THERMODYNAMICS OF DT-DT BASE-PAIR MISMATCHING IN LINEAR DNA DUPLEXES AND 3-ARM DNA JUNCTIONS

We have used a combination of magnetic-suspension densimetry and calor imetry to derive complete thermodynamic profiles, including volume cha nges, for the formation of linear DNA duplexes and three-arm branched DNA junctions, from their component strands, with and without dT-dT mi smatches. The formation of each type of complex at 20 degrees C is acc ompanied by a favorable free energy, with a favorable enthalpy term pa rtially compensated by an unfavorable entropy. Formation is associated also with net uptake of water molecules. Using the formation of the f ully-paired linear duplex or three-arm junction as reference states, w e can establish a thermodynamic cycle in which the contribution of the single-strand species cancels. From this cycle, we determine that sub stitution of dA for dT has a differential free energy of Delta Delta G 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 di fferential free energies result from an unfavorable enthalpy, partiall y compensated by a favorable entropy, and a negative Delta Delta V. Th e free energies in the two cases have signs opposed to those of Delta Delta V, a situation that implicates hydration changes in creating the mismatch. When the Delta Delta V terms are normalized by the total nu mber of base pairs involved, the immobilization of structural water mo lecules (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 DN A structures than of duplexes.