title: Synthesis and properties of a Hoechst-like minor-groove binding agent tethered to an oligodeoxynucleotide.
abstract: A small Hoechst-like DNA groove-binding fluorophore carrying a terminal bromoacetimido linker has been synthesized. Individual diastereomeric oligodeoxynucleotide dodecamers containing a thiol-based linker attached to an internucleotide phosphoramidate within a sequence of dA-dT residues were each covalently labeled with the new fluorophore. One isomer of the DNA-fluorophore conjugate (Isomer B) hybridizes to the complementary single-stranded target DNA and the presence of the tethered fluorophore results in both increased duplex stability and an enhanced fluorescent signal, presumably due to the fluorophore binding in the dA-dT rich minor groove. Duplex stability is increased by 2-3 degrees C and the fluorescence quantum yield for the fluorophore increases four-fold. In contrast, the other diastereomer (Isomer A) exhibits reduced helix stability (approximately 2 degrees C) and only slight changes in fluorescence intensity upon hybridization.
authors.affiliation: Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02167, USA.
authors.forename: M J
authors.initials: MJ
authors.lastname: O'Donnell
authors.forename: S B
authors.initials: SB
authors.lastname: Rajur
authors.forename: L W
authors.initials: LW
authors.lastname: McLaughlin
mesh_terms: D001483:Base Sequence; D001562:Benzimidazoles / Q000737:chemistry / Q000494:pharmacology; D006690:Bisbenzimidazole / Q000031:analogs & derivatives* / Q000737:chemistry; D004247:DNA / Q000187:drug effects*; D015195:Drug Design; D005456:Fluorescent Dyes / Q000737:chemistry / Q000494:pharmacology*; D008969:Molecular Sequence Data; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*
chemical_list: D001562:Benzimidazoles; D005456:Fluorescent Dyes; D009838:Oligodeoxyribonucleotides; D004247:DNA; D006690:Bisbenzimidazole; C017807:bisbenzimide ethoxide trihydrochloride