Synthesis and properties of guanidine-based peptide nucleic acids

This thesis presents the results of the development of a new class of guanidine-based peptide nucleic acid (GPNA), which can be readily taken up by different cell lines and bind sequence specifically to DNA.; Chapter I includes an introduction to peptide nucleic acid, hybridization of PNA to oligonucleotides, structure of PNA-oligonucleotide complex and application of PNA. Background information on the structurally modified PNA analogues is provided.; Chapter II covers the synthesis of GPNA monomers containing the four natural nucleobases Boc-Arg(Tos)-T-OH, Boc-Arg(Tos)-A-OH, Boc-Arg(Tos)-C-OH and Boc-Arg(Tos)-G-OH. The oligomers of GPNA have been prepared by solid phase synthesis.; Chapter III demonstrates the GPNAs bind sequence specifically to DNA and are taken up by cells and dispersed in different compartment of the cells. The GPNAs are capable of recognizing and binding to a complementary DNA sequence with higher stability that the unmodified PNA. CD and Job-plot indicates that both homopyrimidine and mix-sequence GPNAs bind to complementary DNAs to form a GPNA-DNA duplexex, while unmodified homopyrimidine PNA binds to its complementary DNA strand in a 2:1 ratio to form a PNA2-DNA triplex. Cellular uptake experiments in HCT 116 cells show that GPNA traverses the cell membrane as effectively as the TAT transduction domain under identical conditions, while unmodified PNA did not show any cellular uptake. The uptake of GPNA is not cell line dependent, since GPNA shows uptake in three other three cell lines.; Chapter IV explores the use of both backbone and nucleobase modified GPNA to target double-stranded DNA under the double duplex invasion mode. GPNA monomers and oligomers containing unnatural nucleobases 2, 6-diaminopurine (D) and 2-thiourasil (SU) have been synthesized. These pseudo-complementary GPNA oligomers bind to complementary DNAs with higher stability than PNAs while do not bind to each other. Double-stranded DNA can be efficiently and sequence specifically targeted by pseudocomplementary PNA-GPNA hybrid. These developments, along with the inherent cellular uptake property of GPNA described in the previous chapter, may form the basis for the application of antigene GPNA live cells and intact organisms.