PNA hybridization by strand invasion
One of the important properties of PNAs is their  ability to recognize DNA sequence by strand invasion. This facilitates complex formation with a DNA strand that is already base paired with its complementary strand. The initiation of strand invasion by PNAs is facilitated by rapid hybridization of PNAs to transiently unpaired duplex targets. If this hybridization persists long enough, a second PNA can bind by Hoogstein pairing, thus stabilizing a four stranded complex. However, addition of millimolar concentrations of divalent cations prevents strand invasion by PNAs in vitro, since it stabilizes the parent duplex. This factor can be controlled in vitro, but creates problems in vivo, where a variety of factors will determine strand invasion.