A versatile approach to modeling the conformations and energetics of DNA loops is presented. The model is based on the classical theory of elasticity, modified to describe the intrinsic twist and curvature of DNA, the DNA bending anisotropy, and electrostatic properties. All the model parameters are considered to be functions of the loop arclength, so that the DNA sequence-specific properties can be modeled. The developed theory is applied to predict the structure of the DNA loop connecting the protein-bound DNA segments in the crystal structure of the lac repressor-DNA complex. The lac repressor system is used to extensively analyze the parameters and approximations of the model. The capabilities of the model are used to mimic the binding of catabolite gene activator protein (CAP) within the lac repressor loop and to explain the cooperativity in DNA binding between the two proteins. The possibilities for further development of the model and its general applicability in biomolecular modeling are discussed, especially with regard to multi-scale simulations of protein-DNA complexes.
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