Characterizing an RNA aptamer and binding studies with synthetic porphyrazines

Part I. Characterization of the secondary structure and stability of an RNA aptamer that binds vascular endothelial growth factor. Thermal denaturation studies and spectroscopic studies were employed to investigate the secondary structure and stability of an RNA/PEG conjugate commercially called Macugen(TM). The RNA aptamer is conjugated to a pegylated moiety and the majorities of its 2" hydroxyl group are methlyated or otherwise modified. UV optical melting studies and Differential Scanning Calorimetry (DSC) were carried out under different conditions to evaluate the effects of Na + and oligomer concentrations on the stability of the secondary structure of the RNA oligomer. The results of these studies indicated that the melting temperature (Tm) of the RNA is independent of oligomer concentration but dependent on the salt concentration, in a predictable fashion.; Part II. Synthetic porphyrazines: A new class of DNA binding molecules. We have investigated the interaction specificities of a series of synthetic porphyrazines with synthetic DNA oligomers (CG) 2ATAT (CG)2, T4G4, and (TTAGGG) 4. The porphyrazines were prepared as previously described as either unmetallated or metallated with Mn2+, Cu2+ , Co2+, Mg2+ or Zn2+. It is hoped that the expanded ring system of the porphyrazine will lead to a greater specificity to the quadruplex telomer sequence. A preliminary investigation of the interactions between DNAs of different secondary structure with the porphyrazines via UV/Vis and CD absorption studies as well as calorimetric studies was hence initiated. To date, these studies provide evidence that porphyrazines generally interact with each of the oligonucleotides examined through formation of an external electrostatic complex. The results of these initial studies will be presented. (Abstract shortened by UMI.)...