Hairpin Polyamides That use Parallel and Antiparallel Side-by-Side Peptide Motifs in Binding to DNA

Abstract

Pt-bis-netropsin is a synthetic sequence-specific DNA-binding ligand comprizing two netropsin-like fragments which are linked in a tail-to-tail manner via a cis-diammineplatinum (II) residue. The CD studies and thermodynamic characterization of the DNA-binding properties exhibited by this compound reveal that it forms two types of complexes with poly[d(AT)].poly[d(AT)] and DNA oligomers containing nucleotide sequences 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 molecule per 9 AT-base pairs. The second type of the complex corresponds to the binding of Pt-bis-netropsin to DNA in the folded hairpin form. The binding approaches saturation level when one Pt-bis-netropsin molecule 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 spectral profiles reflecting the binding of Pt-bis-netropsin in the hairpin form are different from those observed for binding of another bis-netropsin with the sequence Lys-Gly-Py-Py-Gly-Gly-Gly-Py-Py-Dp, where Py is a N-propylpyrrole amino acid residue and Dp is a dimethylaminopropylamino residue. The hairpin form of this bis-netropsin is formed on the basis of antiparallel side-by-side peptide motif. The CD spectra obtained for complexes of this polyamide in the hairpin form with poly[d(AT)].poly[d(AT)] exhibit positive CD band with a peak at 325 nm, whereas the CD spectral profiles for the second complex of Pt-bis-Nt with poly[d(AT)].poly[d(AT)] and short DNA oligomers have two intense positive CD bands near 290 nm and 328 nm. This reflects the fact that two bis-netropsins use different structural motifs on binding to DNA in the hairpin form.

Abstracts: Eleventh Conversation

“…Further increase in ligands concentration leads to a sharp increase of the width of transition of the complexes. In this case transition point of the complexes decreases which indicates that former stabilizer becomes a destabilizer of double stranded DNA (1). We are going to present the experimental data proving the prediction of the theory at the case of Ethidium bromide and Actinomycine D. We experimentally established the value of concentration at which these well-known stabilizers of the double helix of DNA begin to destabilize it.…”

“…The human genome has more than 100,000 factors of pyr-pur tracts, which are 200-300 bp long ( 4 ). This raises the possibility that triplex DNA may have a biological function ( 1 ). Triplex DNA may be involved in the in vivo regulation of gene expression and in chromosome organization ( 1 ).…”

“…Triplex DNA has become the topic of exhaustive research, and these nucleic acids can be developed from synthetic pyrimidine-purine (pyr-pur) DNA (1)." Triplexes based on T-A-T and C-G-C base triads can be formed easily and are stabilized in the presence of physiological concentration of polyamine (2).…”

“…Triplexes based on T-A-T and C-G-C base triads can be formed easily and are stabilized in the presence of physiological concentration of polyamine (2). Supercoiling provides the energy needed to drive the unwinding of the DNA molecule for triplex DNA development (1). Long tracts of pyr-pur occur in eukaryotic chromosomes and could constitute 1% of the genome (3).…”

“…The minimal requirements for components of designed crystals are [ 1] programmable interactions, [2] predictable local intermolecular structures and [3] rigidity. The stickyended association of DNA molecules fulfills the first two criteria, because it is specific and diverse, and it results in the formation of B-ONA Stable branched DNA molecules permit the formation of networks, but simple branches are too flexible.…”