Development of cell-permeable and helically preorganized peptide nucleic acids

The research described in this thesis focuses on modification of an important oligonucleotide analogue, peptide nucleic acid (PNA). These modifications were made in an attempt to improve PNA's cellular uptake and hybridization properties. PNAs have a great potential to act as antisense and antigene agents by interacting via classic Watson-Crick base pairing with mRNA and dsDNA, respectively; but lack intrinsic cellular uptake properties.; Herein we describe a simple modification made at the alpha-position of the PNA backbone that renders PNA cell-permeable. This modification involves the incorporation of the guanidinium group by replacing the glycine unit of the PNA backbone with arginine. The resulting guanidine-containing cationic PNA oligomers (GPNAs) that incorporate alternating units derived from D-arginine bind to their RNA targets with high affinity and specificity. Moreover, these oligomers are efficiently taken up by both human somatic and embryonic stem cells, and exhibit an antisense effect against our chosen target, the E-cadherin transcript. The positively-charged guanidinium group is also utilized as a tool to modulate PNA-DNA and PNA-PNA interaction; thus GPNA's potential for sequence-unrestricted recognition of dsDNA via double-strand invasion is investigated.; Lastly, we describe the modification of the PNA backbone performed at the gamma-position and the dramatic effect that this modification has on the conformational properties of the resulting oligomers. We demonstrate that this modification induces preorganization of the PNA oligomers into a right- or left-handed helix, depending on the configuration of the chiral center at this position. Moreover, we show that the preorganized oligomers derived from amino acids with L-configuration bind to RNA and DNA with significant increased affinity, as compared to unmodified PNA.; The studies regarding GPNAs described in this thesis could have a significant impact on the future design of novel antisense and antigene agents. Alternatively, the findings obtained with the preorganized gamma-substituted peptide nucleic acids have important implication not only in the future design of nucleic acid analogues with high binding affinity and selectivity but also in the development of novel materials that require a defined spatial organization for efficient electronic coupling. These materials could have applications in molecular electronic and photonic devices.