Modeling the Lac repressor-operator assembly: the influence of DNA looping on Lac repressor conformation.

Repression of transcription of the Escherichia coli Lac operon by the Lac repressor (LacR) is accompanied by the simultaneous binding of LacR to two operators and the formation of a DNA loop. A recently developed theory of sequence-dependent DNA elasticity enables one to relate the fine structure of the LacR-DNA complex to a wide range of heretofore-unconnected experimental observations. Here, that theory is used to calculate the configuration and free energy of the DNA loop as a function of its length and base-pair sequence, its linking number, and the end conditions imposed by the LacR tetramer.

Implications of the dependence of the elastic properties of DNA on nucleotide sequence.

Recent advances in structural biochemistry have provided evidence that not only the geometric properties but also the elastic moduli of duplex DNA are strongly dependent on nucleotide sequence in a way that is not accounted for by classical rod models of the Kirchhoff type. A theory of sequence-dependent DNA elasticity is employed here to calculate the dependence of the equilibrium configurations of circular DNA on the binding of ligands that can induce changes in intrinsic twist at a single base-pair step. Calculations are presented of the influence on configurations of the assumed values and distribution along the DNA of intrinsic roll and twist and a modulus coupling roll to twist.

Theory of self-contact in Kirchhoff rods with applications to supercoiling of knotted and unknotted DNA plasmids.

There are circumstances under which it is useful to model a molecule of duplex DNA as a homogeneous, inextensible, intrinsically straight, impenetrable elastic rod of circular cross-section obeying the theory of Kirchhoff. For such rods recent research has yielded exact analytical solutions of Kirchhoff's equations of mechanical equilibrium with the effects of impenetrability taken into account, and criteria have been derived for determining whether an equilibrium configuration is stable in the sense that it gives a strict local minimum to the elastic energy. This paper contains a summary of published results on equilibrium configurations for the case in which a rod has been pre-twisted and closed to form a knot-free ring.