title: Four base recognition by triplex-forming oligonucleotides at physiological pH.
abstract: We have achieved recognition of all 4 bp by triple helix formation at physiological pH, using triplex-forming oligonucleotides that contain four different synthetic nucleotides. BAU [2'-aminoethoxy-5-(3-aminoprop-1-ynyl)uridine] recognizes AT base pairs with high affinity, (Me)P (3-methyl-2 aminopyridine) binds to GC at higher pHs than cytosine, while (A)PP (6-(3-aminopropyl)-7-methyl-3H-pyrrolo[2,3-d]pyrimidin-2(7H)-one) and S [N-(4-(3-acetamidophenyl)thiazol-2-yl-acetamide)] bind to CG and TA base pairs, respectively. Fluorescence melting and DNase I footprinting demonstrate successful triplex formation at a 19mer oligopurine sequence that contains two CG and two TA interruptions. The complexes are pH dependent, but are still stable at pH 7.0. BAU, (Me)P and (A)PP retain considerable selectivity, and single base pair changes opposite these residues cause a large reduction in affinity. In contrast, S is less selective and tolerates CG pairs as well as TA.
authors.affiliation: School of Biological Sciences, University of Southampton Bassett Crescent East, Southampton SO16 7PX, UK.
authors.forename: David A
authors.initials: DA
authors.lastname: Rusling
authors.forename: Vicki E C
authors.initials: VE
authors.lastname: Powers
authors.forename: Rohan T
authors.initials: RT
authors.lastname: Ranasinghe
authors.forename: Yang
authors.initials: Y
authors.lastname: Wang
authors.forename: Sadie D
authors.initials: SD
authors.lastname: Osborne
authors.forename: Tom
authors.initials: T
authors.lastname: Brown
authors.forename: Keith R
authors.initials: KR
authors.lastname: Fox
mesh_terms: D020029:Base Pairing; D004247:DNA / Q000737:chemistry*; D018983:DNA Footprinting; D003850:Deoxyribonuclease I / Q000378:metabolism; D006863:Hydrogen-Ion Concentration; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009705:Nucleosides / Q000737:chemistry; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D013050:Spectrometry, Fluorescence
chemical_list: D009705:Nucleosides; D009838:Oligodeoxyribonucleotides; C051802:triplex DNA; D004247:DNA; D003850:Deoxyribonuclease I