HAIRPIN POLYAMIDES THAT USE PARALLEL AND ANTIPARALLEL SIDE-BY-SIDE PEPTIDE MOTIFS IN BINDING TO DNA

Pt-bis-netropsin is a synthetic sequence-specific DNA-binding ligand c omprizing two netropsin,like fragments which are linked in a tail-to-t ail manner via a cis-diammineplatinum (II) residue. The CD studies and thermodynamic characterization of the DNA-binding properties exhibite d by this compound reveal that it forms two types of complexes with po ly[d(AT)].poly[d(AT)] and DNA oligomers containing nucleotide sequence s 5'-CC(TA)(n) CC-3', with n = 4, 5 and 6. The first type corresponds to the binding of Pt-bis-netropsin in the extended conformation and is characterized by the saturating ratio of one bound Pt-bis-netropsin m olecule per 9 AT-base pairs. The second type of the complex correspond s to the binding of Pt-bis-netropsin to DNA in the folded hairpin form . The binding approaches saturation level when one Pt-bis-netropsin mo lecule is bound per four or five AT-base pairs. The hairpin form of Pt -bis-netropsin complex is built on the basis of parallel side-by-side peptide motif which is inserted in the minor DNA groove. The CD spectr al profiles reflecting the binding of Pt-bis-netropsin in the hairpin form are different from those observed for binding of another bis-netr opsin with the sequence Lys-Gly-Py-Py-Gly-Gly-Gly-Py-Py-Dp, where Py i s a N-propylpyrrole amino acid residue and Dp is a dimethylaminopropyl amino residue. The hairpin form of this bis-netropsin is formed on the basis of antiparallel side-by side peptide motif. The CD spectra obta ined for complexes of this polyamide in the hair-pin form with poly[d( AT)].poly[d(AT)] exhibit positive CD band with a peak at 325 nm, where as the CD spectral profiles for the second complex of Pt-bis-Nt with p oly[d(AT)].poly[d(AT)] and short DNA oligomers have two intense positi ve CD bands near 290 nm and 328 nm. This reflects the fact that two bi s-netropsins use different structural motifs on binding to DNA in the hairpin form.