Operator regions base pair

Approximately 10 base pairs are required to make one turn in B-DNA. The centers of the palindromic sequences in the DNA-binding regions of the operator are also separated by about 10 base pairs (see Table 8.1). Thus if one of the recognition a helices binds to one of the palindromic DNA sequences, the second recognition a helix of the protein dimer is poised to bind to the second palindromic DNA sequence. 

Figure 8.15 Sequence-specific protein-DNA interactions provide a general recognition signal for operator regions in 434 bacteriophage, (a) In this complex between 434 repressor fragment and a synthetic DNA there are two glutamine residues (28 and 29) at the beginning of the recognition helix in the helix-turn-helix motif that provide such interactions with the first three base pairs of the operator region.

The sequence of bases in the operator region shows a remarkable symmetry property. Twenty-eight out of 36 of the base pairs in this region of the promoter are located on a twofold (dyad) axis of symmetry (see fig. 30.7). We shall see that dyad symmetry is a common property for repressor or activator binding sites and that it relates to the way in which DNA and regulatory proteins interact. 

Sequence Similarities - DNA sequence analysis of operators that respond to LexA has yielded a consensus sequence, with 7 highly conserved bases in a 20-base-pair region. Different LexA-sensitive genes have this sequence located quite differently with respect to the transcriptional start site. Therefore, it appears that the exact location of bound repressor is not critical to ensure that transcription will be inhibited. 

---