DNA-protein complexes are the biologically relevant DNA species par excellence. Thus, while previous electrophoretic DNA characterization has dealt with conformational analysis of free DNA, this year's project aimed at such analysis of DNA-protein complexes. Two classical, well-studied complexes provided suitable models for such work: The nucleosome and the E.coli-DNA-CAP complex. It was found that in contrast with the free nucleosomal or standard linear DNA which are stretched in proportion to gel concentration, the nucleosome maintains its globular conformation, brought about by the wrapping of 1.5 superhelical turns around histone octomer, independently of gel concentration, i.e. the conformation of the complex in a gel is that of a protein, not of DNA. Electrophoretic conformational analysis of DNA-protein complexes was also applied to the problem of distinguishing peripherally and centrally bound CAP promoter on a 146 bp DNA fragment by transverse pore gradient gel electrophoresis. A difference in deformability by the gel was found. It is due to differences in curvature of the DNA fragment carrying the specific binding site on which the well-known DNA bending by CAP is superimposed.
