In contrast to DNA-DNA duplex formation, no salt is necessary to facilitate and stabilize the formation of a PNA-DNA (or RNA) duplex. For this reason, the Tm of a PNA-DNA-duplex is almost independent of ionic strength. For example, the Tm of a 15-mer duplex has been shown to decrease by only 5¡ÆC as the NaCl concentration was raised from 10 mM to 1 M. Thus a PNA, when used at low ionic strength (e.g. 10 mM phosphate buffer with no NaCl), will effectively bind to a target under low salt conditions in the presence of a competing DNA strand because the stability of the DNA-DNA duplex is relatively small.

It is important, however, NOT to perform the hybridization in the absence of a buffer since PNA/DNA duplexes precipitate at low pH or when no counter-ions present.

In the case of RNA, low salt conditions serve to destabilize intramolecular hybridization (tertiary structure) favoring hybridization of the PNA. Therefore hybridization conditions should be chosen so that the PNA can compete better with DNA or RNA for hybridization to the target.