Recognition of DNA by Modified Peptide Nucleic Acids (PNA) for Gene Targeting and Analysis

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We propose a study aimed at novel chemistry and technology for gene analysis and gene specific targeting by PNA. The DNA mimic PNA (peptide nucleic acid) is finding widespread applications within genetic diagnostics, molecular biology and drug discovery. This is due to the very favourable DNA and RNA recognition properties of PNA combined with very high biological (and chemical) stability, as well as "chemical flexibility". Thus PNA oligomers can be "tailor made" to a variety of applications. In this project we propose to explore and exploit PNA chemical modifications and conjugates for gene detection and targeting. Specifically, we plan to design and synthesize novel nucleobases for sequence specific recognition of duplex DNA by triplex formation and helix invasion. Such PNA oligomers will be analysed in cellular gene targeting (antisense and antigene) assays using the Ha-ras and c-myc oncogenes as model genes. Furthermore, conjugates of PNA with lipids, peptides, fluorophores and DNA intercalators will be prepared and characterized in terms of DNA recognition, cellular uptake and (antisense and antigene) gene knock down activity. The structure of novel PNA oligomer complexes with DNA and PNA will be studied by X-ray crystallography. Finally, the capacity to tailor make PNA oligomers will be exploited to design and analyse PNA capture and detection probes for development of novel on line, solid support analysis of DNA molecules in hybridisation array formats.