title: Theoretical study of ethidium intercalation in triple-stranded DNA and at triplex-duplex junctions.
abstract: The contribution of different factors in the interaction of ethidium intercalated into various sequences of a triple helix, or in the region of the junction between the double- and triple-stranded DNA has been studied by energy minimization. It is found that in the total energy of the ethidium- triple helix complexes, a particular electrostatic contribution emerges due to the presence of protonated cytosines in the triple helix. This parameters is determinant in the sequence-specificity of ethidium binding to the triple helix. The preferred intercalation sites of ethidium in the triple helix are proposed. The interaction of ethidium at the triplex-duplex junction, and its effects are also discussed. This study is aimed at searching for new drugs specific for the triple helix, or for the triplex-duplex junctions.
authors.affiliation: Laboratoire de Biophysique, INSERM U201, CNRS UA481, Paris, France.
authors.forename: J S
authors.initials: JS
authors.lastname: Sun
authors.forename: R
authors.initials: R
authors.lastname: Lavery
authors.forename: J
authors.initials: J
authors.lastname: Chomilier
authors.forename: K
authors.initials: K
authors.lastname: Zakrzewska
authors.forename: T
authors.initials: T
authors.lastname: Montenay-Garestier
authors.forename: C
authors.initials: C
authors.lastname: Hélène
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure; D003854:Deoxyribonucleotides / Q000737:chemistry; D004996:Ethidium / Q000737:chemistry*; D006860:Hydrogen Bonding; D007364:Intercalating Agents / Q000737:chemistry*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011685:Purine Nucleotides / Q000737:chemistry; D011742:Pyrimidine Nucleotides / Q000737:chemistry; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D013816:Thermodynamics
chemical_list: D003854:Deoxyribonucleotides; D007364:Intercalating Agents; D011685:Purine Nucleotides; D011742:Pyrimidine Nucleotides; D004247:DNA; D004996:Ethidium