Spectroscopic study on interaction of nucleic acid base with tryptophan-containing tripeptides: acetyl-Trp-X-Trp-NHCH3 (X = Gly, Asn, Asp, Gln and Glu).

As part of a series of peptides designed to have binding ability selective for each of the nucleic acid bases, five tripeptides consisting of N-acetyl-Trp-X-Trp-NHCH3 (X = Gly, Asn, Asp, Gln and Glu) were synthesized, and their abilities to form complexes with four different nucleotides were examined by the fluorescence and phase distribution methods. The association constants obtained indicated that, depending on the sort of X residue, the peptides showed a variation in their interaction with guanosine monophosphate (GMP), while no noticeable selectivity was observed for other nucleotides adenosine monophosphate (AMP), uridine monophosphate (UMP) and cytidine monophosphate (CMP). The binding mode of N-acetyl-Trp-Asp-Trp-NHCH3 for the guanine base was further investigated using the proton nuclear magnetic resonance (1H-NMR) method. The mode was suggested to involve intimate cooperation of (1) the hydrogen bond formation between the carboxyl group of the Asp side chain and the guanine C2-amino group, and (2) the stacking interaction of the base with two terminal Trp residues of the peptide. Such interaction was strengthened by the protonation of the guanine base. A tentative binding mode is proposed based on these results.