Reaction of nucleic acid bases with α-acetylenic esters: Part IV. Preparation of an alkylating derivative of tRNA Phe by conformation-specific chemical modification

Abstract

The reaction of yeast tRNA Phe with methyl chlorotetrolate, ClCH 2-C≡C-COOCH 3, was studied. This reagent converts adenine and cytosine rings into derivatives in which an additional heterocycle bearing the alkylating chloromethyl group is fused to the original base; these derivatives can exist in two isomeric forms. Modified nucleosides of this type can be easily identified by reverse-phase HPLC. It was found that under native conditions, the modification of tRNA involves the anticodon loop and the 3′-end. The isomers of adenine derivatives formed in the anticodon loop were different from those formed in the 3′-end. It is suggested that the isomeric structure of the derivatives is related to the fine conformational differences between these two regions of tRNA Phe. Methyl chlorotetrolate could thus be used as a conformational probe of single-stranded nucleic acids. Preliminary assays showed that modified tRNA Phe binds irreversibly to yeast phenylalanyl-tRNA synthetase.