PD-LOOP - A COMPLEX OF DUPLEX DNA WITH AN OLIGONUCLEOTIDE

A stable complex between duplex DNA and an oligonucleotide is assemble d with the aid of a DNA synthetic mimic, peptide nucleic acid (PNA). H omopyrimidine PNAs are known to invade into short homopurine tracts in duplex DNA forming P-loops, We have found that P-loops, formed at two closely located purine tracts in the same DNA strand separated by a m ixed purine-pyrimidine sequence, merge and open the double helix betwe en them, The opposite DNA strand, which is not bound with PNA, exposes and becomes accessible for complexing with an oligonucleotide via Wat son-Crick pairing. As a result, the PD-loop emerges, which consists of locally open duplex DNA, PNA ''openers,'' and an oligonucleotide, The PD-loop stability and sequence specificity are demonstrated by affini ty capture of duplex DNAs by using biotinylated oligonucleotides and s treptavidin-covered magnetic beads. The type of complex formed by PNAs , an oligonucleotide and duplex DNA we describe, opens ways for develo pment of various in vitro and in situ hybridization techniques with du plex DNA and may find applications in DNA nanotechnology and genomics.