title: The role of the minor groove substituents in indirect readout of DNA sequence by 434 repressor.
abstract: The sequence of non-contacted bases at the center of the 434 repressor binding site affects the strength of the repressor-DNA complex by influencing the structure and flexibility of DNA (Koudelka, G. B., and Carlson, P. (1992) Nature 355, 89-91). We synthesized 434 repressor binding sites that differ in their central sequence base composition to test the importance of minor groove substituents and/or the number of base pair hydrogen bonds between these base pairs on DNA structure and strength of the repressor-DNA complex. We show here that the number of base pair H-bonds between the central bases apparently has no role in determining the relative affinity of a DNA site for repressor. Instead we find that the affinity of DNA for repressor depends on the absence or presence the N2-NH(2) group on the purine bases at the binding site center. The N2-NH(2) group on bases at the center of the 434 binding site appears to destabilize 434 repressor-DNA complexes by decreasing the intimacy of the specific repressor-DNA contacts, while increasing the reliance on protein contacts to the DNA phosphate backbone. Thus, the presence of an N2-NH(2) group on the purines at the center of a binding site globally alters the precise conformation of the protein-DNA interface.
authors.affiliation: Department of Biological Sciences, University at Buffalo, Buffalo, New York 14260-1300, USA.
authors.forename: Steven A
authors.initials: SA
authors.lastname: Mauro
authors.forename: David
authors.initials: D
authors.lastname: Pawlowski
authors.forename: Gerald B
authors.initials: GB
authors.lastname: Koudelka
mesh_terms: D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D020029:Base Pairing; D001483:Base Sequence; D001665:Binding Sites; D002942:Circular Dichroism; D017665:Hydroxyl Radical; D007700:Kinetics; D009690:Nucleic Acid Conformation; D009994:Osmolar Concentration; D011487:Protein Conformation; D012097:Repressor Proteins / Q000737:chemistry* / Q000235:genetics*; D013816:Thermodynamics; D014764:Viral Proteins
chemical_list: C063367:434-repressor protein, Bacteriophage 434; D012097:Repressor Proteins; D014764:Viral Proteins; D017665:Hydroxyl Radical