying additives and reactional partners, and most often offering better alternatives with faster rates and lower toxicity of employed reactants. Among these, the copper-free strain-promoted cycloaddition reactions have been demonstrated to be more promising, offering a reaction without toxic metal catalysts and with faster inherent kinetic rate constants. The strain-promoted alkyne-nitrone cycloadditions are easily tunable from both the (strained) alkyne and nitrone perspective, both compounds giving the opportunity to modulate the rate of reaction by substituting various positions. Previously, acyclic nitrones have been evaluated in the strain-promoted alkyne-nitrone reactions; however, they were notably prone to hydrolysis. Some five-membered ring endocyclic nitrones developed concomitantly offered the advantage of relatively fast kinetics and better resistance to degradation in aqueous conditions and have been successfully used for labelling of biomolecules in living systems. Herein, we have prepared and studied nitrones inspired by the phenanthridine scaffold that efficiently undergo strain-promoted alkyne-nitrone reactions. Phenanthridine nitrones react fast with strained cyclooctynes with large bimolecular rate constants while maintaining bioorthogonality and resistance to hydrolysis.
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Affiliation(s)
- Miroslava Strmiskova
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, ON K1N 6N5, Canada
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, ON K1N 6N5, Canada
| | - Didier A. Bilodeau
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, ON K1N 6N5, Canada
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, ON K1N 6N5, Canada
| | - Mariya Chigrinova
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, ON K1N 6N5, Canada
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, ON K1N 6N5, Canada
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, ON K1N 6N5, Canada
- Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, ON K1N 6N5, Canada
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15
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1 H-[1,2,4]Triazolo[4,3- a]pyridin-4-ium and 3 H-[1,2,4]triazolo[4,3- a]quinolin-10-ium derivatives as new intercalating agents for DNA. ZEITSCHRIFT FUR NATURFORSCHUNG SECTION B-A JOURNAL OF CHEMICAL SCIENCES 2018. [DOI: 10.1515/znb-2018-0089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractTwo new cationic DNA intercalators, 3-phenyl-1-(6-phenylpyridin-2-yl)-1H-[1,2,4]triazolo[4,3-a]pyridin-4-ium (1a)+and 1-phenyl-3-(6-phenylpyridin-2-yl)-3H-[1,2,4]triazolo[4,3-a]quinolin-10-ium (1b)+, were synthesized from 2-chloropyridine and 2-chloroquinoline, respectively, in a four-step procedure. Generation of the hydrazine, followed by condensation with an aldehyde to give a hydrazone and subsequent Buchwald-Hartwig amination gave a mixture ofE- andZ-configuredN,N-functionalized hydrazones. Finally, oxidative cyclisation gave rise to the formation of the cationic DNA intercalators, whose molecular structures were determined by single-crystal X-ray diffraction analysis of the hexafluorophosphate and tribromide salt of (1a)+and (1b)+, respectively. The intercalative binding of (1a)PF6and (1b)PF6to ctDNA was confirmed by means of UV, CD and luminescence spectroscopy, determination of the DNA melting temperature and by rheology measurements.
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16
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Haniff HS, Graves A, Disney MD. Selective Small Molecule Recognition of RNA Base Pairs. ACS COMBINATORIAL SCIENCE 2018; 20:482-491. [PMID: 29966095 PMCID: PMC6325646 DOI: 10.1021/acscombsci.8b00049] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Many types of RNAs exist in the human transcriptome, yet only the bacterial ribosome has been exploited as a small molecule drug target. Aside from rRNA, other cellular RNAs such as noncoding RNAs have primarily secondary structure and limited tertiary structure. Within these secondary structures of noncanonically paired and unpaired regions, more than 50% are base paired, with most efforts to target these structures focused on looped regions. A void exists in the availability of small molecules capable of targeting RNA base pairs. Using chemoinformatics, an RNA-focused library enriched for nitrogen-containing heterocycles was developed and tested for binding RNA base pairs, leading to the identification of six selective and previously unknown binders. While all binders were derivatives of benzimidazoles, those with expanded aromatic polycycles bound selectively to AU pairs, while those with flexible urea side chains bound selectively to GC pairs. Two of the three selective GC pair binders can distinguish between two different orientations, 5'GG/3'CC and 5'GC/3'CG pairs. Furthermore, all six molecules showed >50-fold selectivity for RNA over DNA. These studies provide foundational knowledge to better exploit RNA as targets for small molecule chemical probes or lead therapeutics by using modules that target RNA base pairs.
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Affiliation(s)
- Hafeez S Haniff
- Department of Chemistry , The Scripps Research Institute , Jupiter , Florida 33458 , United States
| | - Amanda Graves
- Department of Chemistry , The Scripps Research Institute , Jupiter , Florida 33458 , United States
| | - Matthew D Disney
- Department of Chemistry , The Scripps Research Institute , Jupiter , Florida 33458 , United States
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17
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Mal A, Mishra RK, Praveen VK, Khayum MA, Banerjee R, Ajayaghosh A. Supramolecular Reassembly of Self‐Exfoliated Ionic Covalent Organic Nanosheets for Label‐Free Detection of Double‐Stranded DNA. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801352] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Arindam Mal
- Photosciences and Photonics Section Chemical Sciences and Technology Division and Academy of Scientific and Innovative Research (AcSIR) CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST) Thiruvananthapuram 695019 India
| | - Rakesh K. Mishra
- Photosciences and Photonics Section Chemical Sciences and Technology Division and Academy of Scientific and Innovative Research (AcSIR) CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST) Thiruvananthapuram 695019 India
| | - Vakayil K. Praveen
- Photosciences and Photonics Section Chemical Sciences and Technology Division and Academy of Scientific and Innovative Research (AcSIR) CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST) Thiruvananthapuram 695019 India
| | - M. Abdul Khayum
- Physical/Materials Chemistry Division and Academy of Scientific and Innovative Research (AcSIR) CSIR-National Chemical Laboratory (CSIR-NCL) Pune 411008 India
| | - Rahul Banerjee
- Physical/Materials Chemistry Division and Academy of Scientific and Innovative Research (AcSIR) CSIR-National Chemical Laboratory (CSIR-NCL) Pune 411008 India
| | - Ayyappanpillai Ajayaghosh
- Photosciences and Photonics Section Chemical Sciences and Technology Division and Academy of Scientific and Innovative Research (AcSIR) CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST) Thiruvananthapuram 695019 India
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18
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Mal A, Mishra RK, Praveen VK, Khayum MA, Banerjee R, Ajayaghosh A. Supramolecular Reassembly of Self-Exfoliated Ionic Covalent Organic Nanosheets for Label-Free Detection of Double-Stranded DNA. Angew Chem Int Ed Engl 2018; 57:8443-8447. [PMID: 29714817 DOI: 10.1002/anie.201801352] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Indexed: 11/07/2022]
Abstract
Ionic covalent organic nanosheets (iCONs), a member of the two-dimensional (2D) nanomaterials family, offer a unique functional platform for a wide range of applications. Herein, we explore the potential of an ethidium bromide (EB)-based covalent organic framework (EB-TFP) that self-exfoliates in water resulting in 2D ionic covalent organic nanosheets (EB-TFP-iCONs) for the selective detection of double-stranded DNA (dsDNA). In an aqueous medium, the self-exfoliated EB-TFP-iCONs reassemble in the presence of dsDNA resulting in hybrid EB-TFP-iCONs-DNA crystalline nanosheets with enhanced fluorescence at 600 nm. Detailed steady-state and time-resolved emission studies revealed that the reassembly phenomenon was highly selective for dsDNA when compared to single-stranded DNA (ssDNA), which allowed us to use the EB-TFP-iCONs as a 2D fluorescent platform for the label-free detection of complementary DNA strands.
