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Gaier AJ, Ghimire S, Fix SE, McMillin DR. Internal Versus External Binding of Cationic Porphyrins to Single-Stranded DNA. Inorg Chem 2014; 53:5467-73. [PMID: 24828700 DOI: 10.1021/ic403105q] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Abby J. Gaier
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, Indiana 47907, United States
| | - Srijana Ghimire
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, Indiana 47907, United States
| | - Sarah E. Fix
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, Indiana 47907, United States
| | - David R. McMillin
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, Indiana 47907, United States
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Biver T, Venturini M, Jares-Erijman EA, Jovin TM, Secco F. 7-Aminoactinomycin Binding to DNA Sequences Lacking GpC Sites: A Thermodynamic and Kinetic Study. Biochemistry 2008; 48:173-9. [DOI: 10.1021/bi801671c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tarita Biver
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy, Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria Pabellón II/3, 1428 Buenos Aires, Argentina, and Laboratory of Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, am Fassberg 11, 37077 Göttingen, Germany
| | - Marcella Venturini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy, Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria Pabellón II/3, 1428 Buenos Aires, Argentina, and Laboratory of Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, am Fassberg 11, 37077 Göttingen, Germany
| | - Elizabeth A. Jares-Erijman
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy, Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria Pabellón II/3, 1428 Buenos Aires, Argentina, and Laboratory of Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, am Fassberg 11, 37077 Göttingen, Germany
| | - Thomas M. Jovin
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy, Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria Pabellón II/3, 1428 Buenos Aires, Argentina, and Laboratory of Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, am Fassberg 11, 37077 Göttingen, Germany
| | - Fernando Secco
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa, Italy, Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria Pabellón II/3, 1428 Buenos Aires, Argentina, and Laboratory of Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, am Fassberg 11, 37077 Göttingen, Germany
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Bendic C, Enache M, Volanschi E. Analysis of actinomycin D-DNA model complexes using a quantum-chemical criterion: Mulliken overlap populations. J Mol Graph Model 2008; 24:10-6. [PMID: 15936964 DOI: 10.1016/j.jmgm.2005.03.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2005] [Revised: 03/30/2005] [Accepted: 03/31/2005] [Indexed: 10/25/2022]
Abstract
The binding of the antitumoral drug actinomycin D to single- and double-stranded DNA was investigated using molecular modeling in the frame of MM+ molecular mechanics and AM1 semi-empirical method. Two other programs, especially conceived to analyze hydrogen-bonding patterns in biological macromolecules, HBexplore, based on geometrical criteria and SHB_interactions, based on quantum-chemical criteria (Mulliken overlap populations), were also used. The results account for the non-cooperative intercalative binding process previously investigated, and outline the contribution of specific hydrogen bonding as well as CH...O(N) and other atom-atom intermolecular interactions to the stabilization of the actinomycin D-DNA complexes. They also support the hemi-intercalation model proposed in literature for the actinomycin D-ssDNA complex.
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Affiliation(s)
- Cezar Bendic
- Department of Physical Chemistry, Faculty of Chemistry, University of Bucharest, Blvd. Elisabeta 4-12, Bucharest RO-70346, Romania
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Wadkins RM, Tung CS, Vallone PM, Benight AS. The role of the loop in binding of an actinomycin D analog to hairpins formed by single-stranded DNA. Arch Biochem Biophys 2000; 384:199-203. [PMID: 11147831 DOI: 10.1006/abbi.2000.2113] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Our recent work has indicated that the potent antibiotic and antitumor agent actinomycin D has the ability to selectively bind and stabilize single-stranded DNA that is capable of adopting a hairpin conformation. This mechanism of DNA binding has been implicated in the drug's ability to inhibit transcription by HIV reverse transcriptase from single-stranded DNA templates. In this report, we studied the importance of the hairpin loop on the ability of the 7-amino analog of actinomycin D to selectively bind DNA hairpins. Binding dissociation constant (Kd) values were determined to be 0.22 +/- 0.11 microM for the hairpin formed from the single-stranded DNA 5'-AAAAAAATAGTTTTAAATATTTTTTT-3' (dubbed HP1). The hairpin stem without the loop resulted in binding with Kd = 2.6 +/- 0.9 microM. The drug showed low affinity for the HP1 strand fully duplexed to its complementary sequence (estimated to be at least Kd > 21 microM). Evaluation of 7-aminoactinomycin D binding to a library of thermodynamically characterized DNA hairpins revealed an affinity for the hairpin-forming sequence 5'-GGATACCCCCGTATCC-3' (dubbed ACC4) of Kd = 6.8 +/- 2.2 microM. Replacement of the terminal guanines of this sequence to generate 5'-ATATACCCCCGTATAT-3' resulted in a 10-fold increase in affinity for this hairpin compared to ACC4, to Kd = 0.74 +/- 0.06 microM. A molecular model of the ACC4actinomycin D complex reveals that significant interactions between the hairpin loop and the pentapeptide rings of the drug must occur during drug binding. Taken together, our data indicate that the composition of the stem-loop interface is critical for the selectivity of actinomycin D and its 7-amino analog for DNA hairpins and suggests that novel drugs may be designed based on selection for the desired hairpin composition.
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Affiliation(s)
- R M Wadkins
- Johns Hopkins University School of Medicine, Department of Oncology, Baltimore, Maryland 21231, USA.
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