DNA Recognition and Induced Genome Modification by a Hydroxymethyl-γ Tail-Clamp Peptide Nucleic Acid

Abstract

Peptide nucleic acids (PNA) can target and stimulate recombination reactions in genomic DNA. We have reported that gamma ({gamma})-PNA oligomers possessing the diethylene glycol {gamma}-substituent show improved efficacy over unmodified PNAs in stimulating recombination-induced gene modification. However, this structural modification poses a challenge because of the inherent racemization risk in O-alkylation of the precursory serine side chain. To circumvent this risk and improve {gamma}PNA accessibility, we explore the utility of {gamma}PNA oligomers possessing the hydroxymethyl-{gamma} moiety for gene editing applications. We demonstrate that a {gamma}PNA oligomer possessing the hydroxymethyl modification, despite weaker preorganization, retains the ability to form a hybrid with the double-stranded DNA target of comparable stability and with higher affinity to that of the diethylene glycol-{gamma}PNA. When formulated into poly(lactic-co-glycolic acid) nanoparticles, the hydroxymethyl-{gamma}PNA stimulates higher frequencies ([≥] 1.5-fold) of gene modification than the diethylene glycol {gamma}PNA in mouse bone marrow cells.