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Affiliation(s)
- Arindam Mal
- Photosciences and Photonics Section, Chemical Sciences and Technology Division and Academy of Scientific and Innovative Research (AcSIR), CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, 695019, India
| | - Rakesh K Mishra
- Photosciences and Photonics Section, Chemical Sciences and Technology Division and Academy of Scientific and Innovative Research (AcSIR), CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, 695019, India
| | - Vakayil K Praveen
- Photosciences and Photonics Section, Chemical Sciences and Technology Division and Academy of Scientific and Innovative Research (AcSIR), CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, 695019, India
| | - M Abdul Khayum
- Physical/Materials Chemistry Division and Academy of Scientific and Innovative Research (AcSIR), CSIR-National Chemical Laboratory (CSIR-NCL), Pune, 411008, India
| | - Rahul Banerjee
- Physical/Materials Chemistry Division and Academy of Scientific and Innovative Research (AcSIR), CSIR-National Chemical Laboratory (CSIR-NCL), Pune, 411008, India
| | - Ayyappanpillai Ajayaghosh
- Photosciences and Photonics Section, Chemical Sciences and Technology Division and Academy of Scientific and Innovative Research (AcSIR), CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, 695019, India
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19
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Kwak MI, Jeon BR, Kim SK, Jang YJ. Binding Mode of Cationic Porphyrin with CT-DNA: Importance of the Location and the Number of Positively Charged of Periphery Cationic Ions of Porphyrin. ACS OMEGA 2018; 3:946-953. [PMID: 31457940 PMCID: PMC6641333 DOI: 10.1021/acsomega.7b01627] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 12/25/2017] [Indexed: 05/24/2023]
Abstract
The binding modes of o-, m-, and p-trans-BMPyP with DNA were studied using their spectroscopic properties. Also, the binding modes were compared based on the location and number of periphery cationic methylpyridine ions of the cationic porphyrins. The optical absorption spectra of the o-, m-, and p-trans-BMPyP when bound to DNA presented red shifts and hypochromicity compared to the optical absorption spectrum of DNA-free cationic porphyrins. m-trans-BMPyP-DNA presented the largest red shifts and hypochromicity. The results of the circular dichroism spectral analysis indicated positive and negative bisignate absorption bands in the Soret band of the porphyrins in the case of all concentration ratios of o- and p-trans-BMPyP-DNA, and two negative absorption bands were observed in m-trans-BMPyP-DNA. Compared to the size of the absorption band of the DNA optical absorption spectrum, the results of the reduced linear (LDr) spectral analysis indicated mainly small sizes of Soret absorption bands (the absorption spectrum of porphyrins) and positive LDr values for o- and p-trans-BMPyP-DNA. In consideration of several of such spectroscopic properties, the binding of o- and p-trans-BMPyP with DNA can be said to be distant to insertion modes. Although the case of m-trans-BMPyP to DNA is an insertion mode, the m-trans-BMPyP molecular surface presented much tilt within the intercalation pocket. The results of comparing the binding modes of TMPyP having four periphery cationic methylpyridine ions of cationic porphyrin indicated that regardless of the number of periphery cationic methylpyridine ions of cationic porphyrin, in the case of the ortho-position, nonplanarity due to steric hindrance of the periphery cationic methylpyridine ions presented outside or groove-binding modes indicative of interaction with DNA phosphates. Unlike the ortho-position, the para-position presented different binding modes based on the number of periphery cationic methylpyridine ions. Only cationic porphyrins having four periphery cationic methylpyridine ions were inserted into the DNA. Lastly, regardless of the number of periphery cationic methylpyridine ions, all meta-positions were inserted into the DNA. This indicated that at the least the location and the number of periphery cationic methylpyridine ions of the porphyrins used in this experiment were important elements that determine insertion into DNA base pairs.
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Affiliation(s)
- Min Ik Kwak
- Department of Chemistry and College of Basic Education, Yeungnam University, Dae-dong, Gyeongsan City, Gyeong-buk 38541, Republic of Korea
| | - Bo Ram Jeon
- Department of Chemistry and College of Basic Education, Yeungnam University, Dae-dong, Gyeongsan City, Gyeong-buk 38541, Republic of Korea
| | - Seog K Kim
- Department of Chemistry and College of Basic Education, Yeungnam University, Dae-dong, Gyeongsan City, Gyeong-buk 38541, Republic of Korea
| | - Yoon Jung Jang
- Department of Chemistry and College of Basic Education, Yeungnam University, Dae-dong, Gyeongsan City, Gyeong-buk 38541, Republic of Korea
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20
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Shchepinova MM, Cairns AG, Prime TA, Logan A, James AM, Hall AR, Vidoni S, Arndt S, Caldwell ST, Prag HA, Pell VR, Krieg T, Mulvey JF, Yadav P, Cobley JN, Bright TP, Senn HM, Anderson RF, Murphy MP, Hartley RC. MitoNeoD: A Mitochondria-Targeted Superoxide Probe. Cell Chem Biol 2017; 24:1285-1298.e12. [PMID: 28890317 PMCID: PMC6278870 DOI: 10.1016/j.chembiol.2017.08.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 06/06/2017] [Accepted: 08/01/2017] [Indexed: 12/29/2022]
Abstract
Mitochondrial superoxide (O2⋅-) underlies much oxidative damage and redox signaling. Fluorescent probes can detect O2⋅-, but are of limited applicability in vivo, while in cells their usefulness is constrained by side reactions and DNA intercalation. To overcome these limitations, we developed a dual-purpose mitochondrial O2⋅- probe, MitoNeoD, which can assess O2⋅- changes in vivo by mass spectrometry and in vitro by fluorescence. MitoNeoD comprises a O2⋅--sensitive reduced phenanthridinium moiety modified to prevent DNA intercalation, as well as a carbon-deuterium bond to enhance its selectivity for O2⋅- over non-specific oxidation, and a triphenylphosphonium lipophilic cation moiety leading to the rapid accumulation within mitochondria. We demonstrated that MitoNeoD was a versatile and robust probe to assess changes in mitochondrial O2⋅- from isolated mitochondria to animal models, thus offering a way to examine the many roles of mitochondrial O2⋅- production in health and disease.
