title: Secondary binding sites for heavily modified triplex forming oligonucleotides.
abstract: In order to enhance DNA triple helix stability synthetic oligonucleotides have been developed that bear amino groups on the sugar or base. One of the most effective of these is bis-amino-U (B), which possesses 5-propargylamino and 2'-aminoethoxy modifications. Inclusion of this modified nucleotide not only greatly enhances triplex stability, but also increases the affinity for related sequences. We have used a restriction enzyme protection, selection and amplification assay (REPSA) to isolate sequences that are bound by the heavily modified 9-mer triplex-forming oligonucleotide B(6)CBT. The isolated sequences contain A(n) tracts (n = 6), suggesting that the 5'-end of this TFO was responsible for successful triplex formation. DNase I footprinting with these sequences confirmed triple helix formation at these secondary targets and demonstrated no interaction with similar oligonucleotides containing T or 5-propargylamino-dU.
authors.affiliation: Centre for Biological Sciences, Life Sciences Building, University of Southampton, Southampton SO17 1BJ, UK.
authors.forename: Antonia S
authors.initials: AS
authors.lastname: Cardew
authors.forename: Tom
authors.initials: T
authors.lastname: Brown
authors.forename: Keith R
authors.initials: KR
authors.lastname: Fox
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry*; D018983:DNA Footprinting; D003850:Deoxyribonuclease I; D015252:Deoxyribonucleases, Type II Site-Specific; D003857:Deoxyuridine / Q000031:analogs & derivatives / Q000737:chemistry; D009841:Oligonucleotides / Q000737:chemistry*; D014529:Uridine / Q000031:analogs & derivatives* / Q000737:chemistry
chemical_list: C488802:2'-aminoethoxy-5-(3-aminoprop-1-ynyl)uridine; C119290:5-(1-propargylamino)-2'-deoxyuridine; D009841:Oligonucleotides; C051802:triplex DNA; D004247:DNA; C035042:endodeoxyribonuclease FokI; D003850:Deoxyribonuclease I; D015252:Deoxyribonucleases, Type II Site-Specific; D003857:Deoxyuridine; D014529:Uridine