Analysis of the competition between nucleosome formation and transcription factor binding

We have studied the competitive binding of histones and the Rous sarcoma virus internal enhancer binding factor (IBF) factor (which recent studies indicate is almost certainly cEBP beta). We find that histones and IBF are incapable of forming a ternary complex with a 159-base pair (bp) fragment of DNA containing a single IBF binding site and that histones and factor are mutually exclusive in binding. We have analyzed the various physical parameters of binding, in an attempt to understand how the factor might establish an exclusive binding in the cell. The stability of the nucleosome and the factor-DNA complex have been determined, and in addition a minimum value for the affinity of the histone octamer has been computed. We find that in simple competition the IBF can successfully compete, only if the substrate DNA is shorter than 140 bp. The relevance of these results is discussed in terms of a kinetic model for successful factor competition during the replication of the factor binding site in the cell.