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Carvalho J, Cruz C. Forster resonance energy transfer for studying nucleic acids denaturation: A chemical and biological sciences laboratory experiment. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 48:329-336. [PMID: 32268010 DOI: 10.1002/bmb.21353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 02/25/2020] [Accepted: 03/29/2020] [Indexed: 06/11/2023]
Abstract
The Förster resonance energy transfer (FRET) melting assay intends to evaluate the unfolding, denaturation process of DNA secondary structures, and its stabilization using compounds known as DNA binders, some of which are highly specific for G-quadruplex DNAs versus duplex DNAs. First, students determined the melting temperature (Tm ) of DNA sequences double labeled with 5'-FAM (fluorescein) and 3'-TAMRA (tetramethylrhodamine) in the absence of DNA binders. Second, they determined the melting temperature of the DNAs in the presence of DNA binders by monitoring fluorescence. After completing this experiment, students understood that this method allows a semiquantitative analysis to test a variety of DNA binders against DNA secondary structures, and it can be used to rapidly identify the most promising drug candidates in the drug development stages at the basic research level.
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Affiliation(s)
- Josué Carvalho
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
| | - Carla Cruz
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
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2
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Roy S, Ali A, Kamra M, Muniyappa K, Bhattacharya S. Specific stabilization of promoter G-Quadruplex DNA by 2,6-disubstituted amidoanthracene-9,10-dione based dimeric distamycin analogues and their selective cancer cell cytotoxicity. Eur J Med Chem 2020; 195:112202. [PMID: 32302880 DOI: 10.1016/j.ejmech.2020.112202] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/19/2020] [Accepted: 03/01/2020] [Indexed: 10/24/2022]
Abstract
We have designed and synthesized anthraquinone containing compounds which have oligopyrrole side chains of varying lengths. These compounds stabilized the G-quadruplex DNA formed in the promoter regions of c-MYC oncogenes selectively over the duplex DNA. These observations were recorded using UV-vis spectroscopic titrations, fluorescence measurements and circular dichroism (CD) spectral titrations. The potency of the compounds to stabilize the G4 DNA has been shown from the thermal denaturation experiments. The compound interacts with c-MYC G-quadruplex DNA through stacking mode as obtained from ethidium bromide displacement assay, cyclic voltammetric titration, and docking experiments. Molecular modeling studies suggested that the stacking of the anthraquinone moiety over the G-tetrad of the G4 structures are responsible for the stability of such quadruplex secondary structure. Furthermore, polymerase stop assay also supported the formation of stable G4 structures in the presence of the above-mentioned compounds. The compounds have shown selective cancer cell (HeLa and HEK293T) cytotoxicity over normal cells (NIH3T3 and HDFa) under in vitro conditions as determined from MTT based cell viability assay. Apoptosis was found to be the mechanistic pathway underlying the cancer cell cytotoxicity as obtained from Annexin V-FITC and PI dual staining assay which was further substantiated by nuclear morphological changes as observed by AO/EB dual staining assay. Cellular morphological changes, as well as nuclear condensation and fragmentation upon treatment with these compounds, were observed under bright field and confocal microscopy.
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Affiliation(s)
- Soma Roy
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Asfa Ali
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Mohini Kamra
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Kalappa Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Santanu Bhattacharya
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, India; School of Applied & Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India.
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Kleoff M, Suhr S, Sarkar B, Zimmer R, Reissig H, Marin‐Luna M, Zipse H. Efficient Syntheses of New Super Lewis Basic Tris(dialkylamino)‐Substituted Terpyridines and Comparison of Their Methyl Cation Affinities. Chemistry 2019; 25:7526-7533. [DOI: 10.1002/chem.201900450] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/27/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Merlin Kleoff
- Institut für Chemie und BiochemieFreie Universität Berlin Takustr. 3 14195 Berlin Germany
| | - Simon Suhr
- Institut für Chemie und BiochemieFreie Universität BerlinAnorganische Chemie Fabeckstr. 34–36 14195 Berlin Germany
| | - Biprajit Sarkar
- Institut für Chemie und BiochemieFreie Universität BerlinAnorganische Chemie Fabeckstr. 34–36 14195 Berlin Germany
| | - Reinhold Zimmer
- Institut für Chemie und BiochemieFreie Universität Berlin Takustr. 3 14195 Berlin Germany
| | - Hans‐Ulrich Reissig
- Institut für Chemie und BiochemieFreie Universität Berlin Takustr. 3 14195 Berlin Germany
| | - Marta Marin‐Luna
- Department ChemieLudwig-Maximilians-Universität München Butenandtstr. 5–13 81377 München Germany
| | - Hendrik Zipse
- Department ChemieLudwig-Maximilians-Universität München Butenandtstr. 5–13 81377 München Germany
