Differential scanning calorimetry, temperature-dependent absorbance, and circular dichroic spectroscopy were used to study the thermodynamics of the B-Z transition in poly(m5dG-dC). In sodium phosphate buffer (pH 7.0) containing 50 mM NaCl and 1.0 mM MgCl2, the reversible B-Z transition of the polymer is centered at 38.2 degrees C and is characterized by delta Hcal = 0.61 +/- 0.07 kcal/(mol X base pair) (1 cal = 4.184 J), delta HvH = 68 +/- 7 kcal/mol, and a cooperative unit of length 110 +/- 20 base pairs. A second transition centered at 53.6 degrees C is observed and represents a conformational change of poly(m5dG-dC) from the Z to an alternate left-handed form of unknown structure. This transition does not arise from aggregation to the Z form, or from the helix-coil transition. The left-handed helix-coil transition is observed at 120.9 +/- 0.3 degrees C and is characterized by delta Hcal = 9.1 +/- 1.0 kcal/(mol X base pair). These results indicate a substantial enthalpic contribution to the B-Z transition, in contrast to previous assertions that the process is entropically driven.