Four base recognition by triplex-forming oligonucleotides at physiological pH

David A. Rusling, Vicki E. C. Powers, Rohan T. Ranasinghe, Yang Wang, Sadie D. Osborne, Tom Brown, Keith R. Fox

Research output: Contribution to journalArticlepeer-review


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, (Me)P (3-methyl-2 aminopyridine) binds to GC at higher pHs than cytosine, while (A)PP (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, (Me)P and (A)PP 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.

Original languageEnglish
Pages (from-to)3025-3032
JournalNucleic Acids Research
Issue number9
Publication statusPublished - 1 May 2005


  • Base Pairing
  • DNA/chemistry
  • DNA Footprinting
  • Deoxyribonuclease I/metabolism
  • Hydrogen-Ion Concentration
  • Nucleic Acid Conformation
  • Nucleic Acid Denaturation
  • Nucleosides/chemistry
  • Oligodeoxyribonucleotides/chemistry
  • Spectrometry, Fluorescence


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