title: Activation volume of DNA duplex formation.
abstract: The denaturation-renaturation thermal hysteresis was used to investigate the kinetics of the helix-coil equilibrium of four 22-base pair homopurine-homopyrimidine duplex oligonucleotides with fractional G x C base pair content (f(G x C)) between 0.14 and 0.5. In 20 mM NaCl and 20 mM Tris-HCl at pH 7.0 and at hydrostatic pressures up to 200 MPa, a two-state bimolecular reaction mechanism adequately described the observed kinetics. At 1 MPa and 47 degrees C, the rate constant for helix formation, k1, increased by a factor of 210, and the reverse rate constant, k(-1), decreased by a factor of 420 upon increasing f(G x C) from 0.14 to 0.5. The activation energies for formation of the duplexes were negative and relatively insensitive to f(G x C). The pressure-induced change in the rate constants is related to the activation volume of the reaction step. Pressure causes k1 to become larger, and the magnitude of the change in k1 with pressure increases the lower the f(G x C) value. Thus, when f(G x C) = 0.14, the activation volume for forward reaction, delta V++(1), equals -20 mL/mol, while when f(G x C) = 0.5, delta V++(1) = -6.7 mL/mol. The rate constant for strand separation, k(-1), decreases at high pressure. The activation volume for this step, delta V++(1), varies from 17 to 1.6 mL/mol when f(G x C) = 0.14 and 0.5, respectively. The delta V for helix formation calculated from the activation parameters changed from -23 mL/mol when f(G x C) = 0.14 to -5.8 mL/mol when f(G x C) = 0.5. From extrapolation, it is estimated that the molar volume change for formation of G x C base pairs in homopurine-homopyrimidine sequences is approximately 0 mL/mol. Parameters calculated from kinetics of other two duplex molecules, when f(G x C) = 0.23 and 0.32, lie between these extremes.
authors.affiliation: Department of Pharmaceutical Sciences, University of Toronto, Ontario, Canada.
authors.forename: M C
authors.initials: MC
authors.lastname: Lin
authors.forename: R B
authors.initials: RB
authors.lastname: Macgregor
mesh_terms: D001482:Base Composition; D004247:DNA / Q000737:chemistry*; D006851:Hydrochloric Acid; D007700:Kinetics; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry*; D009841:Oligonucleotides / Q000737:chemistry; D012965:Sodium Chloride; D013053:Spectrophotometry; D013816:Thermodynamics; D014325:Tromethamine
chemical_list: D009692:Nucleic Acid Heteroduplexes; D009841:Oligonucleotides; D014325:Tromethamine; D012965:Sodium Chloride; D004247:DNA; D006851:Hydrochloric Acid