title: Structural foundation for DNA behavior in hydrated ionic liquid: An NMR study.
abstract: A well known rule of high thermal stability of GC-rich DNA helices can be reversed with the use of certain ions, rendering AT-rich duplexes more stable. We have sought to elucidate the structural basis of this phenomenon for choline dihydrogen phosphate, an ionic liquid known for extension of long-term chemical stability of biomolecules. NMR experiments complemented with CD spectroscopy revealed subtle changes of GC and AT-rich double helix structures in choline dihydrogen phosphate compared to NaCl solution. Chemical shift changes observed for different environments were used as a guide to determine choline ions' localization hotspots. For d(5'-AAATATATTT-3') choline ions are localized in the central part, especially in the minor groove near sugar protons of thymidine and H2 protons of adenine residues. In agreement with NMR data, thermodynamic analysis points to the involvement of choline ions in the hydration network as a crucial part of thermal stabilization of AT-rich helices. Analysis for GC-rich d(5'-GGGCGCGCCC-3') oligonucleotide showed preference of choline ions for major groove with less clearly defined localizations spots than in the case of its AT-rich counterpart.
authors.affiliation: Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.
authors.forename: Maja
authors.initials: M
authors.lastname: Marušič
authors.affiliation: Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 8-9-1 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.
authors.forename: Hisae
authors.initials: H
authors.lastname: Tateishi-Karimata
authors.affiliation: Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 8-9-1 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan; Graduate School of Frontier of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.
authors.forename: Naoki
authors.initials: N
authors.lastname: Sugimoto
authors.affiliation: Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; EN-FIST Center of Excellence, SI-1000 Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia. Electronic address: janez.plavec@ki.si.
authors.forename: Janez
authors.initials: J
authors.lastname: Plavec
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D052578:Ionic Liquids / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry / Q000235:genetics; D013696:Temperature
chemical_list: D052578:Ionic Liquids; D009838:Oligodeoxyribonucleotides; D004247:DNA
keywords: Base-pair; Choline dihydrogen phosphate; DNA; Ionic liquids; NMR