Modified peptide nucleic acids (PNA) and amonafide derivatives: Synthesis and applications of trans-cyclopentane and trans-pyrrolidine PNAs and small molecules derived from amonafide

Peptide nucleic acids were discovered by Nielsen and coworkers in 1991 as nucleic acid analogues where the sugar-phosphate backbone is replaced with an uncharged, achiral backbone. PNAs hybridize to complementary DNA and RNA via Watson-Crick hydrogen bonds with higher affinity than corresponding oligonucleotides. These properties make PNA a promising molecule for DNA diagnostic and biological applications. In unmodified PNAs, the aminoethyl-glycine backbone is flexible and, as a result, there is entropic loss associated with duplex formation. The incorporation of (S,S)-trans-1,2-cyclopentane diamine into the PNA backbone increases the binding affinity compared to unmodified PNAs, due to a decrease in entropic loss. Efficient synthetic routes to cyclopentane PNA monomers containing the four standard DNA nucleobases have been developed. These monomers have then been incorporated into PNA strands utilizing a mixed protecting group strategy, and have shown increases in binding affinity and sequence specifity in comparison to unmodified PNA strands. Similar to the (S,S)-trans-1,2-cyclopentane PNA, ( S,S)-trans-pyrrolidine modified PNAs showed an increase in binding affinity and sequence specificty. The (S,S)- trans-pyrrolidine PNA should aid in aqueous solubility, an aspect of PNA technology that can be problematic.; To prepare PNA monomers containing guanine, it was necessary to prepare N-9 guanine acetic acid. Methodology to produce either the N-9 or N-7 alkylated guanine has been developed. The N-7 alkylated product can be incorporated into PNA monomers and used as a protonated cytosine mimic. Insertion of N-7 alkylated guanine monomers into the Hoogsteen binding strand of bis-PNA hairpins produces compounds that can undergo strand invasion of double stranded DNA, forming a stable PNA2/DNA triplex. By installing a fluorescent probe onto the bis-PNA hairpin, it is possible to mark plasmid DNA and monitor its migration through the cell.; An efficient 2-step synthetic route to 4-substituted amonafide derivatives was developed. The synthesis allowed for a wide range of analogues to be prepared quickly and also allowed for the cursory production of multi-gram quantities of amonafide analogues. These molecules were tested for anticancer activity in collaboration with Professor Sui Huang at Northwestern Medical School.