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Nucleic Acids Research 2004 32(15):4439-4447; doi:10.1093/nar/gkh776
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Published online 18 August 2004

Nucleic Acids Research, Vol. 32 No. 15 © Oxford University Press 2004; all rights reserved

Selectivity and affinity of triplex-forming oligonucleotides containing 2'-aminoethoxy-5-(3-aminoprop-1-ynyl)uridine for recognizing AT base pairs in duplex DNA

Sadie D. Osborne, Vicki E. C. Powers, David A. Rusling1, Oliver Lack, Keith R. Fox1 and Tom Brown*

School of Chemistry, University of Southampton, Highfield, Southampton SC17 1BJ, UK and 1 School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK

* To whom correspondence should be addressed. Tel: +44 23 8059 2974; Fax: +44 23 8059 2291; Email: tb2{at}soton.ac.uk
Present address: Sadie D. Osborne, Department of Chemistry, University of Sheffield, Sheffield S3 7HF, UK
The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors

Received July 2, 2004; Revised and Accepted July 30, 2004

We have used DNase I footprinting, fluorescence and ultraviolet (UV) melting experiments and circular dichroism to demonstrate that, in the parallel triplex binding motif, 2'-aminoethoxy-5-(3-aminoprop-1-ynyl)uridine (bis-amino-U, BAU) has very high affinity for AT relative to all other Watson–Crick base pairs in DNA. Complexes containing two or more substitutions with this nucleotide analogue are stable at pH 7.0, even though they contain several C.GC base triplets. These modified triplex-forming oligonucleotides retain exquisite sequence specificity, with enhanced discrimination against YR base pairs (especially CG). These properties make BAU a useful base analogue for the sequence-specific creation of stable triple helices at pH 7.0.


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