Extending the Scope of Pna With Non-standard Base Pairs

Period of Performance: 01/01/2000 - 06/30/2000


Phase 1 SBIR

Recipient Firm

Eragen Biosciences, Inc.
Madison, WI 53717
Principal Investigator


This research aims to expand the scope of Peptide Nucleic Acid (PNA) by adding artificial nucleobases which form stable non-standard base pairs to the currently available natural nucleobase PNA repertoire. PNAs based on an expanded nucleobase alphabet are anticipated to have significant potential in conjunction with the established properties of an expanded genetic information system (AEGIS). Incorporation of AEGIS non- standard DNA base pairs has improved bDNA diagnostic technology and led to a novel commercial DNA diagnostic product (bDNA 3.0 QuantiplexTM) with sensitivity comparable to PCR. Nevertheless, the scope of the DNA-AEGIS technology is limited by the difficult synthesis and attenuated chemical stability for several of the non-standard base reagents. PNA reagents and oligomers containing AEGIS non-standard nucleobases are anticipated to be more amenable to chemical synthesis and more stable. Furthermore, PNA has intrinisic properties which yield advantages for PNA:DNA based diagnostic systems relative to those based on DNA:DNA recognition (hybridization) complexes. These include greater stability and greater sensitivity to base mismatches for PNA:DNA duplexes relative to DNA:DNA hybrids. Taking the above together, inclusion of AEGIS non-standard nucleobases into PNA can be expected to greatly increase the scope and utility of both PNA and DNA-AEGIS technologies. Useful diagnostic applications can be already be conceived for the combination of these technologies. Specific examples include: coding for DNA microarrays, oligonucleotide ligation based DNA diagnostics. PROPOSED COMMERCIAL APPLICATIONS: Peptide Nucleic Acid (PNA) based on an expanded Watson:Crick rule based molecular recognition code will increase the scope and potential of PNA based diagnostic systems. Greater specificity for hybridization based assays taking advantage of DNA:PNA non-standard base pairing is expected. Specific applications with significant potential include the spatial address"zip coding" for DNA microarrays and other sandwich assays based on oligonucleotide ligation assay (OLA) in conjunction with the expanded code.