1H NMR Studies of the Binding of Bacteriophage‐M13‐Encoded Gene‐5 Protein to Oligo(deoxyadeny1ic acid)s of Varying Length

Abstract

The binding of gene-5 protein to oligo(deoxyadenylic acid)s varying in length from 2-16 nucleotides was studied by titrating the protein with the oligonucleotides and recording the 1H NMR spectra at 360 MHz. To obtain information about the mode of binding of the protein, the aromatic parts of the spectra wre analyzed by performing spectral simulations, starting from the assignments obtained from nuclear Overhauser enhancements at 500 MHz. The 1H NMR spectra of the complexes of gene-5 protein with (dA)8, (dA)12 and (dA)16 appear to be identical except for differnces in linewidth. The 1H NMR spectra of the complexes with the smaller oligonucleotides (dA)2, (dA)3 and (dA)4 differ from each other and from the spectra obtained from the complexes with longer oligonucleotides. Binding of all oligonulceotides basically influences the same aromatic residues, namely 2 tyrosines and 1 phenylalanine. In the protein-oligonucleotide complexes, 1 protein monomer covers 3 nucleotide residues, in contrast to the stoichiometry of 1:4 found for protein-polynucleotide complexes. The binding to oligonucleotides apparently is cooperative and ionic-strength-dependent but far less so than found for the binding to polynucleotides.