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Affiliation(s)
| | - Andrew G Cairns
- WestCHEM School of Chemistry, University of Glasgow, Glasgow G12 8QQ, UK
| | - Tracy A Prime
- MRC Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Angela Logan
- MRC Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Andrew M James
- MRC Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Andrew R Hall
- MRC Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Sara Vidoni
- MRC Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Sabine Arndt
- MRC Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Stuart T Caldwell
- WestCHEM School of Chemistry, University of Glasgow, Glasgow G12 8QQ, UK
| | - Hiran A Prag
- MRC Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Victoria R Pell
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - Thomas Krieg
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - John F Mulvey
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - Pooja Yadav
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - James N Cobley
- Division of Sport and Exercise Sciences, Abertay University, Dundee DD1 1HG, UK
| | - Thomas P Bright
- MRC Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Hans M Senn
- WestCHEM School of Chemistry, University of Glasgow, Glasgow G12 8QQ, UK
| | - Robert F Anderson
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Michael P Murphy
- MRC Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK.
| | - Richard C Hartley
- WestCHEM School of Chemistry, University of Glasgow, Glasgow G12 8QQ, UK.
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21
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Saftić D, Radić Stojković M, Žinić B, Glavaš-Obrovac L, Jukić M, Piantanida I, Tumir LM. Impact of linker between triazolyluracil and phenanthridine on recognition of DNA and RNA. Recognition of uracil-containing RNA. NEW J CHEM 2017. [DOI: 10.1039/c7nj02699d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A phenanthridine-triazolyluracilyl multifunctional ligand, linked by a lysine–glycine peptide, binds to poly rA–poly rU with micromolar affinity and selective fluorescence response.
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Affiliation(s)
- Dijana Saftić
- Laboratory for Biomolecular Interactions and Spectroscopy
- Division of Organic Chemistry & Biochemistry
- Ruđer Bošković Institute
- P.O.B. 180
- HR 10002 Zagreb
| | - Marijana Radić Stojković
- Laboratory for Biomolecular Interactions and Spectroscopy
- Division of Organic Chemistry & Biochemistry
- Ruđer Bošković Institute
- P.O.B. 180
- HR 10002 Zagreb
| | - Biserka Žinić
- Laboratory for Biomolecular Interactions and Spectroscopy
- Division of Organic Chemistry & Biochemistry
- Ruđer Bošković Institute
- P.O.B. 180
- HR 10002 Zagreb
| | - Ljubica Glavaš-Obrovac
- Department of Medicinal Chemistry and Biochemistry
- School of Medicine Osijek
- 31000 Osijek
- Croatia
| | - Marijana Jukić
- Department of Medicinal Chemistry and Biochemistry
- School of Medicine Osijek
- 31000 Osijek
- Croatia
| | - Ivo Piantanida
- Laboratory for Biomolecular Interactions and Spectroscopy
- Division of Organic Chemistry & Biochemistry
- Ruđer Bošković Institute
- P.O.B. 180
- HR 10002 Zagreb
| | - Lidija-Marija Tumir
- Laboratory for Biomolecular Interactions and Spectroscopy
- Division of Organic Chemistry & Biochemistry
- Ruđer Bošković Institute
- P.O.B. 180
- HR 10002 Zagreb
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23
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Tumir LM, Radić Stojković M, Piantanida I. Come-back of phenanthridine and phenanthridinium derivatives in the 21st century. Beilstein J Org Chem 2014; 10:2930-54. [PMID: 25550761 PMCID: PMC4273281 DOI: 10.3762/bjoc.10.312] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 11/21/2014] [Indexed: 12/23/2022] Open
Abstract
Phenanthridine derivatives are one of the most intensively studied families of biologically active compounds with efficient DNA binding capability. Attracting attention since DNA structure discovery (1960s), they were early recognized as a symbol of DNA intercalative binding, for many decades applied as gold-standard DNA- and RNA-fluorescent markers (ethidium bromide), probes for cell viability (propidium iodide), but also “ill-famed” for various toxic (genotoxic) and mutagenic effects. After two decades of low interest, the discovery of phenanthridine alkaloids and new studies of antiparasitic/antitumor properties of phenanthridine derivatives resulted in the strong increase of the scientific interest about the turn of this century. Here are summarized phenanthridine-related advances in the 21st century (2000-present period) with emphasis on the supramolecular interactions and bioorganic chemistry, as well as novel or improved synthetic approaches.
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Affiliation(s)
- Lidija-Marija Tumir
- Laboratory for Study of Interactions of Biomacromolecules, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, PO Box 180, HR-10002 Zagreb, Croatia
| | - Marijana Radić Stojković
- Laboratory for Study of Interactions of Biomacromolecules, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, PO Box 180, HR-10002 Zagreb, Croatia
| | - Ivo Piantanida
- Laboratory for Study of Interactions of Biomacromolecules, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, PO Box 180, HR-10002 Zagreb, Croatia
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Cairns AG, Senn HM, Murphy MP, Hartley RC. Expanding the palette of phenanthridinium cations. Chemistry 2014; 20:3742-51. [PMID: 24677631 PMCID: PMC4164275 DOI: 10.1002/chem.201304241] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 01/03/2014] [Indexed: 01/01/2023]
Abstract
5,6-Disubstituted phenanthridinium cations have a range of redox, fluorescence and biological properties. Some properties rely on phenanthridiniums intercalating into DNA, but the use of these cations as exomarkers for the reactive oxygen species (ROS), superoxide, and as inhibitors of acetylcholine esterase (AChE) do not require intercalation. A versatile modular synthesis of 5,6-disubstituted phenanthridiniums that introduces diversity by Suzuki–Miyaura coupling, imine formation and microwave-assisted cyclisation is presented. Computational modelling at the density functional theory (DFT) level reveals that the novel displacement of the aryl halide by an acyclic N-alkylimine proceeds by an S(N)Ar mechanism rather than electrocyclisation. It is found that the displacement of halide is concerted and there is no stable Meisenheimer intermediate, provided the calculations consistently use a polarisable solvent model and a diffuse basis set.
