title: Nuclease resistance of oligonucleotides containing the tricyclic cytosine analogues phenoxazine and 9-(2-aminoethoxy)-phenoxazine ("G-clamp") and origins of their nuclease resistance properties.
abstract: The tricyclic cytosine analogues phenoxazine and 9-(2-aminoethoxy)-phenoxazine ("G-clamp") are known to significantly enhance the binding affinity of oligonucleotides to their complementary target DNA or RNA strands. To investigate their effect on the nuclease resistance, they were incorporated into model oligomers with a natural phosphodiester backbone, and enzymatic degradation was monitored in an in vitro assay with snake venom phosphodiesterase as the hydrolytic enzyme. In both cases, a single incorporation at the 3'-terminus completely protected the oligonucleotides against 3'-exonuclease attack. Further investigations indicate that the observed high nuclease resistance is not due to the lack of binding affinity to the enzyme's active site, since these modified oligonucleotides were able to inhibit degradation of a natural DNA fragment by bovine intestinal mucosal phosphodiesterase in a dose-dependent manner.
authors.affiliation: Department of Medicinal Chemistry, Isis Pharmaceuticals, 2292 Faraday Avenue, Carlsbad, California 92008, USA.
authors.forename: Martin A
authors.initials: MA
authors.lastname: Maier
authors.forename: Janet M
authors.initials: JM
authors.lastname: Leeds
authors.forename: Guity
authors.initials: G
authors.lastname: Balow
authors.forename: Robert H
authors.initials: RH
authors.lastname: Springer
authors.forename: Ramesh
authors.initials: R
authors.lastname: Bharadwaj
authors.forename: Muthiah
authors.initials: M
authors.lastname: Manoharan
mesh_terms: D000818:Animals; D002417:Cattle; D003596:Cytosine / Q000031:analogs & derivatives*; D006868:Hydrolysis; D009841:Oligonucleotides / Q000737:chemistry*; D010078:Oxazines / Q000737:chemistry*
chemical_list: D009841:Oligonucleotides; D010078:Oxazines; D003596:Cytosine; C039203:phenoxazine