Quaternary structure of DNA-dependent RNA polymerase from Escherichia coli. Measurement of distances by fluorescence energy transfer

Fluorescence resonance energy transfer analysis of escherichia coli RNA polymerase and polymerase-DNA complexes

Fluorescence resonance energy transfer (FRET) is a technique allowing measurements of atomic-scale distances in diluted solutions of macromolecules under native conditions. This feature makes FRET a powerful tool to study complicated biological assemblies. In this report we review the applications of FRET to studies of transcription initiation by Escherichia coli RNA polymerase. The versatility of FRET for studies of a large macromolecular assembly such as RNA polymerase is illustrated by examples of using FRET to address several different aspects of transcription initiation by polymerase. FRET has been used to determine the architecture of polymerase, its complex with single-stranded DNA, and the conformation of promoter fragment bound to polymerase. FRET has been also used as a binding assay to determine the thermodynamics of promoter DNA fragment binding to the polymerase. Functional conformational changes in the specificity subunit of polymerase responsible for the modulation of the promoter binding activity of the enzyme and the mechanistic aspects of the transition from the initiation to the elongation complex were also investigated.

Antibodies against the subunits of E. coli RNA polymerase as probes for subunit-specific binding of DNA and other ligands

Antibodies against the isolated subunits alpha, beta, and beta' of DNA-dependent RNA polymerase from E. coli have been prepared. They have been used to compare the extent of antibody-binding, as measured by complement fixation, to the isolated subunits and to the intact enzyme, in the absence and presence of ligands, such as inhibitors, nucleotides, nucleosides, oligo- and poly-nucleotides, and DNA of different composition. In many cases the results show a subunit-specific dependence of complement fixation upon the presence of a ligand and suggest a functional topography of the interaction between the subunits alpha, beta, and beta' of RNA polymerase and defined nucleotide sequences and small ligands.