title: Effect of cytosine protonation and cation on thermodynamic properties of parallel DNA triplex family.
abstract: The conformational and thermodynamic properties of three modified parallel triplexes, which have the same base composition but differ in the orientation of the Hoogsteen third strand with respect to the core duplex, were comparatively discussed. The results show that the intermolecular triplex is unstable relatively to the intramolecular triplex and the thermodynamic properties are slightly dependent on the 3' or/and 5' junctions. Furthermore, mono- and divalent cations compete each other in stabilizing the triple helix structure and a higher concentration of the monovalent cation would shield the effect of divalent cations on the triplex stability.
authors.affiliation: High Technology Research Center, Faculty of Science and Engineering, Konan University, 8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan.
authors.forename: P
authors.initials: P
authors.lastname: Wu
authors.forename: H
authors.initials: H
authors.lastname: Hara
authors.forename: Y
authors.initials: Y
authors.lastname: Kawamoto
authors.forename: N
authors.initials: N
authors.lastname: Sugimoto
mesh_terms: D001483:Base Sequence; D002412:Cations / Q000737:chemistry; D003596:Cytosine / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009841:Oligonucleotides / Q000737:chemistry; D011522:Protons; D013816:Thermodynamics
chemical_list: D002412:Cations; D009841:Oligonucleotides; D011522:Protons; C051802:triplex DNA; D003596:Cytosine; D004247:DNA