Intercalator conjugates of pyrimidine locked nucleic acid-modified triplex-forming oligonucleotides: improving DNA binding properties and reaching cellular activities

Nucleic Acids Res. 2005 Jul 27;33(13):4223-34. doi: 10.1093/nar/gki726. Print 2005.

Abstract

Triplex-forming oligonucleotides (TFOs) are powerful tools to interfere sequence-specifically with DNA-associated biological functions. (A/T,G)-containing TFOs are more commonly used in cells than (T,C)-containing TFOs, especially C-rich sequences; indeed the low intracellular stability of the non-covalent pyrimidine triplexes make the latter less active. In this work we studied the possibility to enhance DNA binding of (T,C)-containing TFOs, aiming to reach cellular activities; to this end, we used locked nucleic acid-modified TFOs (TFO/LNAs) in association with 5'-conjugation of an intercalating agent, an acridine derivative. In vitro a stable triplex was formed with the TFO-acridine conjugate: by SPR measurements at 37 degrees C and neutral pH, the dissociation equilibrium constant was found in the nanomolar range and the triplex half-life approximately 10 h (50-fold longer compared with the unconjugated TFO/LNA). Moreover to further understand DNA binding of (T,C)-containing TFO/LNAs, hybridization studies were performed at different pH values: triplex stabilization associated with pH decrease was mainly due to a slower dissociation process. Finally, biological activity of pyrimidine TFO/LNAs was evaluated in a cellular context: it occurred at concentrations approximately 0.1 microM for acridine-conjugated TFO/LNA (or approximately 2 microM for the unconjugated TFO/LNA) whereas the corresponding phosphodiester TFO was inactive, and it was demonstrated to be triplex-mediated.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA / chemistry*
  • DNA / metabolism
  • DNA-Binding Proteins / antagonists & inhibitors*
  • HeLa Cells
  • Humans
  • Hydrogen-Ion Concentration
  • Intercalating Agents / chemistry*
  • Intercalating Agents / pharmacology*
  • Oligonucleotides
  • Oligonucleotides, Antisense / chemistry*
  • Oligonucleotides, Antisense / metabolism
  • Oligonucleotides, Antisense / pharmacology*
  • Pyrimidines / chemistry*
  • Transcription, Genetic / drug effects*

Substances

  • DNA-Binding Proteins
  • Intercalating Agents
  • Oligonucleotides
  • Oligonucleotides, Antisense
  • Pyrimidines
  • locked nucleic acid
  • triplex DNA
  • DNA