Specificity and Dynamics of Protein-Nucleic Acid Interactions

Abstract

First, a survey is given on model experiments, which provide information on the contribution of individual amino acid side chains to interactions of amino acids with nucleic acids. The most sensitive approach proved to be an analysis of helix-coil transitions in the presence of various ligands. Measurements for different RNA and DNA helices in the presence of amino acid amides demonstrate the existence of an affinity scale for the interaction of amino acid residues with nucleic acids, which is mainly determined by the hydrophobicity. The data indicate a direct pathway for the evolution of melting proteins and can be used to construct a simple model for the evolution of the genetic code. Recent experiments also demonstrate a selective interaction of amino acid residues with tRNA^Phe.

In the second part, the dynamics of nucleic acid ligand interactions is discussed. As shown by electric field jump experiments, simple oligonucleotide-oligopeptide complexes are formed at a diffusion controlled rate, whereas “insertion” of aromatic residues between stacked bases is already a relatively slow reaction. An example is also given for the use of electro-optical procedures for analysis of structures in solution: rotation time constants demonstrate that binding of cyclic AMP receptor to specific DNA fragments leads to strong bending of the double helix around the protein. The importance of ligand mobility along nucleic acid chains is demonstrated for the example of a melting protein. Finally, the dynamics of a repressor-operator recognition is compared for the lac- and the tet-system; some mechanisms for the motion of ligands along polynucleotides are discussed.