Thermodynamics of the Helix‐Coil Transition of (dG‐dC) Oligomers

The dissociation of short double‐helical DNA with the alternating sequence (dG‐dC) n . (dG‐dC) n into the corresponding single strands was studied as a function of chain length, oligomer concentration and temperature in 1.0M NaCl, pH 7.2 by hypochromicity and equilibrium centrifugation. The melting curves are analyzed according to an “all‐or‐none” model and the following thermodynamic parameters were deduced. The change in free energy for formation of a dG · dC base pair adjacent to another one, ΔG 0 s , =−2.2 kcal/mol at 37°C; the corresponding change in enthaply, ΔH 0 s , =−11.1 ± 0.5kcal/mol and in entropy, ΔS 0 s , =−27.9 ± 1 cal · K −1 · mol base pair −1 . The stability constant, s , is 104 ± 5 at 25°C. The formation of the first base pair from two single strands involves a nucleation parameter, β, = 1.6 10 −4 M −1 at 25°C, which is similar to the corresponding values determined for different RNA oligomers. The enthaply change associated with the formation of the first base pair, −Δ H 0 βs , =+3±5 kcal/mol which is very close to zero. These thermodynamic parameters are compared with those for the dA · dT base pair. At physiological conditions, it is estimated that the stability of one dG · dC pair is very close to that of two dA.dT pairs. The data imply that the opening of a unique sequence of DNA in a cell is a very improbable event.