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Nucleic Acids Research 2005 33(9):3025-3032; doi:10.1093/nar/gki625
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Published online 23 May 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

Four base recognition by triplex-forming oligonucleotides at physiological pH

David A. Rusling, Vicki E. C. Powers1, Rohan T. Ranasinghe1, Yang Wang1, Sadie D. Osborne1, Tom Brown1 and Keith R. Fox*

School of Biological Sciences, University of Southampton Bassett Crescent East, Southampton SO16 7PX, UK 1School of Chemistry, University of Southampton Highfield, Southampton SO17 1BJ, UK

*To whom correspondence should be addressed. Tel: +44 23 8059 4374; Fax: +44 23 8059 4459; Email: k.r.fox{at}soton.ac.uk

Received April 6, 2005. Revised April 29, 2005. Accepted May 12, 2005.

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, MeP (3-methyl-2 aminopyridine) binds to GC at higher pHs than cytosine, while APP (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, MeP and APP 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.

Present address: Sadie D. Osborne, Department of Chemistry, University of Sheffield, Sheffield S3 7HF, UK


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