Published online 4 October 2005
Methods Online |
End invasion of peptide nucleic acids (PNAs) with mixed-base composition into linear DNA duplexes
Center for Advanced Biotechnology, Boston University 36 Cummington Street, Boston, MA 02215, USA 1Department of Radiation Medicine, Lombardi Comprehensive Cancer, Georgetown University Medical Center 3970 Reservoir Rd. N.W., Washington, DC 20057, USA
*To whom correspondence should be addressed. Tel: +1 617 353 8492; Fax: +1 617 353 8501; Email: ismolina{at}bu.edu
Received July 26, 2005. Revised August 31, 2005. Accepted September 18, 2005.
Peptide nucleic acid (PNA) is a synthetic DNA mimic with valuable properties and a rapidly growing scope of applications. With the exception of recently introduced pseudocomplementary PNAs, binding of common PNA oligomers to target sites located inside linear double-stranded DNAs (dsDNAs) is essentially restricted to homopurine–homopyrimidine sequence motifs, which significantly hampers some of the PNA applications. Here, we suggest an approach to bypass this limitation of common PNAs. We demonstrate that PNA with mixed composition of ordinary nucleobases is capable of sequence-specific targeting of complementary dsDNA sites if they are located at the very termini of DNA duplex. We then show that such targeting makes it possible to perform capturing of designated dsDNA fragments via the DNA-bound biotinylated PNA as well as to signal the presence of a specific dsDNA sequence, in the case a PNA beacon is employed. We also examine the PNA–DNA conjugate and prove that it can initiate the primer-extension reaction starting from the duplex DNA termini when a DNA polymerase with the strand-displacement ability is used. We thus conclude that recognition of duplex DNA by mixed-base PNAs via the end invasion has a promising potential for site-specific and sequence-unrestricted DNA manipulation and detection.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors