We have achieved recognition of all 4 bp by triple helix<br/>formation at physiological pH, using triplex-forming<br/>oligonucleotides that contain four different synthetic<br/>nucleotides. BAU [20-aminoethoxy-5-(3-aminoprop-1-<br/>ynyl)uridine] recognizesATbase pairs with high affinity,<br/>MeP (3-methyl-2 aminopyridine) binds to GC at<br/>higher pHs than cytosine, while APP (6-(3-aminopropyl)-<br/>7-methyl-3H-pyrrolo[2,3-d]pyrimidin-2(7H)-one)<br/>and S [N-(4-(3-acetamidophenyl)thiazol-2-yl-acetamide)]<br/>bind to CG and TA base pairs, respectively.<br/>Fluorescence melting and DNase I footprinting demonstrate<br/>successful triplex formation at a 19mer oligopurine<br/>sequence that contains two CG and two TA<br/>interruptions. The complexes are pH dependent, but<br/>are still stable at pH 7.0. BAU, MeP and APP retain considerable<br/>selectivity, and single base pair changes<br/>opposite these residues cause a large reduction in<br/>affinity. In contrast, S is less selective and tolerates<br/>CG pairs as well as TA
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