Binding of triple helix forming oligonucleotides to sites in gene promoters

Biochemistry. 1991 Sep 24;30(38):9246-55. doi: 10.1021/bi00102a017.


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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Base Sequence
  • Deoxyribonuclease I / pharmacology
  • ErbB Receptors / genetics
  • Genes, myc*
  • Humans
  • Hydrogen Bonding
  • In Vitro Techniques
  • Mice
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Oligonucleotides / chemistry*
  • Promoter Regions, Genetic*
  • Proto-Oncogene Proteins c-myc / genetics*
  • Receptor, Insulin / genetics


  • Oligonucleotides
  • Proto-Oncogene Proteins c-myc
  • ErbB Receptors
  • Receptor, Insulin
  • Deoxyribonuclease I