Individual‐site binding data and the energetics of protein–DNA interactions

Individual‐site isotherms for the binding of bacteriophage λ repressor to the left and right λ operators have been determined [D. F. Senear, M. Brenowitz, M. A. Shea, and G. K. Ackers (1986) Biochemistry , Vol. 25, pp. 7344–7354.] using the DNAse protection technique [ footprinting; D. J. Galas and A. Schmitz (1978) Nucleic Acids Research , Vol. 5, pp. 3157–3170]. These extensive data have been interpreted with a quantitative model that emphasized cooperative interactions between adjacently bound ligands [occupied ↔ occupied interactions; G. K. Ackers, A. D. Johnson, and M. A. Shea (1982) Proceedings of the National Academy of Science, USA , Vol. 79, pp. 1129–1133]. Overlooked in this model are the effects of cooperative interactions between a site containing a bound ligand and its neighboring unoccupied site (occupied ↔ unoccupied interactions). This paper reinterprets the existing data with a model that considers occupied ↔ unoccupied as well as occupied ↔ occupied interactions. The results yield parameters that differ substantially from those already reported. A discussion on the advisability of ignoring occupied ↔ unoccupied interactions is included. © 1993 John Wiley & Sons, Inc.