Propidium binding to a ribonuclease-DNA complex: X-ray and fluorescence studies.

Propidium iodide, an antitumor compound, was diffused into crystals of a complex between RNase A and deoxytetraadenylate (dpA)4). This complex has four deoxyoligomers bound per protein molecule. A difference Fourier analysis at 2.9 A showed that the principal binding site for the propidium in the crystals was a hydrophobic depression on the side of RNase away from the active site and apparently involves methionine 13 and phenylalanine 8. Binding of propidium at this site produces small conformational changes that effect binding of nucleotides at the active site of the enzyme. Fluorescence titrations in the presence and absence of nucleotide inhibitors suggested that propidium iodide is a competitive inhibitor of the enzyme with a Kl of approximately 1 mM. No significant binding of propidium to the 16 nucleotides of single-stranded DNA associated with each protein molecule was observed.