title: Detection of PCR products using PNA strand invasion.
abstract: The unique ability of homopyrimidine peptide nucleic acid (PNA) to strand invade homopurine sites of duplex DNA offers a potential alternative to existing techniques for rapid detection of PCR products. From gel shift studies, PNA was found to specifically strand invade homopurine sites that had been incorporated into an amplicon during the PCR cycle. This was achieved by adding a homopyrimidine sequence to the 5'-terminus of a PCR primer. The position of the strand invasion sites at the termini of the DNA duplex offers kinetic advantages for PNA strand invasion, since the termini of DNA duplexes are known to be unwound. This unwound state was demonstrated using a novel assay that determined single-stranded regions within the amplicon. The presence of the PNA moiety in strand invasion complexes was confirmed by a novel electroblot, an Enzyme Linked Nucleic Acid assay and by an increase in stability as demonstrated by T(m)studies with the Idaho RapidCycler. Since the strand invasion sites can be controlled through selection of the homopurine sequence there is great flexibility for designing strand invasion motifs unique to a particular PCR amplicon, thus providing a huge potential for differentiating and detecting multiplex PCR products.
authors.affiliation: DERA CBD Porton Down, Salisbury, Wiltshire, SP4 0JQ, UK. ldrewe@dra.hmg.gb
authors.forename: L J
authors.initials: LJ
authors.lastname: Drewe
authors.forename: G
authors.initials: G
authors.lastname: Brightwell
authors.forename: E A
authors.initials: EA
authors.lastname: Hall
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry; D015342:DNA Probes / Q000737:chemistry; D008969:Molecular Sequence Data; D020135:Peptide Nucleic Acids / Q000032:analysis / Q000737:chemistry*; D016133:Polymerase Chain Reaction / Q000379:methods*; D011687:Purines / Q000737:chemistry; D011743:Pyrimidines / Q000737:chemistry
chemical_list: D015342:DNA Probes; D020135:Peptide Nucleic Acids; D011687:Purines; D011743:Pyrimidines; D004247:DNA; C030986:pyrimidine; C030985:purine