Biochemistry 1992,31, 10969-10975 10969 Evidence That a Minor Groove-Binding Peptide and a Major Groove-Binding Protein Can Simultaneously Occupy a Common Site on DNA+

ABSTRACT: Affinity cleaving proteins have been synthesized based on the DNA-binding domain of the yeast transcriptional activator GCN4 with the DNA cleaving moiety Fe-EDTA attached a t the NH2 terminus [Oakley, M. G., & Dervan, P. B. (1990) Science 248, 8471. Cleavage patterns generated by Fe-EDTA-GCN4(226-28 1) bound to the DNA sites 5’-CTGACTAAT-3 ’ and 5’-ATGACTCTT-3 ’ reveal that the NH2 termini of the GCN4 DNA-binding domain are located in the major groove of DNA, 9-10 base pairs apart, consistent with a Y-shaped dimeric structure. 1-Methylimidazole-Zcarboxamide netropsin (2-ImN) is a designed synthetic peptide which binds in the minor groove of DNA at 5’-TGACT-3 ’ sites a