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Affiliation(s)
- Andrew G Cairns
- WestCHEM School of Chemistry, University of GlasgowGlasgow, G12 8QQ (UK) E-mail:
| | - Hans Martin Senn
- WestCHEM School of Chemistry, University of GlasgowGlasgow, G12 8QQ (UK) E-mail:
| | - Michael P Murphy
- MRC Mitochondrial Biology Unit, Wellcome Trust/MRC BuildingCambridge, CB2 0XY (UK)
| | - Richard C Hartley
- WestCHEM School of Chemistry, University of GlasgowGlasgow, G12 8QQ (UK) E-mail:
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Sánchez MI, Penas C, Vázquez ME, Mascareñas JL. Metal-catalyzed uncaging of DNA-binding agents in living cells†Electronic supplementary information (ESI) available: Synthesis and characterization of the studied molecules and required precursors. NMR, UV, and fluorescence spectra, titrations, control experiments, and detailed procedures for cell uptake and co-staining experiments. See DOI: 10.1039/c3sc53317dClick here for additional data file. Chem Sci 2014; 5:1901-1907. [PMID: 25632343 PMCID: PMC4304260 DOI: 10.1039/c3sc53317d] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 01/30/2014] [Indexed: 12/27/2022] Open
Abstract
Ruthenium-catalyzed activation of DNA-binding compounds in aqueous buffers and in cellular environments.
Attachment of alloc protecting groups to the amidine units of fluorogenic DNA-binding bisbenzamidines or to the amino groups of ethidium bromide leads to a significant reduction of their DNA affinity. More importantly, the active DNA-binding species can be readily regenerated by treatment with ruthenium catalysts in aqueous conditions, even in cell cultures. The catalytic chemical uncaging can be easily monitored by fluorescence microscopy, because the protected products display both different emission properties and cell distribution to the parent compounds.
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Affiliation(s)
- Mateo I Sánchez
- Departamento de Química Orgánica e Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS) , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain . ; Tel: +34 881 81 44 05
| | - Cristina Penas
- Departamento de Química Orgánica e Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS) , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain . ; Tel: +34 881 81 44 05
| | - M Eugenio Vázquez
- Departamento de Química Orgánica e Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS) , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain . ; Tel: +34 881 81 44 05
| | - José L Mascareñas
- Departamento de Química Orgánica e Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS) , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain . ; Tel: +34 881 81 44 05
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Grabar Branilović M, Tomić S, Tumir LM, Piantanida I. The bis-phenanthridinium system flexibility and position of covalently bound uracil finely tunes the interaction with polynucleotides. MOLECULAR BIOSYSTEMS 2013; 9:2051-62. [PMID: 23681361 DOI: 10.1039/c3mb25578f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of structurally similar bis-phenanthridinium derivatives, some with uracil at different positions, revealed different interactions with various polynucleotides. The uniform binding of mononucleotides to all studied compounds by "cyclobisintercaland" binding type indicated that compound-polynucleotide interaction selectivity was the consequence of polynucleotide secondary structure and not direct nucleobase recognition. Although affinity and fluorimetric response of all studied compounds toward ds-DNA/RNA was similar, the thermal denaturation and ICD signal-based sensing was highly sensitive to polynucleotide basepair composition and secondary structure. In particular, for the specific poly rAH(+)-poly rAH(+) double helix MD parameters are newly developed and used for analysis of its complexes. The highly sensitive orientation of phenanthridinium as well as the role of the uracil substituent, both binding interactions finely tuned by the steric and binding properties of the DNA/RNA-ligand interaction site, offer novel structural information about binding and steric properties of particular DNA-RNA systems.
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Affiliation(s)
- Marina Grabar Branilović
- Laboratory for Chemical and Biological Crystallography, Division of Physical Chemistry, Ruđer Bošković Institute, HR 10002 Zagreb, P.O.B. 180, Croatia.
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Phukan S, Mitra S. Fluorescence behavior of ethidium bromide in homogeneous solvents and in presence of bile acid hosts. J Photochem Photobiol A Chem 2012. [DOI: 10.1016/j.jphotochem.2012.06.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Osadchii SA, Shubin VG, Kozlova LP, Varlamenko VS, Filipenko ML, Boyarskikh UA. Improvement of ways to obtain ethidium bromide and synthesis of ethidium ethyl sulfate, a new fluorescent dye for detection of nucleic acids. RUSS J APPL CHEM+ 2011. [DOI: 10.1134/s107042721109014x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Rounds CM, Lubeck E, Hepler PK, Winship LJ. Propidium iodide competes with Ca(2+) to label pectin in pollen tubes and Arabidopsis root hairs. PLANT PHYSIOLOGY 2011; 157:175-87. [PMID: 21768649 PMCID: PMC3165868 DOI: 10.1104/pp.111.182196] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 07/14/2011] [Indexed: 05/02/2023]
Abstract
We have used propidium iodide (PI) to investigate the dynamic properties of the primary cell wall at the apex of Arabidopsis (Arabidopsis thaliana) root hairs and pollen tubes and in lily (Lilium formosanum) pollen tubes. Our results show that in root hairs, as in pollen tubes, oscillatory peaks in PI fluorescence precede growth rate oscillations. Pectin forms the primary component of the cell wall at the tip of both root hairs and pollen tubes. Given the electronic structure of PI, we investigated whether PI binds to pectins in a manner analogous to Ca(2+) binding. We first show that Ca(2+) is able to abrogate PI growth inhibition in a dose-dependent manner. PI fluorescence itself also relies directly on the amount of Ca(2+) in the growth solution. Exogenous pectin methyl esterase treatment of pollen tubes, which demethoxylates pectins, freeing more Ca(2+)-binding sites, leads to a dramatic increase in PI fluorescence. Treatment with pectinase leads to a corresponding decrease in fluorescence. These results are consistent with the hypothesis that PI binds to demethoxylated pectins. Unlike other pectin stains, PI at low yet useful concentration is vital and specifically does not alter the tip-focused Ca(2+) gradient or growth oscillations. These data suggest that pectin secretion at the apex of tip-growing plant cells plays a critical role in regulating growth, and PI represents an excellent tool for examining the role of pectin and of Ca(2+) in tip growth.
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Affiliation(s)
| | | | - Peter K. Hepler
- Department of Biology, University of Massachusetts, Amherst, Massachusetts 01003 (C.M.R., P.K.H.); School of Natural Science, Hampshire College, Amherst, Massachusetts 01002 (E.L., L.J.W.)
