title: Formation and temperature stability of G-quadruplex structures studied by electronic and vibrational circular dichroism spectroscopy combined with ab initio calculations.
abstract: Variations in the structure of d(GGGA)(5) oligonucleotide in the presence of Li(+), Na(+), and K(+) ions and its temperature stability were studied using electronic and vibrational circular dichroism, IR absorption, and ab initio calculations with the Becke 3-Lee-Yang-Parr functional at the 6-31G** level. The samples were characterized by nondenaturing gel electrophoresis. Oligonucleotide d(GGGA)(5) in the presence of Li(+) forms a nonplanar single tetramer, with angles of 102 degrees and 171 degrees between neighboring guanine bases. This tetramer changes its geometry at temperatures >50 degrees C, but does not form a quadruplex structure. In the presence of Na(+), the d(GGGA)(5) structure was optimized to almost planar tetramers with an angle of 177 degrees between neighboring guanines. The spectral results suggest that it stacks into a quadruplex helical structure. This quadruplex structure decayed to a single tetramer at temperatures >60 degrees C. The Hartree-Fock energies imply that d(GGGA)(5) prefers to form complexes with Na(+) rather than Li(+). The d(GGGA)(5) structure in the presence of monovalent ions is stabilized against thermal denaturation in the order Li(+) < Na(+) < K(+).
authors.affiliation: Department of Analytical Chemistry, Institute of Chemical Technology, Prague, Technická 5, 166 28 Prague, Czech Republic.
authors.forename: Jakub
authors.initials: J
authors.lastname: Nový
authors.forename: Stanislav
authors.initials: S
authors.lastname: Böhm
authors.forename: Jarmila
authors.initials: J
authors.lastname: Králová
authors.forename: Vladimír
authors.initials: V
authors.lastname: Král
authors.forename: Marie
authors.initials: M
authors.lastname: Urbanová
mesh_terms: D002942:Circular Dichroism / Q000295:instrumentation* / Q000379:methods*; D004581:Electronics; D054856:G-Quadruplexes; D006147:Guanine / Q000737:chemistry; D007477:Ions; D008094:Lithium / Q000737:chemistry; D008958:Models, Molecular; D008968:Molecular Conformation; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000737:chemistry; D009841:Oligonucleotides / Q000737:chemistry; D011188:Potassium / Q000737:chemistry; D012964:Sodium / Q000737:chemistry; D013055:Spectrophotometry, Infrared / Q000379:methods; D013696:Temperature
chemical_list: D007477:Ions; D009711:Nucleotides; D009841:Oligonucleotides; D006147:Guanine; D008094:Lithium; D012964:Sodium; D011188:Potassium