title: DNA junction structure stabilized by molecular crowding conditions.
abstract: We examined the effects of molecular crowding conditions on the structures and thermodynamics of three-way junctions (TWJs) of DNA. To explore the crowding effects on the junction point, we further evaluated the number of water molecules associated with the whole TWJ as well as the individual arms. It was found that the number of water molecules taken up by the whole TWJ was significantly smaller than the sum of the individual arms. These results clearly show the dehydration from the junction point of the TWJ structure. Therefore, molecular crowding should be favourable for the junction point of TWJ structure and unfavourable for the duplex structure. From these results, it can be concluded that a cell-mimicking molecular crowding condition in which the activity of water decreases and hydration becomes less favourable, might facilitate the formation of junction structures in comparison with duplexes.
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.
authors.forename: Daisuke
authors.initials: D
authors.lastname: Miyoshi
authors.forename: Sanjukta
authors.initials: S
authors.lastname: Muhuri
authors.forename: Kenta
authors.initials: K
authors.lastname: Mimura
authors.forename: Naoki
authors.initials: N
authors.lastname: Sugimoto
mesh_terms: D004247:DNA / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D011092:Polyethylene Glycols / Q000737:chemistry; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D014867:Water; D011092:Polyethylene Glycols; D004247:DNA