ANALYSIS OF THE COMPETITION BETWEEN NUCLEOSOME FORMATION AND TRANSCRIPTION FACTOR-BINDING

We have studied the competitive binding of histones and the Rous sarco ma virus internal enhancer binding factor (IBF) factor (which recent s tudies indicate is almost certainly cEBP beta). We find that histones and IBF are incapable of forming a ternary complex with a 159- base pa ir (bp) fragment of DNA containing a single IBF binding site and that histones and factor are mutually exclusive in binding. We have analyze d the various physical parameters of binding, in an attempt to underst and how the factor might establish an exclusive binding in the cell. T he stability of the nucleosome and the factor-DNA complex have been de termined, and in addition a minimum value for the affinity of the hist one octamer has been computed. We find that in simple competition the IBF can successfully compete, only if the substrate DNA is shorter tha n 140 bp. The relevance of these results is discussed in terms of a ki netic model for successful factor competition during the replication o f the factor binding site in the cell.