title: Investigations of the cation binding to nucleotides by monitoring the hairpin-duplex equilibrium of a self-complementary sequence.
abstract: Nucleotide folding accompanies cation binding that shields the electronegative potential of phosphate groups, and metal ions in the condensation layer predominantly associate diffusely with base-paired nucleotides. Although metal ions bound at specific sites have been well studied, information of diffusely bound cations, that usually have a weak binding affinity than those associating at specific sites, have not been thoroughly studied. We explored a convenient experimental system using a self-complementary nucleotide sequence for analyzing cationic ligands diffusely bound to DNA or RNA base pairs. To study the metal ion-nucleotide interaction under a non-homologous aqueous condition, solutions containing a large amount of PEG (polyethylene glycol) were examined. We found that PEG (e.g., 20 wt%) substantially influenced the metal ion binding to nucleotides, suggesting significances of the molecular environment on nucleotide-cation interactions.
authors.affiliation: Faculty of Frontiers of Innovative Research in Science and Technology and Frontier Institute for Biomolecular Engineering Research, Konan University, Kobe, 650-0047, Japan. shuichi@center.konan-u.ac.jp
authors.forename: Shu-ichi
authors.initials: S
authors.lastname: Nakano
authors.forename: Hidenobu
authors.initials: H
authors.lastname: Hirayama
authors.forename: Naoki
authors.initials: N
authors.lastname: Sugimoto
mesh_terms: D001483:Base Sequence; D002412:Cations / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D008670:Metals / Q000737:chemistry*; D011092:Polyethylene Glycols / Q000737:chemistry; D012313:RNA / Q000737:chemistry*
chemical_list: D002412:Cations; D008670:Metals; D011092:Polyethylene Glycols; D012313:RNA; D004247:DNA