Detection of conformational and net charge differences in DNA‐protein complexes by quantitative electrophoresis on polyacrylamitie‐agarose copolymer gels

The Galactosidase repressor (GalR) of Escherichia coli modulates the expression of the gal operon by binding to two DNA operators, O_E and O₁. The O_E and O₁ elements are 16 by pallindromic DNA sequences, differing in four of the base pairs (Fig. 1). O_E and O₁ DNA fragments, both free and complexed with repressor, were analyzed by “quantitative gel electrophoresis”. By the criteria of that method, applied to the linear Ferguson plots of both DNA fragments and the linear ranges of those of the DNA‐GalR complexes, it was shown that the apparent size of DNA increases upon repressor binding. Moreover, this size increase is greater for the complex with the O₁ operator than for the complex with the O_E operator in the case that GalR is located in the center of a 155 bp DNA fragment. This is not the case when GalR is located in a peripheral position. By contrast with their size differences, the centrally located GalR‐O₁ and GalR‐O_E complexes appear to possess indistinguishable net surface charge densities as judged from the intercepts with the mobility axis. The larger size of the complex with centrally located O₁ fragment, as compared with that bearing the O_E fragment, is interpreted as being due to bending of the DNA‐protein complex, since an authentically bent fragment of a plasmid with bent upstream activator sequence also exhibits a larger slope of the Ferguson plot, and thus the larger size, than predicted on the basis of its DNA chain length (bp). Thus, the apparently larger size of the GalR‐O₁ complex at the center of DNA, compared to that of the GalR‐O_E complex, supports the previous conclusion that the Gal repressor induces a larger degree of bending in O₁ DNA than in O_E DNA. DNA fragments bearing O_E and O₁ when complexed with the Gal repressor show convex Ferguson plots at polyacrylamide concentrations below that of gelation and in the presence of 0.5 % agarose, while the plots of the corresponding free 155 bp DNA fragments are linear in that range. The curvature presumably reflects the size increase concomitant with complex formation, since DNA larger than 155 bp also exhibits that curvature on polyacrylamide stabilized by nonrestrictive agarose gels.