Stabilization of G-quadruplex in the BCL2 promoter region in double-stranded DNA by invading short PNAs

Nucleic Acids Res. 2009 Dec;37(22):7570-80. doi: 10.1093/nar/gkp840.

Abstract

Numerous regulatory genes have G-rich regions that can potentially form quadruplex structures, possibly playing a role in transcription regulation. We studied a G-rich sequence in the BCL2 gene 176-bp upstream of the P1 promoter for G-quadruplex formation. Using circular dichroism (CD), thermal denaturation and dimethyl sulfate (DMS) footprinting, we found that a single-stranded oligonucleotide with the sequence of the BCL2 G-rich region forms a potassium-stabilized G-quadruplex. To study G-quadruplex formation in double-stranded DNA, the G-rich sequence of the BCL2 gene was inserted into plasmid DNA. We found that a G-quadruplex did not form in the insert at physiological conditions. To induce G-quadruplex formation, we used short peptide nucleic acids (PNAs) that bind to the complementary C-rich strand. We examined both short duplex-forming PNAs, complementary to the central part of the BCL2 gene, and triplex-forming bis-PNAs, complementary to sequences adjacent to the G-rich BCL2 region. Using a DMS protection assay, we demonstrated G-quadruplex formation within the G-rich sequence from the promoter region of the human BCL2 gene in plasmid DNA. Our results show that molecules binding the complementary C-strand facilitate G-quadruplex formation and introduce a new mode of PNA-mediated sequence-specific targeting.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Circular Dichroism
  • DNA / chemistry*
  • DNA Footprinting
  • G-Quadruplexes*
  • Genes, bcl-2*
  • Humans
  • Nucleic Acid Denaturation
  • Peptide Nucleic Acids / chemistry*
  • Plasmids / chemistry
  • Promoter Regions, Genetic*

Substances

  • Peptide Nucleic Acids
  • DNA