Recognition of nucleic acid base by tryptophan-containing peptides: spectroscopic study on interaction of N-acetylTrp-(Gly)m-Asp-(Gly)n-TrpNHCH3 (m = 0-2, n = 0-2) with guanine base.

As part of the designs of tryptophan-containing peptides which possess specific binding ability for each nucleic acid base, a series of N-acetylTrp-(Gly)m-Asp-(Gly)n-TrpNHCH3 (m = 0-2, n = 0-2) were chemically synthesized, and their abilities to form complexes with a guanine base were examined by the fluorescence and 1H-NMR methods. Fluorescence titration suggested the most preferential stacking interaction of the Trp-Gly-Asp-Trp sequence with the base. Analysis of low-field shifts of guanine N2-amino protons showed the hydrogen bond pairing with the Asp carboxyl side chain and its favorable formation for the -Gly-Asp-Trp peptide sequence. On the other hand, the largest up-field shift of guanine H8 proton was observed for Trp-Gly-Asp-Trp peptide, although its shifting degree caused by the stacking interaction with the Trp indole ring was not so significant. Thus, both spectroscopic methods indicated the Trp-Gly-Asp-Trp sequence to be most suitable for the guanine base recognition, which is constituted with the intimate cooperation of the hydrogen bond formation between the Asp carboxyl and guanine NH2 groups and the stacking interaction of the base with two neighboring Trp indole rings. This sequence preference would also be possible in acidic circumstances where the guanine N7 atom is protonated. A tentative interaction model is proposed based on these spectroscopic results.