DNA triplex formation with 5-dimethylaminopropargyl deoxyuridine

Rusling, David A., Peng, Guomei, Srinivasan, Natarajan, Fox, Keith R and Brown, Tom (2009) DNA triplex formation with 5-dimethylaminopropargyl deoxyuridine. Nucleic Acids Research, 37 (4), 1288-1296. (doi:10.1093/nar/gkn1060).

Abstract

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.

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Contributors

Author: David A. Rusling

Author: Keith R Fox

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