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Radić Stojković M, Miljanić S, Mišković K, Glavaš-Obrovac L, Piantanida I. The phenanthridine biguanides efficiently differentiate between dGdC, dAdT and rArU sequences by two independent, sensitive spectroscopic methods. MOLECULAR BIOSYSTEMS 2011; 7:1753-65. [DOI: 10.1039/c1mb05030c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Dukši M, Baretić D, Čaplar V, Piantanida I. Novel bis-phenanthridine derivatives with easily tunable linkers, study of their interactions with DNA and screening of antiproliferative activity. Eur J Med Chem 2010; 45:2671-6. [DOI: 10.1016/j.ejmech.2010.02.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Revised: 12/28/2009] [Accepted: 02/04/2010] [Indexed: 10/19/2022]
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Zielonka J, Kalyanaraman B. Hydroethidine- and MitoSOX-derived red fluorescence is not a reliable indicator of intracellular superoxide formation: another inconvenient truth. Free Radic Biol Med 2010; 48:983-1001. [PMID: 20116425 PMCID: PMC3587154 DOI: 10.1016/j.freeradbiomed.2010.01.028] [Citation(s) in RCA: 393] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Revised: 01/20/2010] [Accepted: 01/21/2010] [Indexed: 12/15/2022]
Abstract
Hydroethidine (HE; or dihydroethidium) is the most popular fluorogenic probe used for detecting intracellular superoxide radical anion. The reaction between superoxide and HE generates a highly specific red fluorescent product, 2-hydroxyethidium (2-OH-E(+)). In biological systems, another red fluorescent product, ethidium, is also formed, usually at a much higher concentration than 2-OH-E(+). In this article, we review the methods to selectively detect the superoxide-specific product (2-OH-E(+)) and the factors affecting its levels in cellular and biological systems. The most important conclusion of this review is that it is nearly impossible to assess the intracellular levels of the superoxide-specific product, 2-OH-E(+), using confocal microscopy or other fluorescence-based microscopic assays and that it is essential to measure by HPLC the intracellular HE and other oxidation products of HE, in addition to 2-OH-E(+), to fully understand the origin of red fluorescence. The chemical reactivity of mitochondria-targeted hydroethidine (Mito-HE, MitoSOX red) with superoxide is similar to the reactivity of HE with superoxide, and therefore, all of the limitations attributed to the HE assay are applicable to Mito-HE (or MitoSOX) as well.
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Affiliation(s)
- Jacek Zielonka
- Department of Biophysics and Free Radical Research Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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33
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Monaco RR. Capture of a Transition State Using Molecular Dynamics: Creation of an Intercalation Site in dsDNA with Ethidium Cation. J Nucleic Acids 2010; 2010. [PMID: 20798766 PMCID: PMC2925101 DOI: 10.4061/2010/702317] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Revised: 11/17/2009] [Accepted: 01/28/2010] [Indexed: 11/24/2022] Open
Abstract
The mechanism of intercalation and the ability of double stranded DNA (dsDNA) to accommodate a variety of ligands in this manner has been well studied. Proposed mechanistic steps along this pathway for the classical intercalator ethidium have been discussed in the literature. Some previous studies indicate that the creation of an intercalation site may occur spontaneously, with the energy for this interaction arising either from solvent collisions or soliton propagation along the helical axis. A subsequent 1D diffusional search by the ligand along the helical axis of the DNA will allow the ligand entry to this intercalation site from its external, electrostatically stabilized position. Other mechanistic studies show that ethidium cation participates in the creation of the site, as a ligand interacting closely with the external surface of the DNA can cause unfavorable steric interactions depending on the ligands' orientation, which are relaxed during the creation of an intercalation site. Briefly, such a site is created by the lengthening of the DNA molecule via bond rotation between the sugars and phosphates along the DNA backbone, causing an unwinding of the dsDNA itself and separation between the adjacent base pairs local to the position of the ligand, which becomes the intercalation site. Previous experimental measurements of this interaction measure the enthalpic cost of this part of the mechanism to be about −8 kcal/mol. This paper reports the observation, during a computational study, of the spontaneous opening of an intercalation site in response to the presence of a single ethidium cation molecule in an externally bound configuration. The concerted motions between this ligand and the host, a dsDNA decamer, are clear. The dsDNA decamer AGGATGCCTG was studied; the central …GATG… site was the intercalation site.
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Affiliation(s)
- Regina R Monaco
- Department of Environmental Chemistry, Mailman School of Public Health, Columbia University, New York NY, 10032, USA
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34
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Prunkl C, Pichlmaier M, Winter R, Kharlanov V, Rettig W, Wagenknecht HA. Optical, Redox, and DNA-Binding Properties of Phenanthridinium Chromophores: Elucidating the Role of the Phenyl Substituent for Fluorescence Enhancement of Ethidium in the Presence of DNA. Chemistry 2010; 16:3392-402. [DOI: 10.1002/chem.200902823] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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35
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Neto BAD, Lapis AAM, Mancilha FS, Batista Jr. EL, Netz PA, Rominger F, Basso LA, Santos DS, Dupont J. On the selective detection of duplex deoxyribonucleic acids by 2,1,3-benzothiadiazole fluorophores. MOLECULAR BIOSYSTEMS 2010; 6:967-75. [DOI: 10.1039/b919155k] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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36
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de la Loza MCD, Wellinger RE. A novel approach for organelle-specific DNA damage targeting reveals different susceptibility of mitochondrial DNA to the anticancer drugs camptothecin and topotecan. Nucleic Acids Res 2009; 37:e26. [PMID: 19151088 PMCID: PMC2651790 DOI: 10.1093/nar/gkn1087] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
DNA is susceptible of being damaged by chemicals, UV light or gamma irradiation. Nuclear DNA damage invokes both a checkpoint and a repair response. By contrast, little is known about the cellular response to mitochondrial DNA damage. We designed an experimental system that allows organelle-specific DNA damage targeting in Saccharomyces cerevisiae. DNA damage is mediated by a toxic topoisomerase I allele which leads to the formation of persistent DNA single-strand breaks. We show that organelle-specific targeting of a toxic topoisomerase I to either the nucleus or mitochondria leads to nuclear DNA damage and cell death or to loss of mitochondrial DNA and formation of respiration-deficient ‘petite’ cells, respectively. In wild-type cells, toxic topoisomerase I–DNA intermediates are formed as a consequence of topoisomerase I interaction with camptothecin-based anticancer drugs. We reasoned that targeting of topoisomerase I to the mitochondria of top1Δ cells should lead to petite formation in the presence of camptothecin. Interestingly, camptothecin failed to generate petite; however, its derivative topotecan accumulates in mitochondria and induces petite formation. Our findings demonstrate that drug modifications can lead to organelle-specific DNA damage and thus opens new perspectives on the role of mitochondrial DNA-damage in cancer treatment.
