Binding of triple helix forming oligonucleotides to sites in gene promoters

Ross H. Durland, Donald J. Kessler, Sandy Gunnell, Madeleine Duvic, B. M. Pettitt, Bernard Pettitt

Research output: Contribution to journalArticle

250 Scopus citations


A class of triplex-forming oligodeoxyribonucleotides (TFOs) is described that can bind to naturally occurring sites in duplex DNA at physiological pH in the presence of magnesium. The data are consistent with a structure in which the TFO binds in the major groove of double-stranded DNA to form a three-stranded complex that is superficially similar to previously described triplexes. The distinguishing features of this class of triplex are that TFO binding apparently involves the formation of hydrogen-bonded G·GC and T·AT triplets and the TFO is bound antiparallel with respect to the more purine-rich strand of the underlying duplex. Triplex formation is described for targets in the promoter regions of three different genes: the human c-myc and epidermal growth factor receptor genes and the mouse insulin receptor gene. All three sites are relatively GC rich and have a high percentage of purine residues on one strand. DNase I footprinting shows that individual TFOs bind selectively to their target sites at pH 7.4-7.8 in the presence of millimolar concentrations of magnesium. Electrophoretic analysis of triplex formation indicates that specific TFOs bind to their target sites with apparent dissociation constants in the 10-7-10-9 M range. Strand orientation of the bound TFOs was confirmed by attaching eosin or an iron-chelating group to one end of the TFO and monitoring the pattern of damage to the bound duplex DNA. Possible hydrogen-bonding patterns and triplex structures are discussed.

Original languageEnglish (US)
Pages (from-to)9246-9255
Number of pages10
Issue number38
StatePublished - 1991
Externally publishedYes


ASJC Scopus subject areas

  • Biochemistry

Cite this

Durland, R. H., Kessler, D. J., Gunnell, S., Duvic, M., Pettitt, B. M., & Pettitt, B. (1991). Binding of triple helix forming oligonucleotides to sites in gene promoters. Biochemistry, 30(38), 9246-9255.