Specificity of the Mnt protein: Independent effects of mutations at different positions in the operator

The relative binding affinities of Mnt protein are determined for each possible base-pair at position 15 of the operator sequence, and for all combinations of G - C base-pairs at positions 15 and 17. The partitioning of each operator sequence is determined quantitatively with restriction enzymes. At position 15, the wild-type G - C base-pair provides the highest binding affinity but, unlike position 17, the primary distinction is between purine and pyrimidine bases on the top strand. The information content at position 15 is only about 0.16 bit. In comparison with previous measurements at position 17, it is determined that the interactions of the Mnt protein with positions 15 and 17 are independent, i.e. the specific binding energies for the two positions are additive. The relative binding affinities at position 17 are also determined in the background of a G to T mutation at position 5, the position equivalent to 17 on the other half of the symmetric operator. The relative affinities at position 17 are independent of whether position 5 is wild-type or mutant.