Calorimetric determination of base‐stacking enthalpies in double‐helical DNA molecules

Abstract Differential scanning calorimetry was used to directly determine the transition enthalpies accompanying the duplex‐to‐single‐strand transition of polyd(AT), poly(dA)·poly(dT), polyd(AC)·polyd(TG), and d(GCGCGC). The calorimetric data allow us to define the following average base‐stacking enthalpies: Interaction Δ H (kcal/stack) AC/TG, TG/AC 5.6 AT/TA, TA/AT 7.1 AA/TT 8.6 GC/CG, CG/GC 11.9 Comparison with published data on the corresponding RNA interactions reveals remarkably good agreement. By assuming transition enthalpies to result from the pairwise disruption of nearest‐neighbor stacking interactions, we used the enthalpy data listed above to predict the transition enthalpies for three oligomeric DNA duplexes. Excellent agreement was found between the predicted and the calorimetrically determined values.