title: Stable DNA triple helix formation using oligonucleotides containing 2'-aminoethoxy,5-propargylamino-U.
abstract: We have prepared oligonucleotides containing the novel base analogue 2'-aminoethoxy,5-propargylamino-U in place of thymidine and examined their ability to form intermolecular and intramolecular triple helices by DNase I footprinting and thermal melting studies. The results were compared with those for oligonucleotides containing 5-propargylamino-dU and 2'-aminoethoxy-T. We find that the bis-substituted derivative produces a large increase in triplex stability, much greater than that produced by either of the monosubstituted analogues, which are roughly equipotent with each other. Intermolecular triplexes with 9-mer oligonucleotides containing three or four base modifications generate footprints at submicromolar concentrations even at pH 7.5, in contrast to the unmodified oligonucleotide, which failed to produce a footprint at pH 5.0, even at 30 microM. UV- and fluorescence melting studies with intramolecular triplexes confirmed that the bis-modified base produces a much greater increase in T(m) than either modification alone.
authors.affiliation: Department of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK.
authors.forename: Matthieu
authors.initials: M
authors.lastname: Sollogoub
authors.forename: Richard A J
authors.initials: RA
authors.lastname: Darby
authors.forename: Bernard
authors.initials: B
authors.lastname: Cuenoud
authors.forename: Tom
authors.initials: T
authors.lastname: Brown
authors.forename: Keith R
authors.initials: KR
authors.lastname: Fox
mesh_terms: D001391:Azo Compounds / Q000737:chemistry; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D018983:DNA Footprinting; D003850:Deoxyribonuclease I / Q000378:metabolism; D003857:Deoxyuridine / Q000031:analogs & derivatives* / Q000737:chemistry* / Q000378:metabolism; D019793:Fluorescein / Q000737:chemistry; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009841:Oligonucleotides / Q000138:chemical synthesis* / Q000378:metabolism; D010293:Pargyline / Q000031:analogs & derivatives* / Q000737:chemistry* / Q000378:metabolism; D011437:Propylamines / Q000737:chemistry* / Q000378:metabolism; D013050:Spectrometry, Fluorescence; D014466:Ultraviolet Rays
chemical_list: D001391:Azo Compounds; D009841:Oligonucleotides; D011437:Propylamines; C051802:triplex DNA; C009054:propargylamine; C016081:propynyloxy-2'-deoxyuridine; C008492:methyl red; D004247:DNA; D010293:Pargyline; D003850:Deoxyribonuclease I; D019793:Fluorescein; D003857:Deoxyuridine