title: dC-dG alternating oligonucleotides: thermodynamic and kinetic aspects of the B-Z transformation.
abstract: The alternating cytosine-guanine oligodeoxyribonucleotides (dCdG)n, (dGdC)n, (dCdG)ndC (n = 3,4), (dGdC)7 and dG(dCdG)3 have been studied by UV and CD spectroscopy at different temperatures and NaCl concentrations. The analysis of the melting data, assuming an all-or-none model, reveals that in the B-conformation the 5'G/C3' stacking interactions are enthalpically favoured with respect to the 5'C/G3' one. The CD investigation of the B-Z equilibrium shows that the Z-conformation is enthalpically stabilized, while the B-conformation is entropically favoured, in the range of NaCl concentration considered (1 to 5 M). The kinetic data for the B-Z transformation, obtained with a salt-jump technique for the hexamer (dCdG)3, support a mechanism by which the Watson-Crick hydrogen bonds are broken before the bases flip over separately and eventually stack, reforming the H-bonds, in the new helix.
authors.affiliation: Dept. of Biochemistry, Biophysics and Macromolecular Chemistry, University of Trieste, Italy.
authors.forename: G
authors.initials: G
authors.lastname: Manzini
authors.forename: L E
authors.initials: LE
authors.lastname: Xodo
authors.forename: F
authors.initials: F
authors.lastname: Quadrifoglio
authors.forename: J H
authors.initials: JH
authors.lastname: van Boom
authors.forename: G A
authors.initials: GA
authors.lastname: van der Marel
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000528:radiation effects; D007700:Kinetics; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides; D013816:Thermodynamics; D014466:Ultraviolet Rays
chemical_list: D009841:Oligonucleotides; D004247:DNA