Escherichia coli ribonucleic acid polymerase binding to the deoxyribonucleic acid of the echinoid Paracentrotus lividus: properties of the complexes and distribution of stable binding sites.

We describe the properties of the complexes that form between Escherichia coli RNA polymerase and Paracentrotus lividus DNA: dissociation kinetics, temperature dependence of the complex formation, resistance to heparin, and range of RNA polymerase-DNA weight/weight ratios that give rise to the stable binding events. The amount and distribution of the sites that form stable binding [class A sites as defined by Hinkle & Chamberlin [Hinkle, D., & Chamberlin, M. J. (1972) J. Mol. Biol. 70, 157]] with E. coli RNA polymerase were determined by the analysis of the dissociation of complexes formed by the enzyme on DNA fragments of various length. The P. lividus appears to form 3.1 X 10(5) stable (t1/2 greater than or equal to 15 min) complexes per haploid genome; the great majority of these complexes shows a short-range distribution (1000-2000 base pairs). The observed attributes of the stable binding sites of P. lividus DNA for E. coli RNA polymerase (amount, distribution, and quantitative ability to start in vitro RNA chains) point to the conclusion that E. coli and sea urchin DNA are nearly indistinguishable by the criteria adopted. The behavior of the sea urchin stable binding sites for the E. coli enzyme is not consistent with the expected behavior of the in vivo promoters.