Chemical Approaches to the Study of Protein-tRNA Recognition

Abstract

Chemical modification methods can be used to study the structural requirements for recognition of tRNAs by proteins, provided that alteration of a specific site in the tRNA can be correlated with the presence or absence of an effect on the protein-tRNA interaction. This can often be accomplished by selection of a reagent that attacks a unique target in the tRNA, such as the 3′ or 5′ terminal, or a specific minor base. The amount of structure-function information that can be obtained using such highly selective reagents is obviously limited to a very small number of sites. To probe other internal regions of tRNA structure, reagents can be used that modify major bases. Such reagents normally alter a number of sites simultaneously, making it necessary to carry out additional steps to determine which of the modifications produced are significant in terms of their effect on a particular biological activity. In this paper, I will describe the general methods used in my laboratory to obtain specific information on the structural requirements for recognition of Escherichia coli tRNAs^Met by a number of E. coli proteins following modification of the tRNAs with reagents that alter the structure of major bases.

CONFORMATIONAL EFFECTS ON BIOLOGICAL ACTIVITY
Recognition of tRNAs by proteins is expected to involve interactions between essential ligands located at specific sites in the three-dimensional structure of each macromolecule. Such interactions can be destroyed either by altering the conformation of the tRNA in a manner that changes the spatial orientation of a required functional...