GenixTalk

PNA (Peptide Nucleic Acid) was discovered by Nielsen, Egholm, Berg, and Buchardt in 1991. PNA is a DNA analog in which polyamide backbone replaces the traditional phosphate ribose ring of DNA. Despite a radical change to the natural structure, PNA is capable of sequence-specific binding to DNA or RNA. Due to its superior binding properties and stability, PNA has been widely applied in the field of biology.

The PNA backbone is made of N-(2-aminoethyl)-glycine units linked by peptides bonds. The different bases (purines and pyrimidines) are linked to the backbone by methylene carbonyl linkages. Unlike DNA or other DNA analogs, PNAs do not contain any pentose sugar moieties or phosphate groups. Like amino acids, PNA monomers have amino and carboxyl termini. PNA monomers are linked by peptide bonds into a single chain oligomer. By convention, the PNA oligomer is depicted like a peptide with its N-terminus at the first position. However, this end corresponds to the 3' end of a DNA or RNA strand. Hence, the N-terminus of a PNA hybridizes to the 5'-end of complementary single-stranded DNA. Thus, unlike the 5' to 3' convention in writing nucleic acid sequences, PNA sequences are usually written from 3' to 5'.
PNA monomers are easily synthesized into oligomers as long as 20 bases using protocols for standard peptide synthesis. PNA monomers use fluorenylmethoxycarbonyl (Fmoc) protection of the N-terminal monomer amino group, and benzhydryloxycarbonyl (Bhoc) to protect the A, C and G exocyclic amino groups. The Bhoc group coupled with the XAL synthesis handle allows rapid deprotection and cleavage of the PNA oligomer from the resin. Typical coupling yields are >95 %. Synthesis is completed by TFA cleavage of the oligomer from the resin. The oligomer is purified by reverse phase HPLC. Although the monomers exhibit poor solubility, the oligomers are very soluble, especially if exocyclic amines are present (200-1000 ? of 0.1 % aqueous trifluoroacetic acid (TFA) and fractionnate the solution into aliquots).