PD-loop

A key interest in our lab is the application of Peptide Nucleic Acids (PNAs) for DNA labeling. A special class of PNAs (bis-PNA) can be used to locally and sequence-specifically invade duplex DNA. They bind to one of the two DNA strands of a target sequence, leaving the opposite strand displaced. Once opened, an oligonucleotide probe is used to form a PD-loop.

A PD-loop is an exceptionally stable PNA₂-DNA structure that is formed when the termini of the oligonucleotide (ODN) probe are complementary to the DNA strand displaced by the PNA probes; upon hybridization to the target DNA the probe circularizes and a DNA ligase closes the gap. The ligation reaction is extremely sequence specific and can discriminate single mutations if they are located close to the ligation point. Then, signal amplification and fluorescent labeling can be used to detect the target DNA. PD-loop formation is limited to a pre-selected 20-30-bp-long target site within dsDNA. A significant advantage of PNA-based PD-loop design is the fact that the rest of the DNA retains its duplex structure and is inaccessible for ODN binding.