Tyrosyl-base-phenylalanyl intercalation in gene 5 protein-DNA complexes: proton nuclear magnetic resonance of selectively deuterated gene 5 protein

Abstract

The interactions of oligodeoxynucleotides with the aromatic residues of gene 5 protein [from Escherichia coli] in complexes with d(pA)8 and d(pT)8 were determined by 1H NMR of the protein in which the 5 tyrosyl residues were selectively deuterated either in the 2,6 or the 3,5 positions. Only the 3,5 protons of the 3 surface tyrosyls (26, 41 and 56) interact with the bases. The remainder of the aromatic protons undergoing base-dependent upfield ring-current shifts on complex formation are phenylalanyl protons, assigned to Phe(13) on the basis of model building. 19F NMR of the complexes of the m-fluorotyrosyl-labeled protein with d(pT)4 and d(pA)8 confirms the presence of ring-current perturbations of nuclei at the 3,5-tyrosyl positions of the 3 surface tyrosyls. Differential expression of the 19F{1H} nuclear Overhauser effect confirms the presence of 2 buried and 3 surface tyrosyl residues. A new model of the DNA binding groove is presented involving Tyr(26)-base-Phe(13) intercalation.