title: Single-strand-targeted triplex formation: stability, specificity and RNase H activation properties.
abstract: Single-stranded (ss) oligodeoxyribonucleotides (oligos) containing both Watson-Crick and Hoogsteen hydrogen bonding domains joined by either a 5-nucleotide loop or a flexible hexaethylene-glycol linker, called foldback triplex-forming oligos (FTFOs), are designed and studied for their binding affinity and specificity to their ss DNA/RNA targets. Thermal denaturation studies revealed an increased affinity of FTFOs, due to addition of a Hoogsteen hydrogen bonding domain at the binding site, as the Watson-Crick domain forms a double helix with the target, when compared to conventional antisense and antigene oligos. DNase I hydrolysis and electrophoretic mobility shift analysis confirmed the formation of foldback triplexes relative to conventional double- and triple-stranded structures. The FTFOs showed increased sequence specificity mainly arising from their ability to recognize the target sequence twice, first by Watson-Crick base pairing and a second time by Hoogsteen base pairing. An FTFO with DNA components in both duplex- and triplex-forming domains showed preference for a DNA homopurine target strand.
authors.affiliation: Hybridon, Inc., Worcester, MA 01605.
authors.forename: E R
authors.initials: ER
authors.lastname: Kandimalla
authors.forename: S
authors.initials: S
authors.lastname: Agrawal
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D004277:DNA, Single-Stranded / Q000378:metabolism*; D004591:Electrophoresis, Polyacrylamide Gel; D004789:Enzyme Activation; D006358:Hot Temperature; D006860:Hydrogen Bonding; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry / Q000378:metabolism*; D012313:RNA / Q000378:metabolism*; D016914:Ribonuclease H / Q000378:metabolism*
chemical_list: D004277:DNA, Single-Stranded; D009838:Oligodeoxyribonucleotides; D012313:RNA; D016914:Ribonuclease H