Impact of charges on the hybridization kinetics and thermal duplex stability of PNA

Peptide nucleic acid (PNA) is prominent artificial nucleic acid mimetic and modifications at the g-position of the peptidic backbone are known to further enhance the desirable properties of PNA in terms of duplex stability.  Here, we leveraged a propargyl ether modification at this position for late stage functionalization of PNA to obtain positively charged (cationic amino and guanidinium groups), negatively charged (anionic carboxylate and alkyl phosphonate group) and neutral (PEG) PNA to assess the impact of these charges on DNA:PNA and PNA:PNA duplex formation.  Analysis of the thermal stability concurred prior studies showing PNA:DNA duplex are moderately more stable with cationic PNA than anionic PNA at physiological salt concentrations.  We show that this effect is derived predominately from difference in the association kinetics.