title: Peptide nucleic acid (PNA)/DNA hybrid duplexes: intercalation by an internally linked anthraquinone.
abstract: Peptide nucleic acids (PNA) mimic DNA and RNA by forming complementary duplex structures following Watson-Crick base pairing. A set of reporter compounds that bind to DNA by intercalation are known, but these compounds do not intercalate in PNA/DNA hybrid duplexes. Analysis of the 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 of a PNA oligomer. These are the first non-nucleobase functional groups that have been incorporated into a PNA. The resulting PNA(AQ) conjugates form stable hybrids with complementary DNA oligomers. We find that when the AQ groups are covalently bound to PNA that they stabilize the hybrid duplex and are, at least partially, intercalated.
authors.affiliation: School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.
authors.forename: B
authors.initials: B
authors.lastname: Armitage
authors.forename: T
authors.initials: T
authors.lastname: Koch
authors.forename: H
authors.initials: H
authors.lastname: Frydenlund
authors.forename: H
authors.initials: H
authors.lastname: Orum
authors.forename: G B
authors.initials: GB
authors.lastname: Schuster
mesh_terms: D000880:Anthraquinones / Q000737:chemistry*; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D007364:Intercalating Agents; D008958:Models, Molecular; D015335:Molecular Probes / Q000138:chemical synthesis; D009691:Nucleic Acid Denaturation; D009693:Nucleic Acid Hybridization; D009696:Nucleic Acids / Q000138:chemical synthesis; D010455:Peptides / Q000138:chemical synthesis
chemical_list: D000880:Anthraquinones; D007364:Intercalating Agents; D015335:Molecular Probes; D009696:Nucleic Acids; D010455:Peptides; D004247:DNA