Different interactions of cro repressor dimer with the left and right halves of O(R)3 operator DNA

λ Cro repressor protein is titrated with two half-operator DNA duplexes comprising the right and left halves of the major binding site on phage λ DNA, the O(R)3 operator. The comparison of binding strengths and the conformation of Cro repressor in the two protein-DNA complexes shows that base pair differences between the two halves of the O(R)3 operator affect the binding of Cro repressor protein. Some ¹H NMR resonances are assigned for both protein and DNA in the Cro-operator DNA complexes which are then used to highlight differences between Cro right half and Cro left half protein-operator DNA interactions. These differences are compared to the asymmetry found in the λ C(I) repressor-operator DNA complex. Mechanisms for the recognition of the Cro transcriptional regulatory protein have considered only interactions between a single Cro monomer and a consensus half-operator site with the assumption that the interactions in the remaining half-site are related by the 2-fold symmetry of the complex. A revised model is suggested that allows asymmetry in the two halves of the protein-DNA complex. Methods are proposed to avoid problems in the general use of ¹H NMR spectroscopy to study protein-DNA interaction such as intermediate exchange behavior and sample aggregation.