![]() ![]() Doubts concerning the experimental basis for all these suggestions stimulated the appearance of highly sensitive and precise calorimetric instruments designed for studying viscous and very dilute solutions: the Nano-DSC and Nano-ITC (Privalov 2012). It was expected, however, that a certain contribution to the DNA duplex formation might also result from the compactly packed flat base pairs (Sugimoto et al. These experiments seemed to confirm that the enthalpic contribution of both base pairs does not depend on temperature and is larger for the CG pair, as expected if the DNA double helix is maintained only by the hydrogen bonds between the bases. There were many subsequent attempts to estimate the thermodynamic contribution of base pairing to maintaining the double helix by measuring the heats of melting synthetic polynucleotides using conventional calorimetric instruments for liquids. This seemed to be confirmed by the optical observation that increase of CG content leads to a rise in DNA duplex thermostability (Marmur and Doty 1962). Moreover, it suggested that the physical basis of duplex stability is the hydrogen bonds between conjugate bases: two between A and T and three between C and G. The understanding by Watson and Crick ( 1953) that two complementary strands of DNA are wound together into a double helix was a great discovery in biology, as it explained the mechanism of coding and replication of genetic information (Watson and Crick 1953). 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. 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. Thus, DNA base pairing is entropy driven and is coupled to the enthalpy driven van der Waals base pair stacking. ![]() 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. 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. The temperature dependence results from hydration of the apolar surfaces of bases that become exposed upon duplex dissociation. 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. ![]()
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