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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.

Original publication

DOI

10.1093/nar/gki625

Type

Journal article

Journal

Nucleic Acids Res

Publication Date

2005

Volume

33

Pages

3025 - 3032

Keywords

Base Pairing, DNA, DNA Footprinting, Deoxyribonuclease I, Hydrogen-Ion Concentration, Nucleic Acid Conformation, Nucleic Acid Denaturation, Nucleosides, Oligodeoxyribonucleotides, Spectrometry, Fluorescence