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Affiliation(s)
- M C Díaz de la Loza
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla - CSIC, Avda, Américo Vespucio s/n, 41092, Sevilla, Spain
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Martino L, Virno A, Pagano B, Virgilio A, Di Micco S, Galeone A, Giancola C, Bifulco G, Mayol L, Randazzo A. Structural and Thermodynamic Studies of the Interaction of Distamycin A with the Parallel Quadruplex Structure [d(TGGGGT)]4. J Am Chem Soc 2007; 129:16048-56. [DOI: 10.1021/ja075710k] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Luigi Martino
- Contribution from the Dipartimento di Chimica “P. Corradini”, Università degli Studi di Napoli “Federico II”, via Cintia, I-80126, Napoli, Italy, Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli “Federico II”, via D. Montesano 49, I-80131 Napoli, Italy, and Dipartimento di Scienze Farmaceutiche, Università di Salerno, via Ponte Don Melillo, 84084, Fisciano (SA), Italy
| | - Ada Virno
- Contribution from the Dipartimento di Chimica “P. Corradini”, Università degli Studi di Napoli “Federico II”, via Cintia, I-80126, Napoli, Italy, Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli “Federico II”, via D. Montesano 49, I-80131 Napoli, Italy, and Dipartimento di Scienze Farmaceutiche, Università di Salerno, via Ponte Don Melillo, 84084, Fisciano (SA), Italy
| | - Bruno Pagano
- Contribution from the Dipartimento di Chimica “P. Corradini”, Università degli Studi di Napoli “Federico II”, via Cintia, I-80126, Napoli, Italy, Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli “Federico II”, via D. Montesano 49, I-80131 Napoli, Italy, and Dipartimento di Scienze Farmaceutiche, Università di Salerno, via Ponte Don Melillo, 84084, Fisciano (SA), Italy
| | - Antonella Virgilio
- Contribution from the Dipartimento di Chimica “P. Corradini”, Università degli Studi di Napoli “Federico II”, via Cintia, I-80126, Napoli, Italy, Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli “Federico II”, via D. Montesano 49, I-80131 Napoli, Italy, and Dipartimento di Scienze Farmaceutiche, Università di Salerno, via Ponte Don Melillo, 84084, Fisciano (SA), Italy
| | - Simone Di Micco
- Contribution from the Dipartimento di Chimica “P. Corradini”, Università degli Studi di Napoli “Federico II”, via Cintia, I-80126, Napoli, Italy, Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli “Federico II”, via D. Montesano 49, I-80131 Napoli, Italy, and Dipartimento di Scienze Farmaceutiche, Università di Salerno, via Ponte Don Melillo, 84084, Fisciano (SA), Italy
| | - Aldo Galeone
- Contribution from the Dipartimento di Chimica “P. Corradini”, Università degli Studi di Napoli “Federico II”, via Cintia, I-80126, Napoli, Italy, Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli “Federico II”, via D. Montesano 49, I-80131 Napoli, Italy, and Dipartimento di Scienze Farmaceutiche, Università di Salerno, via Ponte Don Melillo, 84084, Fisciano (SA), Italy
| | - Concetta Giancola
- Contribution from the Dipartimento di Chimica “P. Corradini”, Università degli Studi di Napoli “Federico II”, via Cintia, I-80126, Napoli, Italy, Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli “Federico II”, via D. Montesano 49, I-80131 Napoli, Italy, and Dipartimento di Scienze Farmaceutiche, Università di Salerno, via Ponte Don Melillo, 84084, Fisciano (SA), Italy
| | - Giuseppe Bifulco
- Contribution from the Dipartimento di Chimica “P. Corradini”, Università degli Studi di Napoli “Federico II”, via Cintia, I-80126, Napoli, Italy, Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli “Federico II”, via D. Montesano 49, I-80131 Napoli, Italy, and Dipartimento di Scienze Farmaceutiche, Università di Salerno, via Ponte Don Melillo, 84084, Fisciano (SA), Italy
| | - Luciano Mayol
- Contribution from the Dipartimento di Chimica “P. Corradini”, Università degli Studi di Napoli “Federico II”, via Cintia, I-80126, Napoli, Italy, Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli “Federico II”, via D. Montesano 49, I-80131 Napoli, Italy, and Dipartimento di Scienze Farmaceutiche, Università di Salerno, via Ponte Don Melillo, 84084, Fisciano (SA), Italy
| | - Antonio Randazzo
- Contribution from the Dipartimento di Chimica “P. Corradini”, Università degli Studi di Napoli “Federico II”, via Cintia, I-80126, Napoli, Italy, Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli “Federico II”, via D. Montesano 49, I-80131 Napoli, Italy, and Dipartimento di Scienze Farmaceutiche, Università di Salerno, via Ponte Don Melillo, 84084, Fisciano (SA), Italy
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Abstract
A stably-bound external binding site for ethidium cation in the major groove of B-form DNA is proposed. This complex is stabilized by hydrogen bonding between this ligand and the nucleophilic centers O6 and N7 of guanine, both of which are accessible via the major groove. This binding site is not the same as the well-characterized electrostatically-stabilized external binding site, but rather is seen to be a covalently bound complex which is stabilized by two hydrogen bonds between the ethidium ligand and guanine in the double stranded (ds) B-form DNA. This site [(1), R. Monaco, F. Hasheer. J Biomol Struct Dyn 10, 675 (1993)] can only exist at very low occupancy ratios. The existence of this binding site leads directly to the expectation that there will exist particular mechanistic steps along the pathway of interaction between ethidium and ds B-DNA at low and high ligand concentrations that involve this binding mode. This would not only explain observations published recently [for example, see (2-6), W. Wilson, I. Lopp. Biopolymers 18, 3025 (1979); L. Wakelin, M. Waring. J Mol Biol 144, 183-214 (1980); A. Karpetyan, N. Mehrabian, G. Terzikian, A. Antonian, P. Vardevanian, M. Frank-Kamenetshii. Proceedings of the 10th Conversation, SUNY Albany, 275 (1998); P. Vardevanyan, A. Antonyan, G. Manukyan, A. Karapetyan. Experimental and Molecular Medicine 33, 205 (2001); P. Vardevanyan, A. Antonyan, L. Minasbekan, A. Karapetyan. Proceedings of the 2002 Miami Nature Biotechnology Winter Symposium, 2(S1), 144 (2002)] but also give insight into discrepancies reported in the literature over the years by different workers studying the mechanism of interaction between ethidium and DNA. In this paper this novel binding interaction is discussed, and it is shown how the elucidation of this interaction led to the proposal of two distinct mechanisms of intercalation between ds B-DNA and ethidium cation for high and low concentrations of ligand. Modeling studies show the stability, configuration, and relative energies of this outside binding site. It is expected that this externally bound complex between ethidium cation and ds B-form DNA will be experimentally detectable using fluorescent polarization and/or linear and circular dichroism spectroscopic studies [(7, 8) E. Tuite, U. Sehlstedt, P. Hagmar, B. Norden, M. Takahashi. Euro J Biochem 243, 482-492 (1997); T. Hard. Biopolymers 26, 613-618 (1987)].
