The DNA sequence to which a protein binds can profoundly affect the ability of the protein-DNA complex to participate in gene regulatory processes. Hence, DNA is more than a passive platform onto which proteins assemble, it can play an active, second role as an allosteric effector of protein function. The allosteric effect of DNA is a recently discovered phenomenon. Thus, the goal of understanding how DNA influences the form and function of the transcriptional regulatory protein represents the leading edge of the work on the function of DNA binding proteins. The repressor of bacteriophage 434 appears to undergo two conformational changes, one as it dimerizes in the presence of nonspecific DNA and another as the repressor dimer binds to a specific DNA binding site. The structure and function of the 434 repressor-DNA complex may vary with the identity of the DNA sequence to which it binds. Among other changes these distinct structural forms vary in their abilities to form higher order oligomeric complexes. The conformational differences between these complexes influence 1) sequence recognition by the repressors; 2) cooperative interactions between DNA bound repressors and 3) the interaction of the repressor with RecA. In light of these findings, the basis for the allosteric effect of DNA on repressor function will be determined. Having established the nature of DNA allostery, this information will then be used to probe the allosteric effect of DNA on repressor tetramer formation to provide insight into the mechanism of DNA-dependent cooperative binding of repressor. In addition, this information will guide experiments aimed at providing an understanding of how the distribution of the various oligomeric forms of repressor can be regulated by interaction with other proteins and DNA in the host cell. Insights gained from these results will further the understanding of the critical determinants of function in these and other sequence-specific protein-DNA complexes. In addition to being an archetypal system in which the effect of DNA sequence on function can be investigated, the lambdoid bacteriophages provide a conceptually and practically accessible system in which to study the role of protein-protein interactions in gene regulation. These features have allowed students at all levels, including those at the high school level, to significantly contribute to the battery of observations and understanding in this system. By working in this system, students at the graduate, undergraduate and high school levels, have learned how to ask important biological questions, and used their observations to make important contributions to the understanding of gene regulatory mechanisms. The elegant simplicity of the system ensures that others will do the same.
