Forces maintaining the DNA double helix

Despite the common acceptance that the enthalpy of DNA duplex unfolding does not depend on temperature and is greater for the CG base pair held by three hydrogen bonds than for the AT base pair held by only two, direct calorimetric measurements have shown that the enthalpic and entropic contributions of both base pairs are temperature dependent and at all temperatures are greater for the AT than the CG pair. The temperature dependence results from hydration of the apolar surfaces of bases that become exposed upon duplex dissociation. The larger enthalpic and entropic contributions of the AT pair are caused by water fixed by this pair in the minor groove of DNA and released on duplex dissociation. Analysis of the experimental thermodynamic characteristics of unfolding/refolding DNA duplexes of various compositions shows that the enthalpy of base pairing is negligibly small, while the entropic contribution is considerable. Thus, DNA base pairing is entropy driven and is coupled to the enthalpy driven van der Waals base pair stacking. Each of these two processes is responsible for about half the Gibbs energy of duplex stabilization, but all the enthalpy, i.e., the total heat of melting, results from dissociation of the stacked base pairs. Both these processes tightly cooperate: while the pairing of conjugate bases is critical for recognition of complementary strands, stacking of the flat apolar surfaces of the base pairs reinforces the DNA duplex formed.