Estimation of a Duplex Melting Enthalpy

Estimation of a Duplex Melting Enthalpy. From the average enthalpies given in Table 16.5, one can estimate the melting enthalpies of an oligonucleotide duplex based on its nucleotide sequence. For example, the oligonucleotide duplex d(ATGCAT)2 has the structure 

Breslauer and his colleagues have been able to use this database to predict the energetics associated with the melting of a wide variety of duplexes based on the nucleotide sequence in the oligonucleotide. Conversely, from the known nucleotide sequence and the melting energetics obtained from Table 16.6, they have been able to predict the likelihood that structural features like the hairpin loop of reaction (16.25) would be observed. 

Interaction Af//(kJmol 1 of base stacks) AS/(J-K.-1-mol 1 of base stacks) AG/(kJ-mol 1 of base stacks) 

Data from K. J. Breslauer, R. Frank, H. Blocker, and L. A. Marky, Proc. Natl. Acad. Sci. USA, 83, 3746-3750 (1986). 

One implication of the ability of the database to make reasonable predictions about the thermodynamics of duplex melting is that base sequence, rather than total base composition, determines duplex stability. This conclusion is supported by the observation that the second and third entries in Table 16.6, which involve only A and T, have the same base composition but yield significantly different melting thermodynamics. 

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