title: Monovalent cations regulate DNA sequence recognition by 434 repressor.
abstract: The bacteriophage 434 repressor distinguishes between its six naturally occurring binding sites using indirect readout. In indirect readout, sequence-dependent differences in the structure and flexibility of non-contacted bases in a protein's DNA-binding site modulate the affinity of DNA for protein. The conformation and flexibility of a DNA sequence can be influenced by the interaction of the DNA bases or backbone with solution components. We examined the effect of changing the cation-type present in solution on the stability and structure of 434 repressor complexes with wild-type and mutant OR1 and OR3, binding sites that differ in their contacted and non-contacted base sequences. We find that the affinity of repressor for OR1, but not for OR3, depends remarkably on the type and concentration of monovalent cation. Moreover, the formation of a stable, specific repressor-OR1 complex requires the presence of monovalent cations; however, repressor-OR3 complex formation has no such requirement. Changing monovalent cation type alters the ability of repressor to protect OR1, but not OR3, from *OH radical cleavage. Altering the relative length of the poly(dA) x poly(dT) tract in the non-contacted regions of the OR1 and OR3 can reverse the cation sensitivity of repressor's affinities for these two sites. Taken together these findings show that cation-dependent alterations in DNA structure underlies indirect readout of DNA sequence by 434 repressor and perhaps other proteins.
authors.affiliation: Department of Biological Sciences, State University of New York at Buffalo, 607 Cooke Hall, North Campus, Box 601300, Buffalo, NY 14260-1300, USA.
authors.forename: Steven A
authors.initials: SA
authors.lastname: Mauro
authors.forename: Gerald B
authors.initials: GB
authors.lastname: Koudelka
mesh_terms: D001483:Base Sequence; D002414:Cations, Monovalent; D003090:Coliphages / Q000378:metabolism*; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D012097:Repressor Proteins / Q000378:metabolism*; D012689:Sequence Homology, Nucleic Acid; D014764:Viral Proteins
chemical_list: C063367:434-repressor protein, Bacteriophage 434; D002414:Cations, Monovalent; D012097:Repressor Proteins; D014764:Viral Proteins; D004247:DNA