Eckhard Birch-Hirschfeld

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 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.

Penetration and Antiviral Activity of Coxsackievirus B3 (Cvb3)-Specific Phosphorothioate Oligodeoxynucleotides (Ps-Odn)

Abstract The antiviral activity of PS-ODNs, complementary to different regions of the CVB3 genome, was investigated under in vitro conditions. Inhibition of CVB3 replication was detected only after prolonged pretreatment of HeLa cells with antiviral active PS-ODNs, but not when virus and PS-ODN were applicated simultaneously. Results from flow cytometric analysis indicate that a low cellular uptake of anti-CVB3 oligonucleotides into HeLa cells might be a reason for their moderate antiviral activity.

Selforganization of Nucleic Acids Visualized by Scanning Force Microscopy

Abstract SFM-investigations visualize domains and microdomains of selforganizational DNA- and RNA-adlayer patterns on graphite substrates and contribute by this to general approaches of elucidating biomesogen pre-life states complexity.

Possibilities of Triplex-Formation by 21-Mer Oligodeoxyribonucleotides as Analogs of Tetrahymena Pre-rRNA Fragments

Abstract A potential DNA triple helix of 21-mer oligodeoxyribonucleotides was synthesized and characterized. The strands were chosen to study the interaction of internal guide and intervening sequences analogs as well as adjacent 3′and 5′exon parts around the splicing site of Tetrahymena pre-rRNA. Further in parallel works a series of different RNA and DNA strands was synthesized and combined yielding a suitable order of stability. Here we want to show an isolated examination of a DNA-strand triple helix with defined sequences containing a central mismatched base arrangement and T-A-T bases at the ends.

Stabilization of Double Stranded Homologous Poly(dA)·Poly(dT) by Taxol.

Abstract The nucleic acid activity of taxol and paclitaxel was investigated with synthetic and natural oligo- and polynucleotides. The polynucleotides poly(dA)·poly(dT), poly(dG)·poly(dC), poly [d(A-T)]·poly[d(A-T)], poly[d(G-C)]·poly[d(G-C)] and calf thymus DNA were used. The oligonucleotides are 24-mers with d(purine)24·d(pyrimidine)24 strands, as well as d[(purine)x-(pyrimidine)x]·d[(purine)x-(pyrimidine)x] sequences. The study was performed with spectroscopic and calorimetric methods in dilute and condensed DNA-solutions. In a recent study, taxol and paclitaxel showed molecular recognition of AT nucleotides with a high affinity to homologous (dA)·(dT) sequences; no interaction with GC nucleotides could be observed. An astonishing stabilization of the DNA duplex up to ΔTm = 25°C was measured by thermal denaturation with poly(dA)·poly(dT)/paclitaxel complexes. Circular dichroism signals of DNA (24-mer) containing homologous (dA)·(dT) tracts increased with increasing amount of the drug; for the other oligo- and polynucleotides no change in the spectra could be found. Contrary to this findings, circular dichroism (CD) spectra of poly(dA)·poly(dT)/paclitaxel complexes displayed reduced intensities of the signals at increasing drug concentrations. These findings in dilute solutions were complemented by differential scanning calorimetric investigations in condensed states (only calf thymus DNA tested). Increasing enthalpies by increasing amount of the drug point to a stabilization. Simple phosphate backbone interaction in the narrow groove of (dA)·(dT) tracts could be a sufficient explanation for all the results. Hydrophilic side groups of the drug interact with the phosphate and clip the strands together, while the hydrophobic parts of the molecule may disturb the polynucleobase formation.