Competitive triplex/quadruplex equilibria involving guanine-rich oligonucleotides

Biochemistry. 1995 Jan 10;34(1):278-84. doi: 10.1021/bi00001a034.

Abstract

Oligonucleotide-directed triple helix formation in the purine motif involves the binding of guanine-rich oligonucleotides to duplex DNA. Although this approach has been proposed for in vivo gene inhibition, triple helix formation by guanine-rich oligonucleotides is severely inhibited by physiological concentrations of certain monovalent cations (M+), especially K+. To clarify the mechanism of this inhibition, electrophoretic gel mobility shift titrations were performed to analyze the formation and stability of a purine motif triple helix in the presence of M+ and to monitor oligonucleotide aggregation under these conditions. M+ inhibition of triplex formation exhibited a concentration and ionic radius dependence that correlates with the ability of M+ to stabilize guanine quartet structures. In the presence of inhibitory [M+], guanine-rich oligonucleotides formed aggregates having characteristics consistent with the involvement of guanine quartets. The inhibitory effects of K+ on triplex formation could not be reversed by addition of the physiological polyamines spermidine3+ or spermine4+. M+ reduced the equilibrium concentration of the triplex primarily by decreasing the rate of triplex formation, but M+ also caused a detectable increase in the rate of triplex dissociation. Together, these results suggest that triplex inhibition under physiological ionic conditions is caused by competing equilibria wherein guanine-rich oligonucleotides form aggregates involving guanine quartets. Approaches to destabilizing aggregates of guanine-rich oligonucleotides under physiological conditions will be required before in vivo applications can be realistically considered.

Publication types

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

MeSH terms

  • Base Sequence
  • Cations, Monovalent
  • Electrophoresis, Polyacrylamide Gel
  • Guanine / chemistry*
  • Models, Chemical
  • Molecular Sequence Data
  • Nucleic Acid Conformation*
  • Oligodeoxyribonucleotides / chemistry*

Substances

  • Cations, Monovalent
  • Oligodeoxyribonucleotides
  • Guanine