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Four base recognition by triplex-forming oligonucleotides at physiological pH

By David A. Rusling, Vicki E.C. Powers, Rohan T. Ranasinghe, Yang Wang, Sadie D. Osborne, Tom Brown and Keith R. Fox

Abstract

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

Topics: QD, QH426
Year: 2005
OAI identifier: oai:eprints.soton.ac.uk:24235
Provided by: e-Prints Soton
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