Synthesis, Biophysical and Cellular Uptake Studies of Fluorinated Peptide Nucleic Acid Analogs

Abstract

The thesis entitled “Synthesis, Biophysical and Cellular Uptake Studies of Fluorinated Peptide Nucleic Acid Analogs” comprises of studies on peptide nucleic acids which are fluorinated at different chemical sites. Nucleic acid therapeutics has emerged as effective technology for gene inhibition, but limited by susceptibility to cellular enzymes and poor cell uptake. Hence chemically modified nucleic acids have been used to resist degradation by the cellular enzymes. Peptide nucleic acids are a class of DNA analogs that are stable to cellular enzymes, but suffer from poor aqueous solubility and insufficient cell uptake. During the past two decades several PNA analogs have been reported to address their drawbacks. In the present work PNAs have been modified by substituting hydrogen with bioisosteric fluorine which is well known to increase lipophilicity and bioavailability. The different fluorinated PNA units were incorporated into PNA sequences site specifically using solid phase peptide synthesis protocol. The effect of fluorine on hydrophobicity was studied using HPLC, and their binding affinity to complementary DNA and RNA investigated by various biophysical techniques. This is followed by examining their cell permeation properties in different cell lines.