Thr-Val-Thr Dansyl Hydrazide: The First Fluorescent Tripeptide Preferentially Binding with AT Pairs in DNA

Abstract

In 1991–1993 we amended a DNA-protein recognition model advanced in 1975 [Mol. Biol. (Engl. trans.) 25, 819–836 (1991), J. Biomol. Struct. Dynam. 10, 763–784 (1993)]. Here we test our assumptions with a specially designed tripeptide L-Thr-L-Val-L-Thr-NH-NH-Dns (Dns is 5-dimethylaminonaphthalene-l-sulfonic acid residue). It is shown to dimerize in solution (as evidenced by the nonlinear concentration dependence of its fluorescence) and to bind with DNA mainly in β-dimeric form (S-shaped adsoiption isotherm obtained by equilibrium dialysis). The tripeptide is bound in the DNA minor groove (whence it can be displaced with distamycin A), and such complexes become able to associate into ‘biduplex’ structures (nonlinear dependence of the linear dichroism of bound peptide on DNA concentration). The peptide dimers clearly prefer the AT pairs [half-saturating peptide concentrations are (0.6–0.7)-10 ⁴ M for poly(dA)·poly(dT) but exceed (2.5–2.8)-10⁴ M for poly(dG)·poly(dC)]. These results agree nicely with our earlier suggestions. Since Dnstagged trivaline has been shown [Cold Spring Harbor Symp. Quant. Biol. 47, 361–372 (1983)] to prefer the GC pairs, we think it now becomes possible to design oligopeptides that would specifically bind to any predefined nucleotide sequence.

Key words:

• Threonine
• Tripeptide
• β-dimer
• Protein-DNA recognition