Design, synthesis and physicochemical properties of aromatic peptide nucleic acids

Synthetic methods were developed for the preparation of several structurally diverse aromatic peptide nucleic acid (APNA) monomers containing all four natural DNA bases. This set of building blocks was useful for the preparation of oligomers designed to evaluate the hybridization properties of novel peptide nucleic acid (PNA) analogues, which incorporate aromatic rings into their backbone. Protocols for the solid-phase synthesis of APNA-PNA chimeras and APNA homopolymers were also developed.; Thermal denaturation experiments involving APNA-PNA chimeras demonstrated that APNA backbones comprised of N-(2-aminomethylphenyl) glycine and N-(2-aminobenzyl) glycine as the backbone moiety exhibited good binding affinity for DNA and RNA. Further studies with PNA oligomers composed partly of repeating N-(2-aminobenzyl) glycine APNAs showed that these analogues displayed good sequence recognition for DNA and RNA. Furthermore, continuous tracts of APNA units were well tolerated in both the triplex and duplex binding modes. The binding of APNA modified oligomers was investigated using UV, circular dichroism spectropolarimetry (CD) and complex formation with the cyanine dye 3-ethyl-2-[5-(3-ethyl-3H-benzothiazol-2-ylidene)-penta-1,3-dienyl]-benzothiazol-3-ium iodide (DiSC₂(5)). In the latter experiments, binding of the dye to complexes formed between APNA modified oligomers and DNA or RNA suggested that the minor grooves of these complexes were not drastically different from those formed in the corresponding PNA:DNA or PNA:RNA complexes.; Finally, fully modified APNA homopolymers were prepared in order to investigate their physicochemical properties. These oligomers were found to be essentially insoluble in aqueous buffers, which prohibited study of their binding affinity to nucleic acids. However, a short homothymine oligomer was synthesized which was modified at the C- and N-terminals so that it can be dissolved in water in sufficient quantities to allow for evaluation of its recognition and binding to DNA and RNA. Complex formation was confirmed by CD and DiSC ₂(5) binding experiments. These studies indicated that the APNA homopolymer bound to DNA and RNA, apparently through Watson-Crick base pairing, and formed a complex that was more stable than those formed by the corresponding homothymine DNA oligomer with complementary DNA under similar conditions.