Binding of Escherichia coli ribonucleic acid polymerase holoenzyme to a bacteriophage T7 promoter-containing fragment: evaluation of promoter binding constants as a function of solution conditions.

Abstract

In this paper we obtain thermodynamic and molecular information about the specific complexes formed between Escherichia coli RNA polymerase holoenzyme and a restriction fragment of T7 D111 DNA carrying the A1 and D promoters. Specific binding was observed at both 0 and 37 degrees C over a side range of pH values and ion concentrations [Strauss, H. S., Burgess, R. R., & Record, M. T., Jr. (1980) Biochemistry (first paper of four in this issue)]. The specific complexes formed at these two temperatures may correspond to the closed and open promoter complexes discussed by Chamberlin [Chamberlin, M. J. (1976) RNA Polymerase (Losick, R., & Chamberlin, M., Eds.) pp 159-161, Cold Spring Harbor Laboratory, cold Spring Harbor, NY]. Promoter binding constants KobsdRP are obtained from competition filter binding data by using a statistical analysis and previously determined values of the nonspecific holoenzyme-DNA binding constant KobsdRD. From the magnitudes of KobsdRP at 0 and 37 degrees C, and the dependences of these binding constants on pH and ion concentrations, we conclude that, under physiological ionic conditions, both the 0 and the 37 degrees C complexes are stabilized to a large extent by the formation of ionic interactions and the accompanying release of counterions and that one or two protonation events (pK approximately 7.4) are required for complex formation in both cases. However, the 0 and 37 degrees C complexes differ in their sensitivity to ion concentrations as well as in the magnitude of KobsdRP, and we conclude that the two complexes are distinct. (More counterion release accompanies formation of the 37 degrees C complex). Comparisons of the two complexes with one another and with nonspecific holoenzyme-DNA complexes are drawn from the binding data. We have also examined the equilibrium selectivity ratio (KobsdRP/DobsdRD) and find it to be a sensitive function of temperature and ionic conditions. Selectivity of holoenzyme for promoter sites on the promoter-containing fragment is higher at 37 degrees C than at 0 degrees C under the conditions investigated. Selectivity at either temperature is increased by reducing the pH (in the range 6.1-8.6). At 37 degrees C, selectivity is increased by reducing the salt concentration. Under approximately physiological conditions (0.2 M NaCl and 0.003 M MgCl2, pH 7.4, 37 degrees C), the equilibrium selectivity ratio is found to be of order of magnitude 10(4).