DIFFERENTIAL HYDRATION OF DA-CENTER-DOT-DT BASE-PAIRS IN PARALLEL-STRANDED DNA RELATIVE TO ANTIPARALLEL DNA

Parallel-stranded DNA is a novel double-stranded helical form of DNA. Its secondary structure is established by reverse Watson-Crick base pa iring between the bases of the complementary strands forming a double helix with equivalent grooves. We have used a combination of magnetic suspension densimetry and isothermal titration calorimetry to obtain c omplete thermodynamic profiles for the formation of two DNA 25mer dupl exes. The duplexes contain exclusively dA.dT base pairs in either para llel (ps-d1.D2) or antiparallel (aps-D1.D3) orientation. At 15 degrees C, the formation of each duplex is accompanied by favorable free-ener gy terms resulting from the partial compensation of favorable exotherm ic enthalpies and unfavorable entropies and by an uptake of both count erions and water molecules. By taking into account the contribution of single-strand base-stacking interactions and using the formation of t he aps-D1.D3 duplex as a reference state to establish a thermodynamic cycle in which the similar single strands cancel out, we obtained a De lta Delta G degrees term of +10 kcal mol(-1) duplex formed that result s from a partial differential enthalpy-entropy compensation of +32 kca l mol(-1) and a Delta Delta V of 257 mL mol(-1). The positive sign of this enthalpy-entropy compensation together with the marginal differen tial counterion uptake of 0.2 mol of Na+/mol of duplex is characterist ic of processes driven by differential hydration and strongly suggests that the parallel duplex is much less hydrated than its antiparallel counterpart by similar to 4 mol of water/mol of base pair.