title: Intramolecular triple-helix formation at (PunPyn).(PunPyn) tracts: recognition of alternate strands via Pu.PuPy and Py.PuPy base triplets.
abstract: Triple-helical DNA shows increasing potential for applications in the control of gene expression (including therapeutics) and the development of sequence-specific DNA-cleaving agents. The major limitation in this technology has been the requirement of homopurine sequences for triplex formation. We describe a simple approach that relaxes this requirement, by utilizing both Pu.PuPy and Py.PuPy base triplets to form a continuous DNA triple helix at tandem oligopurine and oligopyrimidine tracts. [Triplex formation at such a sequence has been previously demonstrated only with the use of a special 3'-3' linkage in the third strand [Horne, D. A., & Dervan, P. B. (1990) J. Am. Chem. Soc. 112, 2435-2437].] Supporting evidence is from chemical probing experiments performed on several oligonucleotides designed to form 3-stranded fold-back structures. The third strand, consisting of both purine and pyrimidine blocks, pairs with purines in the Watson-Crick duplex, switching strands at the junction between the oligopurine and oligopyrimidine blocks but maintaining the required strand polarity without any special linkage. Although Mg2+ ions are not required for the formation of Pu.PuPy base triplets, they show enhanced stability in the presence of Mg2+. In the sequences observed. A.AT triplets appear to be more stable than G.GC triplets. As expected, triplex formation is largely independent of pH unless C+.GC base triplets are required.
authors.affiliation: Cell and Molecular Biology Laboratory, SRI International, Menlo Park, California 94025.
authors.forename: S D
authors.initials: SD
authors.lastname: Jayasena
authors.forename: B H
authors.initials: BH
authors.lastname: Johnston
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000187:drug effects; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation / Q000187:drug effects; D011196:Potassium Permanganate / Q000494:pharmacology; D011685:Purine Nucleotides / Q000737:chemistry*; D011742:Pyrimidine Nucleotides / Q000737:chemistry*; D012091:Repetitive Sequences, Nucleic Acid
chemical_list: D011685:Purine Nucleotides; D011742:Pyrimidine Nucleotides; D011196:Potassium Permanganate; D004247:DNA