Ion Effects on the Aggregation and DNA-binding Reactions of Escherichia coli RNA Polymerase (original) (raw)

1. S.L. Shaner*,
2. P. Melançon*,
3. K.S. Lee*,
4. R.R. Burgess†, and
5. M.T. Record, Jr.*
6. *Department of Chemistry and †McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, Wisconsin 53706

Excerpt

Numerous multiple equilibria are involved in the interactions of Escherichia coli RNA polymerase holoenzyme with promoter-containing DNA molecules. These include (1) the interactions of RNA polymerase with nonpromoter sequences (ends, random interior regions, nicks, and “tight-binding” sites), (2) the formation of “closed” (RPC) and “open” (RPo) complexes at promoters, (3) potential conformational equilibria involving the protein and/or the DNA, and (4) changes in the state of aggregation and/or subunit composition of RNA polymerase. An understanding of the interplay between these coupled equilibria is necessary in order to interpret either thermodynamic or kinetic data for an individual reaction. In addition, many or all of these equilibria may be involved in the control of RNA-polymerase-mediated gene expression in vivo.

Work in our laboratories has focused, in part, on the thermodynamics of these coupled equilibria and, in particular, on the origins and implications of the dramatic dependences of these equilibria on the nature...