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Affiliation(s)
- R R Monaco
- Department of Environmental Chemistry, Mailman School of Public Health, Columbia University, New York, NY 10032, USA.
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Basting D, Lorch M, Lehner I, Glaubitz C. Transport cycle intermediate in small multidrug resistance protein is revealed by substrate fluorescence. FASEB J 2007; 22:365-73. [PMID: 17873100 DOI: 10.1096/fj.07-9162com] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Efflux pumps of the small multidrug resistance family bind cationic, lipophilic antibiotics and transport them across the membrane in exchange for protons. The transport cycle must involve various conformational states of the protein needed for substrate binding, translocation, and release. A fluorescent substrate will therefore experience a significant change of environment while being transported, which influences its fluorescence properties. Thus the substrate itself can report intermediate states that form during the transport cycle. We show the existence of such a substrate-transporter complex for the EmrE homolog Mycobacterium tuberculosis TBsmr and its substrate ethidium bromide. The pH gradient needed for antiport has been generated by co-reconstituting TBsmr with bacteriorhodopsin. Sample illumination generates a DeltapH, which results in enhanced ethidium fluorescence intensity, which is abolished when DeltapH or DeltaPsi is collapsed or when the essential residue Glu-13 in TBsmr is exchanged with Ala. This observation shows the formation of a pH-dependent, transient substrate-protein complex between binding and release of ethidium. We have further characterized this state by determining the K(d), by inhibiting ethidium transport through titration with nonfluorescent substrate and by fluorescence anisotropy measurements. Our findings support a model with a single occluded intermediate state in which the substrate is highly immobile.
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Affiliation(s)
- Daniel Basting
- Intitut für Biophysikalische Chemie, J. W. Goethe Universität, Max von Laue Str. 9, 60438 Frankfurt, Germany
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41
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Neto BAD, Lapis AAM, Mancilha FS, Vasconcelos IB, Thum C, Basso LA, Santos DS, Dupont J. New Sensitive Fluorophores for Selective DNA Detection. Org Lett 2007; 9:4001-4. [PMID: 17784767 DOI: 10.1021/ol701708y] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
4,7-Disubstituted benzothiadiazoles containing 1-arylethynyl and 4-methoxyphenyl groups are selective photoluminescent "light up" probes to duplex DNA with unprecedented sensibility in both spectrophotometric and spectrofluorimetric measurements.
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Affiliation(s)
- Brenno A D Neto
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Tecnopuc, PUC-RS, Brazil.
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42
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El-Shishtawy RM, Santos CR, Gonçalves I, Marcelino H, Almeida P. New amino and acetamido monomethine cyanine dyes for the detection of DNA in agarose gels. Bioorg Med Chem 2007; 15:5537-42. [PMID: 17553684 DOI: 10.1016/j.bmc.2007.05.043] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2006] [Revised: 05/11/2007] [Accepted: 05/18/2007] [Indexed: 11/17/2022]
Abstract
Some new monomethine cyanine dyes derived from quinoline and benzothiazole have been prepared and characterized by (1)H and (13)C NMR, FTIR, FABHRMS, and visible spectroscopy. The dyes containing amino and acetamido groups were conveniently synthesized by the condensation of two p-toluenesulfonate heterocyclic quaternary salts and were obtained in the forms of iodide, bromide, and tosylate counteranions. These dyes were compared to ethidium bromide as stains for DNA in electrophoretic gels. The overall results obtained for the sensitivity of these dyes suggest the suitability of acetamido moiety over the amine one and bromide as the counteranion when compared with iodide and tosylate, with a similar capacity of DNA detection in relation to the ethidium bromide stain over the concentration range of 1-3ng.
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Affiliation(s)
- Reda M El-Shishtawy
- Departamento de Química e Unidade de I&D de Materiais Têxteis e Papeleiros, Universidade da Beira Interior, 6201-001 Covilhã, Portugal
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43
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Kubar T, Hanus M, Ryjácek F, Hobza P. Binding of cationic and neutral phenanthridine intercalators to a DNA oligomer is controlled by dispersion energy: quantum chemical calculations and molecular mechanics simulations. Chemistry 2007; 12:280-90. [PMID: 16294358 DOI: 10.1002/chem.200500725] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Correlated ab initio as well as semiempirical quantum chemical calculations and molecular dynamics simulations were used to study the intercalation of cationic ethidium, cationic 5-ethyl-6-phenylphenanthridinium and uncharged 3,8-diamino-6-phenylphenanthridine to DNA. The stabilization energy of the cationic intercalators is considerably larger than that of the uncharged one. The dominant energy contribution with all intercalators is represented by dispersion energy. In the case of the cationic intercalators, the electrostatic and charge-transfer terms are also important. The DeltaG of ethidium intercalation to DNA was estimated at -4.5 kcal mol(-1) and this value agrees well with the experimental result. Of six contributions to the final free energy, the interaction energy value is crucial. The intercalation process is governed by the non-covalent stacking (including charge-transfer) interaction while the hydrogen bonding between the ethidium amino groups and the DNA backbone is less important. This is confirmed by the evaluation of the interaction energy as well as by the calculation of the free energy change. The intercalation affects the macroscopic properties of DNA in terms of its flexibility. This explains the easier entry of another intercalator molecule in the vicinity of an existing intercalation site.
