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.
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