Sequence-dependent differences in DNA structure influence the affinity of P22 operator for P22 repressor

Although the central bases of the P22 operator are not contacted by P22 repressor, the affinity of repressor for operator varies with the sequence of these bases. The KMnO₄ and ^•OH radical susceptibilities of the central bases of the operator vary with their sequence, whether or not the operator is complexed with protein or free in solution. These data show that the minor groove of a lower affinity operator which bears central C-G bases (9C) is more open than that of the higher affinity 9T operator, which bears central T-A bases. This difference in minor groove width is seen both in the absence and presence of repressor. Results of ring closure studies show that, in the absence of repressor, an operator bearing central C·G base pairs operator is overtwisted relative to an operator which contains central T·A base pairs. The binding of P22 repressor unwinds the two operators to similar extents, thereby preserving the relative differences in twists of these DNAs. Although repressor alters the twist of the operator DNA, our results show that differences in DNA torsional flexibility have no role in determining the affinity of operator for protein. Instead, the results indicate that central sequences affect operator affinity for protein by limiting the degree to which the operator can be deformed in the protein-DNA complex. The stability of the complex is apparently modulated, in a central sequence-dependent manner, by alterations in the number and/or geometry of protein-DNA contacts.