Journal
JOURNAL OF BACTERIOLOGY
Volume 191, Issue 18, Pages 5854-5858Publisher
AMER SOC MICROBIOLOGY
DOI: 10.1128/JB.00621-09
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Funding
- National Institutes of Health [R37 GM37048]
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The transcription factor DksA binds in the secondary channel of RNA polymerase ( RNAP) and alters transcriptional output without interacting with DNA. Here we present a quantitative assay for measuring DksA binding affinity and illustrate its utility by determining the relative affinities of DksA for three different forms of RNAP. Whereas the apparent affinities of DksA for RNAP core and holoenzyme are the same, the apparent affinity of DksA for RNAP decreases almost 10-fold in an open complex. These results suggest that the conformation of RNAP present in an open complex is not optimal for DksA binding and that DNA directly or indirectly alters the interface between the two proteins.
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