Journal ArticleDOI
Noncovalent interactions with DNA: an overview.
Lucjan Strekowski,Beth Wilson +1 more
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An overview of the different DNA-binding modes with an emphasis on DNA groove specificity for the groove-binding and intercalation modes is provided.Abstract:
Over the last four decades, intense research has focused on the effects of small organic compounds that noncovalently bind to nucleic acids. These interactions have been shown to disrupt replication and/or transcription culminating in cellular death. Accordingly, DNA binding compounds have potential applications as anti-cancer and anti-viral agents. This report provides an overview of the different DNA-binding modes with an emphasis on DNA groove specificity for the groove-binding and intercalation modes. While most DNA-interacting agents selectively bind to DNA by either groove binding or intercalation, some compounds can exhibit both binding modes. The binding mode with the most favorable free energy for complex formation depends on the DNA sequence and structural features of the bound ligand.read more
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Journal ArticleDOI
DNA-binding of nickel(II), copper(II) and zinc(II) complexes: structure-affinity relationships
Giampaolo Barone,Alessio Terenzi,Antonino Lauria,Anna Maria Almerico,José M. Leal,Natalia Busto,Begoña García +6 more
TL;DR: In this article, a review of the most recent examples of the three metal ions complexed with monodentate and chelating bidentate to tetradentate ligands to DNA is presented, and an attempt has also been made to rationalize the observed trend in the values of the intrinsic DNA-binding constant in terms of structural and chemical features.
Journal ArticleDOI
New hopes from old drugs: revisiting DNA-binding small molecules as anticancer agents.
TL;DR: Evidence is presented that agents capable of targeting DNA without inducing DNA damage would not be limited by the adverse side effects and increased risk of secondary cancers that are consequences of the agents' genotoxicity, and may be as potent as DNA-damaging agents in the killing of tumor cells.
Journal ArticleDOI
Recent advances in small organic molecules as DNA intercalating agents: synthesis, activity, and modeling.
TL;DR: Despite DNA being an important target for several drugs, most of the docking programs are validated only for proteins and their ligands, therefore, a default protocol to identify DNA binding modes which uses a modified canonical DNA as receptor is needed.
Journal ArticleDOI
μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA
Marco Pasi,John H. Maddocks,David L. Beveridge,Thomas C. Bishop,David A. Case,Thomas E. Cheatham,Pablo D. Dans,Bhyravabhotla Jayaram,Filip Lankaš,Charles A. Laughton,Jonathan S. Mitchell,Roman Osman,Modesto Orozco,Alberto Perez,D. Petkevičiūtė,Nad'a Špačková,Jiri Sponer,Jiri Sponer,Krystyna Zakrzewska,Richard Lavery +19 more
TL;DR: The results of microsecond molecular dynamics simulations carried out by the ABC group of laboratories on a set of B-DNA oligomers containing the 136 distinct tetranucleotide base sequences demonstrate that the resulting trajectories have extensively sampled the conformational space accessible to B- DNA at room temperature.
Journal ArticleDOI
Activation of DNA carbon-hydrogen bonds by metal complexes.
TL;DR: The result of this analysis is that for 250 μM O2 and 0.1 mM of glutathione, which are classical concentrations to study DNA cleavage with metal complexes, the pathways involving the C4′peroxide 41 and the heterolytic cleavage forming 56 can be in competition (except if the metal complex favors one pathway).
References
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Book
Principles of Biochemistry
TL;DR: The third edition, coming ten years after the first, emphasizes both the flowering of biochemical research and the prodigious effort by busy teachers and scientists to keep up to date this popular text and reference.
Journal ArticleDOI
Theoretical aspects of DNA-protein interactions: co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous lattice.
TL;DR: The results indicate that the binding of any non-interacting ligand covering more than one lattice residue results in non- linear (convex downward) Scatchard plots, and the introduction of positive ligand-ligand co-operativity antagonizes this non-linearity, and eventually leads to plots of the opposite curvature.
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The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides.
TL;DR: An analogous situation existed in the field of protein chemistry during the period after the formulation and confirmation of the Debye—Huckel theory of ionic solutions but before Scatchard's incorporation of the theory into his analysis of the binding properties of proteins.
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Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity.
TL;DR: The purpose of this review is to examine the various effects of low- molecular-weight electrolytes on the associations and interactions of proteins and nucleic acids through general electrostatic effects rather than chemical effects of particular ions.
Book
Comprehensive natural products chemistry
TL;DR: Collecting together aspects of the chemistry of natural products, this work was conceived as a source of the underlying general principles governing modern natural products physics as discussed by the authors, and was used as a basis for the present paper.