title: Thermodynamics of dT--dT base pair mismatching in linear DNA duplexes and three-arm DNA junctions.
abstract: We have used a combination of magnetic-suspension densimetry and calorimetry to derive complete thermodynamic profiles, including volume changes, for the formation of linear DNA duplexes and three-arm branched DNA junctions, from their component strands, with and without dT-dT mismatches. The formation of each type of complex at 20 degrees C is accompanied by a favorable free energy, with a favorable enthalpy term partially compensated by an unfavorable entropy. Formation is associated also with net uptake of water molecules. Using the formation of the fully-paired linear duplex or three-arm junction as reference states, we can establish a thermodynamic cycle in which the contribution of the single-strand species cancels. From this cycle, we determine that substitution of dA for dT has a differential free energy of deltadeltaG degrees of +2.4 kcal mol(-1) for mismatched duplex and +2.0 kcal mol(-1) (on the average) for the mismatched junction. These unfavorable differential free energies result from an unfavorable enthalpy, partially compensated by a favorable entropy, and a negative deltadeltaV. The free energies in the two cases have signs opposed to those of deltadeltaV, a situation that implicates hydration changes in creating the mismatch. When the deltadeltaV terms are normalized by the total number of base pairs involved, the immobilization of structural water molecules (and/or substitution of electrostricted for hydrophobic water molecules) is about 7 times greater for junctions than duplexes. This is consistent with more extensive hydrophobic hydration of branched DNA structures than of duplexes.
authors.affiliation: Department of Chemistry, New York University 10003, USA.
authors.forename: M
authors.initials: M
authors.lastname: Zhong
authors.forename: L A
authors.initials: LA
authors.lastname: Marky
authors.forename: N R
authors.initials: NR
authors.lastname: Kallenbach
authors.forename: D W
authors.initials: DW
authors.lastname: Kupke
mesh_terms: D001482:Base Composition; D004247:DNA / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D009692:Nucleic Acid Heteroduplexes; D009838:Oligodeoxyribonucleotides; D004247:DNA