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KRAS promoter oligonucleotide with decoy activity dimerizes into a unique topology consisting of two G-quadruplex

Peter Podbevšek1, Janez Plavec2

  • 1Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia EN-FIST Centre of Excellence, Trg OF 13, SI-1000 Ljubljana, Slovenia.

Nucleic Acids Research
|December 15, 2015
PubMed

Insights

The KRAS NHE G-quadruplex structure requires dimerization for anti-cancer activity. This G-quadruplex formation protects the oligonucleotide and enhances its therapeutic potential.

Area of Science:

  • Oncology
  • Molecular Biology
  • Biophysics

Background:

  • KRAS proto-oncogene mutations are linked to various cancers, making it a key target for anti-cancer drug development.
  • The human KRAS promoter possesses a nuclease-hypersensitive element (NHE) that binds nuclear proteins and forms G-quadruplex structures.
  • A 32-nt oligonucleotide (32R-3n) mimicking the KRAS NHE inhibits gene transcription by sequestering the transcription factor MAZ.

Purpose of the Study:

  • To investigate the structural requirements of the 32R-3n oligonucleotide for G-quadruplex formation.
  • To elucidate the role of G-quadruplex structure in the anti-cancer activity of 32R-3n.
  • To characterize the MAZ binding site within the KRAS NHE G-quadruplex.

Main Methods:

  • Nuclear magnetic resonance (NMR) spectroscopy
  • Circular dichroism (CD) and UV spectroscopy
  • Oligonucleotide synthesis and biophysical characterization

Main Results:

  • The 32R-3n oligonucleotide must dimerize to form a stable G-quadruplex structure.
  • The G-quadruplex features two symmetric 5'- and 3'-end units with head-to-head topology and edge-type loops.
  • The MAZ binding site is located within the 3'-end G-quadruplex unit, and its nucleotides exhibit dynamic properties.
  • Both G-quadruplex units contribute to the stability and anti-cancer efficacy of 32R-3n.

Conclusions:

  • Dimerization is essential for the KRAS NHE mimic 32R-3n to fold into a functional G-quadruplex.
  • The dynamic nature of the MAZ binding site suggests potential for sequence- or structure-based recognition.
  • The stable dimeric G-quadruplex structure enhances the anti-cancer potential of 32R-3n by protecting its ends.

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