DNA triplex formation with 5-dimethylaminopropargyl deoxyuridine

David A Rusling, Guomei Peng, Natarajan Srinivasan, Keith R Fox, Tom Brown

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Pages (from-to)1288-1296
Number of pages9
JournalNucleic Acids Research
Issue number4
Early online date12 Jan 2009
Publication statusPublished - 1 Mar 2009


  • Base Sequence
  • DNA/chemistry
  • DNA Footprinting
  • Deoxyuridine/analogs & derivatives
  • Fluorescence
  • Kinetics
  • Methylamines/chemistry
  • Nucleic Acid Denaturation
  • Oligonucleotides/chemistry


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