title: Effects of trimethylamineN-oxide and urea on DNA duplex and G-quadruplex.
abstract: We systematically investigated effects of molecular crowding with trimethylamineN-oxide (TMAO) as a zwitterionic and protective osmolyte and urea as a nonionic denaturing osmolyte on conformation and thermodynamics of the canonical DNA duplex and the non-canonical DNA G-quadruplex. It was found that TMAO and urea stabilized and destabilized, respectively, the G-quadruplex. On the other hand, these osmolytes generally destabilize the duplex; however, it was observed that osmolytes having the trimethylamine group stabilized the duplex at the lower concentrations because of a direct binding to a groove of the duplex. These results are useful not only to predict DNA structures and their thermodynamics under physiological environments in living cells, but also design of polymers and materials to regulate structure and stability of DNA sequences.
authors.affiliation: Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University , Kobe , Japan.
authors.forename: Yu-Mi
authors.initials: YM
authors.lastname: Ueda
authors.affiliation: Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University , Kobe , Japan.
authors.forename: Yu-Ki
authors.initials: YK
authors.lastname: Zouzumi
authors.affiliation: Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology , Yokohama , Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Maruyama
authors.affiliation: Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University , Kobe , Japan.
authors.forename: Shu-Ichi
authors.initials: SI
authors.lastname: Nakano
authors.affiliation: Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, Japan; Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Kobe, Japan.
authors.forename: Naoki
authors.initials: N
authors.lastname: Sugimoto
authors.affiliation: Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University , Kobe , Japan.
authors.forename: Daisuke
authors.initials: D
authors.lastname: Miyoshi
keywords: 101 Self-assembly/Self-organized materials; 208 Sensors and actuators; 30 Bio-inspired and biomedical materials; 505 Optical/Molecular spectroscopy; DNA; G-quadruplex; duplex; molecular crowding; osomolyte