Characterization and application of a DNA aptamer binding to l-tryptophan

Abstract

DNA aptamers for specific recognition of L-tryptophan have been evolved by a SELEX (systematic evolution of ligands by exponential enrichment) technique. Truncation–mutation experiments suggest that a 34-mer sequence, Trp3a-1, possesses the strongest binding ability to L-tryptophan. Trp3a-1 is predicted to adopt a loop–stem secondary structure, in which the loop may further fold into a binding pocket for L-tryptophan with the help of the stem. The specificity investigation shows that Trp3a-1 strongly binds to L-tryptophan, has almost no binding to other amino acids, and weakly binds to some tryptophan analogs and peptides containing the L-tryptophan residue. The binding of Trp3a-1 to L-tryptophan is mainly contributed to by hydrogen bonds and precise stacking formed between the binding pocket of Trp3a-1 and all groups on L-tryptophan. This aptamer has also been proved to be an effective ligand for the chiral separation of D/L-tryptophan. L-Tryptophan and its derivatives are known to play important biological roles; this aptamer ligand could be used as a tool for the analysis of tryptophan and other related studies.