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Fluorescent light-up acridine orange derivatives bind and stabilize KRAS-22RT G-quadruplex. Biochimie 2018; 144:144-152. [DOI: 10.1016/j.biochi.2017.11.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 11/06/2017] [Indexed: 01/17/2023]
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Klein J, Stuckmann A, Sobottka S, Suntrup L, van der Meer M, Hommes P, Reissig HU, Sarkar B. Ruthenium Complexes with Strongly Electron-Donating Terpyridine Ligands: Effect of the Working Electrode on Electrochemical and Spectroelectrochemical Properties. Chemistry 2017; 23:12314-12325. [DOI: 10.1002/chem.201701431] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Indexed: 01/28/2023]
Affiliation(s)
- Johannes Klein
- Institut für Chemie und Biochemie; Anorganische Chemie; Freie Universität Berlin; Fabeckstraße 34-36 14195 Berlin Germany
| | - Alexandra Stuckmann
- Institut für Chemie und Biochemie; Anorganische Chemie; Freie Universität Berlin; Fabeckstraße 34-36 14195 Berlin Germany
| | - Sebastian Sobottka
- Institut für Chemie und Biochemie; Anorganische Chemie; Freie Universität Berlin; Fabeckstraße 34-36 14195 Berlin Germany
| | - Lisa Suntrup
- Institut für Chemie und Biochemie; Anorganische Chemie; Freie Universität Berlin; Fabeckstraße 34-36 14195 Berlin Germany
| | - Margarethe van der Meer
- Institut für Chemie und Biochemie; Anorganische Chemie; Freie Universität Berlin; Fabeckstraße 34-36 14195 Berlin Germany
| | - Paul Hommes
- Institut für Chemie und Biochemie; Organische Chemie; Freie Universität Berlin; Takustraße 3 14195 Berlin Germany
| | - Hans-Ulrich Reissig
- Institut für Chemie und Biochemie; Organische Chemie; Freie Universität Berlin; Takustraße 3 14195 Berlin Germany
| | - Biprajit Sarkar
- Institut für Chemie und Biochemie; Anorganische Chemie; Freie Universität Berlin; Fabeckstraße 34-36 14195 Berlin Germany
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Aroua S, Todorova TK, Hommes P, Chamoreau LM, Reissig HU, Mougel V, Fontecave M. Synthesis, Characterization, and DFT Analysis of Bis-Terpyridyl-Based Molecular Cobalt Complexes. Inorg Chem 2017; 56:5930-5940. [DOI: 10.1021/acs.inorgchem.7b00595] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Safwan Aroua
- Laboratoire de Chimie
des Processus Biologiques, UMR 8229 CNRS, Collège de France, Université Paris 6, 11 Place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Tanya K. Todorova
- Laboratoire de Chimie
des Processus Biologiques, UMR 8229 CNRS, Collège de France, Université Paris 6, 11 Place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Paul Hommes
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Lise-Marie Chamoreau
- Sorbonne Universités, UPMC Université Paris 6, Institut Parisien de
Chimie Moléculaire, UMR 8232 CNRS, 4 Place Jussieu, 75252 Paris Cedex 5, France
| | - Hans-Ulrich Reissig
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Victor Mougel
- Laboratoire de Chimie
des Processus Biologiques, UMR 8229 CNRS, Collège de France, Université Paris 6, 11 Place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Marc Fontecave
- Laboratoire de Chimie
des Processus Biologiques, UMR 8229 CNRS, Collège de France, Université Paris 6, 11 Place Marcelin Berthelot, 75231 Paris Cedex 05, France
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Gueddouda NM, Hurtado MR, Moreau S, Ronga L, Das RN, Savrimoutou S, Rubio S, Marchand A, Mendoza O, Marchivie M, Elmi L, Chansavang A, Desplat V, Gabelica V, Bourdoncle A, Mergny JL, Guillon J. Design, Synthesis, and Evaluation of 2,9-Bis[(substituted-aminomethyl)phenyl]-1,10-phenanthroline Derivatives as G-Quadruplex Ligands. ChemMedChem 2017; 12:146-160. [DOI: 10.1002/cmdc.201600511] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 11/29/2016] [Indexed: 11/09/2022]
Affiliation(s)
| | | | - Stéphane Moreau
- Univ. Bordeaux; ARNA laboratory; CNRS UMR 5320, INSERM U1212; 33076 Bordeaux France
| | - Luisa Ronga
- Univ. Bordeaux; ARNA laboratory; CNRS UMR 5320, INSERM U1212; 33076 Bordeaux France
| | - Rabindra Nath Das
- Univ. Bordeaux; ARNA laboratory; CNRS UMR 5320, INSERM U1212; 33076 Bordeaux France
| | - Solène Savrimoutou
- Univ. Bordeaux; ARNA laboratory; CNRS UMR 5320, INSERM U1212; 33076 Bordeaux France
| | - Sandra Rubio
- Univ. Bordeaux; ARNA laboratory; CNRS UMR 5320, INSERM U1212; 33076 Bordeaux France
| | - Adrien Marchand
- Univ. Bordeaux; ARNA laboratory; CNRS UMR 5320, INSERM U1212; 33076 Bordeaux France
| | - Oscar Mendoza
- Univ. Bordeaux; ARNA laboratory; CNRS UMR 5320, INSERM U1212; 33076 Bordeaux France
| | | | - Lilian Elmi
- Univ. Bordeaux; ARNA laboratory; CNRS UMR 5320, INSERM U1212; 33076 Bordeaux France
| | - Albain Chansavang
- Univ. Bordeaux; ARNA laboratory; CNRS UMR 5320, INSERM U1212; 33076 Bordeaux France
| | - Vanessa Desplat
- Univ. Bordeaux; UFR des Sciences Pharmaceutiques; Biothérapie des Maladies Génétiques Inflammatoires et Cancers; INSERM U1035; 33076 Bordeaux cedex France
| | - Valérie Gabelica
- Univ. Bordeaux; ARNA laboratory; CNRS UMR 5320, INSERM U1212; 33076 Bordeaux France
| | - Anne Bourdoncle
- Univ. Bordeaux; ARNA laboratory; CNRS UMR 5320, INSERM U1212; 33076 Bordeaux France
| | - Jean-Louis Mergny
- Univ. Bordeaux; ARNA laboratory; CNRS UMR 5320, INSERM U1212; 33076 Bordeaux France
| | - Jean Guillon
- Univ. Bordeaux; ARNA laboratory; CNRS UMR 5320, INSERM U1212; 33076 Bordeaux France
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