Synthesis of peptide analogs and the study of their interactions with nucleic acids, by fluorescence, NMR, and Raman spectroscopy

Peptide analogs containing aromatic amino acid residues were synthesized. The interaction of peptide analogs with Calf Thymus DNA, Poly(dA-dT)2, and Poly(A) was studied by Fluorescence, NMR and Raman spectroscopy. The peptide analogs had the general structure X-S-X, where S was a diaminopropane or a diaminoacetone spacer and X an aromatic amino acid. The aromatic residues used were phenylalanine, paranitrophenylalanine, tyrosine, and naphthylalanine. The interaction of the analogs containing diaminoacetone could not be studied due to their decomposition after the final deprotection step. Fluorescence studies of the amide of LysyInaphthylalanine with the nucleic acids allowed the determination of the apparent association constant. In the fluorescence studies, a quenching of the fluorescence of the naphthyl group in the presence of the nucleic acids was observed and attributed to stacking interactions of the aromatic ring with the nucleic acid bases. The stacking interactions of the amide of Lysylnaphthylalanine were greater for double stranded nucleic acids and followed the order: CT-DNA>poly(dA-dT)2>poly(A). Raman studies of the complexes between the amide of Lysylnaphthylalanine and nucleic acids showed a reduction of intensity of the bands assigned to the phosphate vibrations of the nucleic acids. These changes are consistent with the formation of a peptide-DNA complex that causes conformational changes in the DNA. These results are also consistent with previous results from molecular modeling and NMR studies of complexes of the amide of Lysylnaphthylalanine with DNA and Poly(dA-dT)2 in which a strong stacking interaction 0is observed. In addition, the results are consistent with the model proposed by Gabbay and other researchers in which a bending of the DNA double helix occurs when aromatic residues of proteins establish stacking interactions with DNA.