Similar to the production of DNA and RNA oligonucleotides, antisense peptide nucleic acids (PNAs) are commonly synthesized using automated, continuous solid-phase synthesis techniques on peptide synthesizers. Through the utilization of solid-phase Fmoc methods, PNA monomers can be easily assembled in a sequential fashion to form oligomers.

For SPPS fluorenylmethyloxycarbonyl (Fmoc)- and benzhydryloxycarbonyl (Bhoc)-protected PNA monomers are preferred because they allow for mild deprotection of all protecting groups as well as easy cleavage of the resulting PNA oligomer from the resin. The Bhoc protecting group is particular to PNA synthesis (vs. RNA and DNA synthesis), as it is used to protect the primary amines of the heterocyclic bases in PNA monomers which are linked to Fmoc-protected back bone. The benzyloxycarbonyl (Cbz) protecting group on the other hand is combined with Boc-protected back bone. It, too, can be removed under acidic conditions, although they tend to be harsh.

PNA monomers include Cbz- and Bhoc-protected natural nucleobases (cytosine C, guanine G,adenine A, thymine T) attached to N-(2-aminoethyl) glycine units. Newer PNA monomers are developed on a regular basis that include protected synthetic nucleobases such as J, U, thioU, IG, M and D modified to afford certain physicochemical attributes. All PNA monomers are designed to bind to the natural nucleobases present in DNA and RNA.

The modifications to PNA monomers that have been developed help overcome a range of issues with the monomers themselves and those of the highly stable DNA and RNA duplexes formed with PNAs. For instance, some Fmoc/Bhoc-protected PNA monomers exhibit low solubility and tend to precipitate upon storage in solutions. PNA:DNA duplexes, meanwhile, also tend to have lower aqueous solubility and a greater propensity to aggregate than DNA:DNA duplexes.

PNA monomers with modified chemical structures, particularly at the gamma position, have been shown to improve these properties. The synthesis of gamma-modified PNA monomers is based on amino acids bearing exclusively heteroatoms. Modifications that cause changes in the conformations of PNA monomers have also been explored.

Check out our portfolio of PNA monomers here.