The thermodynamic contribution of the 5-methyl group of thymine in the two- and three-stranded complexes formed by poly(dU) and poly(dT) with poly(dA)

To assess the thermodynamic contribution of the 5-methyl group of thymine, we have studied the two-stranded helical complexes poly(dA) . poly(dU) and poly(dA) . poly(dT) and the three-stranded complexes-poly(dA) . 2poly(dU), poly(dA) . poly,(dT) . poly(dU) and poly(dA) . 2poly(dT)-by, differential scanning calorimetry, and uv optical melting experiments. The thermodynamic quantities associated with the 3 --> 2, 2 --> 1, and 3 --> 1 melting transitions are found to vary with salt concentration and temperature in a more complex manner than commonly believed. The transition temperatures, T-m are generally not linear in the logarithm of concentration or activity of NaCl. The change in enthalpy and in entropy, upon melting varies with salt concentration and temperature, and a change in heat capacity accompanies each transition. The poly(dA) . 2poly(dU) triple helix is markedly, different from poly(dA) . 2poly(dT) in both its CD spectrum and thermodynamic behavior, while the poly(dA) . poly(dT) . poly(dU) triple helix resembles poly(dA) 2poly(dT) in these properties. In comparing poly(dA) . 2poly(dT) with either the poly(dA) poly(dT) . poly(dU) or the poly(dA) . 2poly(dU) triplexes, the substitution of thymine for uracil in the third strand results in an enhancement of stability against the 3 --> 2 dissociation of DeltaDeltaGdegrees = -135 +/- 85 cal (mol A)(-1) at 37degreesC. This represents a doubling of the absolute stability toward dissociation compared to the triplexes with poly(dU) as the third strand. The poly (dA) . poly (dT) duplex is more stable than poly(dA) . poly(dU) by DeltaDeltaGdegrees = -350 +/- 60 cal (mol base pair)(-1) at 37degreesC. Poly(dA) . poly(dT) has 50% greater stability than poly(dA) . poly(dU) as a result of the dT for dU substitution in the duplex. (C) 2003 Wiley Periodicals, Inc.