PEPTIDE NUCLEIC-ACID (PNA) DNA HYBRID DUPLEXES - INTERCALATION BY AN INTERNALLY LINKED ANTHRAQUINONE

Peptide nucleic acids (PNA) mimic DNA and RNA by forming complementary duplex structures following Watson-Crick base pairing. A set of repor ter compounds that bind to DNA by intercalation are known, but these c ompounds do not intercalate in PNA/DNA hybrid duplexes. Analysis of th e hybrid PNA duplexes requires development of reporter compounds that probe their chemical and physical properties. We prepared a series of anthraquinone (AQ) derivatives that are linked to internal positions o f a PNA oligomer. These are the first non-nucleobase functional groups that have been incorporated into a PNA. The resulting PNA(AQ) conjuga tes form stable hybrids with complementary DNA oligomers. We find that when the AQ groups are covalently bound to PNA that they stabilize th e hybrid duplex and are, at least partially intercalated.