The effect of the trp repressor from Escherichia coli on the structure and dynamics of dA₂₀dT₂₀

We have determined the effect of the tryptophan (trp) repressor from Escherichia coli on the structure and dynamics of dA₂₀dT₂₀. The structure was determined using time-dependent nuclear Overhauser effects and spin-lattice relaxation times. The deoxyribose conformation is near C3′ endo for the thymine residues, and a mixture of about 30% C3′ endo and 70% C2′ endo for the adenine residues. The glycosidic torsion angles are -50° for T and -60° for A. The roll is 20° and the propellor twist is about 29°. The conformation is consistent with recent calculations (Rao, K. and Kollman, P.A. (1985) J. Am. Chem. Soc. 107, 1507-1511). The rate constant for exchange of the imino protons is similar to that usually found for AT base-pairs, with an activation energy of 20 ± 2 kcal/mol, and an activation entropy of 17 ± 7 cal/mol per K. The repressor greatly retards the exchange of imino protons, and the activation energy increases to 38 kcal/mol. There are small changes in the structure of the DNA on forming the complex, with the adenine and thymidine residues becoming more similar in conformation.