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Affiliation(s)
- Tomás Kubar
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
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Granzhan A, Ihmels H, Viola G. 9-Donor-Substituted Acridizinium Salts: Versatile Environment-Sensitive Fluorophores for the Detection of Biomacromolecules. J Am Chem Soc 2007; 129:1254-67. [PMID: 17263409 DOI: 10.1021/ja0668872] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The absorption and steady-state emission properties of a series of N-alkyl- and N-aryl-9-aminoacridizinium derivatives and two 9-sulfanyl-substituted acridizinium derivatives were investigated. The N-alkyl derivatives and the 9-methylsulfanylacridizinium have an intense intrinsic fluorescence (phi(f) = 0.2-0.6), whereas the N-aryl-substituted compounds are virtually nonfluorescent in liquid solutions (phi(f) < or = 0.01). The emission intensity of the latter compounds significantly increases with increasing viscosity of the medium. It is demonstrated that the excited-state deactivation of the N-aryl-9-aminoacridizinium derivatives is due to two nonradiative processes: (i) torsional relaxation by rotation about the N-aryl bond and (ii) an electron-transfer process from an electron-donor substituted phenyl ring to the photoexcited acridizinium chromophore. The binding of several representative acridizinium derivatives to double-stranded DNA was studied by the spectrophotometric titrations and linear dichroism spectroscopy. The results give evidence that the prevailing binding mode is intercalation with binding constants in the range (0.5-5.0) x 10(5) M(-1) (in base pairs). Notably, the binding of most of the N-aryl-9-aminoacridizinium derivatives leads to a fluorescence enhancement by a factor of up to 50 upon binding to the biomacromolecules. Moreover, the addition of selected proteins, namely albumins, to N-(halogenophenyl)-9-aminoacridizinium ions in the presence of an anionic surfactant (sodium dodecyl sulfate) results in a 20-fold fluorescence enhancement. In each case, the emission enhancement is supposed to result from the hindrance of the torsional relaxation in the corresponding binding site of the biomacromolecule, which in turn suppresses the excited-state deactivation pathway.
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Affiliation(s)
- Anton Granzhan
- University of Siegen, Organic Chemistry II, Adolf-Reichwein-Strasse 2, D-57068 Siegen, Germany
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45
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Piantanida I, Žinić M, Marczi S, Glavaš-Obrovac L. Bis-4,9-diazapyrenium dications: synthesis of the methylenedibenzyl-analogue, interactions with nucleotides, DNA, RNA. The antitumour activity of all till now prepared analogues. J PHYS ORG CHEM 2007. [DOI: 10.1002/poc.1165] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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46
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Robinson KM, Janes MS, Pehar M, Monette JS, Ross MF, Hagen TM, Murphy MP, Beckman JS. Selective fluorescent imaging of superoxide in vivo using ethidium-based probes. Proc Natl Acad Sci U S A 2006; 103:15038-43. [PMID: 17015830 PMCID: PMC1586181 DOI: 10.1073/pnas.0601945103] [Citation(s) in RCA: 618] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The putative oxidation of hydroethidine (HE) has become a widely used fluorescent assay for the detection of superoxide in cultured cells. By covalently joining HE to a hexyl triphenylphosphonium cation (Mito-HE), the HE moiety can be targeted to mitochondria. However, the specificity of HE and Mito-HE for superoxide in vivo is limited by autooxidation as well as by nonsuperoxide-dependent cellular processes that can oxidize HE probes to ethidium (Etd). Recently, superoxide was shown to react with HE to generate 2-hydroxyethidium [Zhao, H., Kalivendi, S., Zhang, H., Joseph, J., Nithipatikom, K., Vasquez-Vivar, J. & Kalyanaraman, B. (2003) Free Radic. Biol. Med. 34, 1359-1368]. However, 2-hydroxyethidium is difficult to distinguish from Etd by conventional fluorescence techniques exciting at 510 nm. While investigating the oxidation of Mito-HE by superoxide, we found that the superoxide product of both HE and Mito-HE could be selectively excited at 396 nm with minimal interference from other nonspecific oxidation products. The oxidation of Mito-HE monitored at 396 nm by antimycin-stimulated mitochondria was 30% slower than at 510 nm, indicating that superoxide production may be overestimated at 510 nm by even a traditional superoxide-stimulating mitochondrial inhibitor. The rate-limiting step for oxidation by superoxide was 4x10(6) M-1.s-1, which is proposed to involve the formation of a radical from Mito-HE. The rapid reaction with a second superoxide anion through radical-radical coupling may explain how Mito-HE and HE can compete for superoxide in vivo with intracellular superoxide dismutases. Monitoring oxidation at both 396 and 510 nm of excitation wavelengths can facilitate the more selective detection of superoxide in vivo.
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Affiliation(s)
- Kristine M. Robinson
- *Linus Pauling Institute, Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331
| | - Michael S. Janes
- *Linus Pauling Institute, Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331
- Invitrogen–Molecular Probes Labeling and Detection Technologies, Eugene, OR 97402
| | - Mariana Pehar
- Departamento de Neurobiología Celular, Instituto de Investigaciones Biológicas Clemente Estable, Av. Italia 3318, 11600 Montevideo, Uruguay
| | - Jeffrey S. Monette
- *Linus Pauling Institute, Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331
| | - Meredith F. Ross
- Medical Research Council, Dunn Human Nutrition Unit, Hills Road, Cambridge CB2 2XY, United Kingdom; and
| | - Tory M. Hagen
- *Linus Pauling Institute, Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331
| | - Michael P. Murphy
- Medical Research Council, Dunn Human Nutrition Unit, Hills Road, Cambridge CB2 2XY, United Kingdom; and
| | - Joseph S. Beckman
- *Linus Pauling Institute, Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331
- To whom correspondence should be addressed. E-mail:
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Di Micco S, Bassarello C, Bifulco G, Riccio R, Gomez-Paloma L. Differential-Frequency Saturation Transfer Difference NMR Spectroscopy Allows the Detection of Different Ligand-DNA Binding Modes. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200501344] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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48
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Tam VK, Liu Q, Tor Y. Extended ethidium bromide analogue as a triple helix intercalator: synthesis, photophysical properties and nucleic acids binding. Chem Commun (Camb) 2006:2684-6. [PMID: 16786087 DOI: 10.1039/b604281c] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ethidium bromide has been extended by fusing an additional aromatic ring resulting in a larger intercalator with increased affinity for poly r(A) x r(U), poly d(A) x d(T) and triple helices when compared to the parent heterocycle.
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Affiliation(s)
- Victor K Tam
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
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49
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Di Micco S, Bassarello C, Bifulco G, Riccio R, Gomez-Paloma L. Differential-Frequency Saturation Transfer Difference NMR Spectroscopy Allows the Detection of Different Ligand-DNA Binding Modes. Angew Chem Int Ed Engl 2006; 45:224-8. [PMID: 16304663 DOI: 10.1002/anie.200501344] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Simone Di Micco
- Dipartimento di Scienze Farmaceutiche, Università di Salerno via Ponte don Melillo, 84084 Fisciano, Salerno, Italy
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