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Nucleic Acids Research Advance Access originally published online on January 12, 2009
Nucleic Acids Research 2009 37(4):1288-1296; doi:10.1093/nar/gkn1060
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Nucleic Acids Research, 2009, Vol. 37, No. 4 1288-1296
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Chemistry and Synthetic Biology

DNA triplex formation with 5-dimethylaminopropargyl deoxyuridine

David A. Rusling1, Guomei Peng1,2, Natarajan Srinivasan2, Keith R. Fox1,* and Tom Brown2

1School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX and 2School 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 November 20, 2008. Revised December 16, 2008. Accepted December 17, 2008.

We have prepared triplex-forming oligonucleotides containing the nucleotide analogue 5-dimethylaminopropargyl deoxyuridine (DMAPdU) in place of thymidine and examined their ability to form intermolecular triple helices by thermal melting and DNase I footprinting studies. The results were compared with those for oligonucleotides containing 5-aminopropargyl-dU (APdU), 5-guanidinopropargyl-dU (GPdU) and 5-propynyl dU (PdU). We find that DMAPdU enhances triplex stability relative to T, though slightly less than the other analogues that bear positive charges (T << PdU < DMAPdU < APdU < GPdU). For oligonucleotides that contain multiple substitutions with DMAPdU dispersed residues are more effective than clustered combinations. DMAPdU will be especially useful as a nucleotide analogue as, unlike APdU and GPdU, the base does not require protection during oligonucleotide synthesis and it can therefore be used with other derivatives that require mild deprotection conditions.

Present address: David A. Rusling, Department of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK


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