Our goal is to develop a thermodynamic library of the sequence-dependent molecular forces that dictate and control DNA secondary structures in solution. These data will be used to predict the sequence-dependent structural preferences of local domains along the DNA polymer chain. Such a predictive ability will allow us to search for correlations between specific structural features and particular functional roles. The thermodynamic data required to achieve this predictive power will be obtained from calorimetric studies on selected oligomeric and polymeric DNA duplexes. Specifically, relative stabilities (DeltaG), temperature-dependent flexibilities (DeltaH, DeltaCp), and melting cooperativities (DeltaHv.H./DeltaHcal.) will be determined as a function of base sequence for fully-bonded duplexes, hairpins, cruciform-like structures, bulge loops, internal loops, and duplexes containing selectively modified bases. Significantly, calorimetry represents the only experimental method by which the relevant thermodynamic data can be obtained in a direct and model-independent manner. The proposed studies will provide us with complete sequence-dependent thermodynamic profiles for each secondary structural feature. Such data will permit the construction of a phase diagram in which DNA secondary structural preferences are mapped as a function of base sequence and temperature. Considering the potential role of conformational heterogeneity as a mechanism for selective, local control of events such as protein-nucleic acid interactions, drug-DNA binding, gene expression, and DNA packing, an ability to predict local conformational prefernces in DNA polymers is of the utmost importance. The calorimetric experiments described in this proposal represent a continuation of our efforts to obtain the thermodynamic data required to achieve this predictive ability.
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