Interaction of Two Peptide-Acridine Conjugates Containing the SPKK Peptide Motif with DNA and Chromatin

Abstract

The interaction between DNA and two peptide-acridine conjugates containing one (1) or two (2) moieties of the Ser-Pro-Lys-Lys (SPKK) minor groove-binding peptide motif has been studied by a combination of hydrodynamic, biochemical and spectroscopic methods including diffusion-enhanced luminescence energy transfer (DELET) measurements with a Tb(III) lanthanide chelate as donor. Viscometric titrations do not reveal any significant difference between the two hybrid molecules which both unwind (by about 15 degrees) and extend the DNA similarly. DELET measurements show that the acridinyl chromophore of compounds 1 and 2 is much more accessible than that of a simple monointercalating drug such as acridine orange or ethidium. The accessibility factor increases proportionally with the peptide length, reflecting the extent of perturbation imposed upon the intercalating chromophore by the binding to DNA of the peptide moiety of the hybrids. Experiments with the osmium tetroxide-bispyridine reagent indicate that the two hybrid compounds both affect the local conformation of DNA rendering certain thymine residues conspicuously accessible to the probe. The drug-induced sites of hyperreactivity towards OsO4 in DNA are very similar with the exception of a short run of three T residues which is attacked more strongly in the presence of tetrapeptide-acridine conjugate 1 than with the octapeptide-acridine conjugate 2. These results are fully in agreement with previous footprinting studies and support the view that a minimum of two SPKK motifs is required to mimic the AT-specific minor groove binding antibiotic netropsin. On the basis of the DNA-binding properties of these two peptide-acridine hybrids, we present DNA-binding models in which the acridinyl moiety of compound 1 protrudes slightly outside the double helix but remains more or less parallel to the plane of the base-pairs. In contrast, with compound 2, where the octapeptide SPKKSPKK is bound to the minor groove, we postulate that the chromophore lies only partially overlapped with the base pairs in the intercalation site and, in addition, the heterocyclic chromophore is significantly tilted with respect to the double helix axis. Electric linear dichroism and DELET measurements with chromatin reveal that the presence of histone proteins affects the intercalative binding of compound 2 while it has practically no effect on the binding of compound 1.

Reaction of a Biscationic Distamycin-Ellipticine Hybrid Ligand with DNA. Mode and Sequence Specificity of Binding

“…Linear dichroism provides a sensitive tool to define the orientation of drugs bound to DNA (Norden et al, 1992) and has the additional advantage that it senses only the orientation of the polymerbound ligand: free ligand is isotropic and does not contribute to the signal. We have shown that electric linear dichroism can be particularly useful as a means of analyzing the structure of hybrid molecule-DNA complexes (Bailly et al, 1990(Bailly et al, , 1992a(Bailly et al, , 1993aFlock et al, 1994). Figure 8a shows the ELD spectra of complexes of Distel (1+) and Distel (2+) with poly(dA-dT)*poly(dA-dT).…”

Oxoazabenzo[de]anthracenes Conjugated to Amino Acids: Synthesis and Evaluation as DNA-Binding Antitumor Agents

“…The design of drugs linked to Lys-containing di- and tripeptides is also considered. In the past, we also successfully elaborated peptide−intercalator conjugates encompassing one or two Ser-Pro-Lys-Lys (SPKK) motifs ( − ). The same motif could also be adequate to optimize the activity of the oxoazabenzo[ de ]anthracene ring system.…”

Peptide Regulation of Gene Expression: A Systematic Review

“…Both peptide conjugates interact with the major and minor grooves of dsDNA. This process is not impacted by the interaction of the dsDNA with histones [85,86]. However, the probability of the SPKKSPKK octapeptide binding to the minor groove of dsDNA depends on the (non-)availability of histone proteins [87].…”