title: Energetics of B-Z junction formation in a sixteen base-pair duplex DNA.
abstract: We report analysis of the NaCl-induced B-Z transition in a 16 base-pair duplex DNA with sequence designed such that when NaCl is increased the left half of the molecule undergoes the B-Z transition while the right half remains in the B-form. An equilibrium thermodynamic model based on the body of available published experimental data and the recent theoretical work of Soumpasis, which indicate, in the salt range above approximately 0.9 M-NaCl, the transition free-energy of B-Z conversion in DNA is a linear function of the NaCl concentration, is employed. Analysis of the B-Z transition of the junction-containing molecule indicates the B-Z junction formed in this 16 base-pair DNA is composed of approximately three base-pairs and has a free energy of formation of approximately 4.7 kcal/mol junction. These values for the junction are in excellent agreement with published estimates of B-Z junction size and energy derived from much longer DNA pieces.
authors.affiliation: Department of Chemistry, University of Illinois, Chicago 60680.
authors.forename: M J
authors.initials: MJ
authors.lastname: Doktycz
authors.forename: A S
authors.initials: AS
authors.lastname: Benight
authors.forename: R D
authors.initials: RD
authors.lastname: Sheardy
mesh_terms: D001483:Base Sequence; D002942:Circular Dichroism; D004247:DNA; D008956:Models, Chemical; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012965:Sodium Chloride; D013816:Thermodynamics
chemical_list: D012965:Sodium Chloride; D004247:DNA