DNA-based positive control mutants in the binding site sequence of 434 repressor

As detected by chemical nuclease treatments, the conformation of the 434 repressor-DNA complex depends on the sequence of the bound DNA (Bell, A. C., and Koudelka, G. B. (1993) J. Mol. Biol. 234, 542-553). We show here that these DNA sequence-dependent conformational changes alter the efficiency with which the repressor activates transcription from 434 P(RM). Several lines of evidence suggest that binding site sequence affects the repressor's ability to activate transcription by altering the accessibility of the activation surface on the repressor to RNA polymerase. The results presented here show that in addition to affecting transcription by altering the overall binding affinity of protein for DNA, DNA sequence may also modulate the activity of the DNA-bound protein.