Characterization of the G-quadruplexes in the duplex nuclease hypersensitive element of the PDGF-A promoter and modulation of PDGF-A promoter activity by TMPyP4

Nucleic Acids Res. 2007;35(22):7698-713. doi: 10.1093/nar/gkm538. Epub 2007 Nov 5.


The proximal 5'-flanking region of the human platelet-derived growth factor A (PDGF-A) promoter contains one nuclease hypersensitive element (NHE) that is critical for PDGF-A gene transcription. On the basis of circular dichroism (CD) and electrophoretic mobility shift assay (EMSA), we have shown that the guanine-rich (G-rich) strand of the DNA in this region can form stable intramolecular parallel G-quadruplexes under physiological conditions. A Taq polymerase stop assay has shown that the G-rich strand of the NHE can form two major G-quadruplex structures, which are in dynamic equilibrium and differentially stabilized by three G-quadruplex-interactive drugs. One major parallel G-quadruplex structure of the G-rich strand DNA of NHE was identified by CD and dimethyl sulfate (DMS) footprinting. Surprisingly, CD spectroscopy shows a stable parallel G-quadruplex structure formed within the duplex DNA of the NHE at temperatures up to 100 degrees C. This structure has been characterized by DMS footprinting in the double-stranded DNA of the NHE. In transfection experiments, 10 microM TMPyP4 reduced the activity of the basal promoter of PDGF-A approximately 40%, relative to the control. On the basis of these results, we have established that ligand-mediated stabilization of G-quadruplex structures within the PDGF-A NHE can silence PDGF-A expression.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Line, Tumor
  • Circular Dichroism
  • DNA / chemistry
  • DNA Footprinting
  • G-Quadruplexes* / drug effects
  • Guanine / chemistry
  • Humans
  • Ligands
  • Mutation
  • Platelet-Derived Growth Factor / genetics*
  • Porphyrins / chemistry
  • Porphyrins / pharmacology*
  • Potassium / chemistry
  • Promoter Regions, Genetic*
  • Single-Strand Specific DNA and RNA Endonucleases / metabolism
  • Transcription, Genetic / drug effects*


  • Ligands
  • Platelet-Derived Growth Factor
  • Porphyrins
  • platelet-derived growth factor A
  • tetra(4-N-methylpyridyl)porphine
  • Guanine
  • DNA
  • Single-Strand Specific DNA and RNA Endonucleases
  • Potassium