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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Effect of SDS Micelles on Actinomycin D - DNA Complexes.
Acta Chim Slov
June 2022
Institute of Physical Chemistry Ilie Murgulescu, Romanian Academy, Splaiul Independentei 202, Bucharest 060021, Romania.
DNA thermal denaturation was evaluated as a measure of the effect of antitumor drug actinomycin D on the stability of the double helix and also the effect of SDS micelles on actinomycin D - DNA complexes. The results indicated that the melting temperature of DNA was dependent on drug concentration, increasing with actinomycin D concentration. High thermal stabilization (about 10 °C) of the DNA helix after the association with actinomycin D clearly demonstrates the intercalative binding mode.
View Article and Find Full Text PDFAnalysis of actinomycin D-DNA model complexes using a quantum-chemical criterion: Mulliken overlap populations.
J Mol Graph Model
September 2005
Department of Physical Chemistry, Faculty of Chemistry, University of Bucharest, Blvd. Elisabeta 4-12, Bucharest RO-70346, Romania.
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.
View Article and Find Full Text PDF7-Azidoactinomycin D: a novel probe for examining actinomycin D-DNA interactions.
J Biol Chem
May 1989
Department of Chemistry, University of Mississippi, University 38677.
The technique of photoaffinity labeling is applied to the actinomycin D system to provide a novel probe for the examination of the interactions of actinomycin D with nucleic acids. The capacity for covalent attachment of actinomycin D will aid greatly in the study of target-site specificities and the correlations of biological effects with biophysical DNA interactions. Through chemical modification of the parent actinomycin D molecule with a photoreactive azido substituent, a functional analog of the parent actinomycin D is generated having equilibrium binding properties identical to those of the parent molecule yet with the capacity to form a covalent attachment to DNA upon photolysis.
View Article and Find Full Text PDFA combined 2D-NMR and molecular dynamics analysis of the structure of the actinomycin D: d(ATGCAT)2 complex.
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Department of Pharmaceutical Chemistry, University of California, San Francisco 94143.
We present a comparative analysis of an NMR experiment and molecular and harmonic dynamics simulations of an actinomycin D: d(ATGCAT)2 complex. A comparison of NOE measurements and 1/R6 weighted proton-proton distances confirm the general correctness of the Actinomycin D-DNA model proposed by Sobell. There are, however, some substantial differences between the proton-proton distances inferred from the NOE results and the molecular and harmonic dynamics simulations.
View Article and Find Full Text PDFWe have analyzed the specificity of the actinomycin D-DNA interaction. The 'footprint' method has been used in this investigation. It is shown that: (i) The presence of dinucleotide GC or GG is required for binding of a single drug molecule.
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