Transfecting RNA quadruplexes results in few transcriptome perturbations

RNA Biol. 2013 Feb;10(2):205-10. doi: 10.4161/rna.22781. Epub 2012 Dec 12.


Guanine-rich nucleic acid sequences can form four-stranded structures called G-quadruplexes. Previous studies showed that transfecting G-quadruplex DNA oligonucleotides inhibits proliferation in many cancer cell lines and can induce apoptosis. However, little is known about the effects of transfecting RNA quadruplexes. In this study, we transfected a G-quadruplex RNA oligonucleotide (GqRNA) into HEK293T cells and observed that it did not alter cell viability. Subsequent transcriptome expression profiling revealed that only two genes, EGR1 and FOS, were significantly altered in the presence of GqRNA (upregulated 2- to 4-fold). Sequence analysis showed that both genes contained putative quadruplex sequences (PQS) in their 3'-UTRs, immediately adjacent to the stop codons. Transfection of the EGR1 PQS as an RNA oligonucleotide also caused an increase in EGR1 expression. Similar motifs are found in a variety of genomes, but are relatively rare and have been missed by previous annotations. A bioinformatic analysis revealed stop codon-proximal enrichment of such motifs compared with the rest of the 3'-UTR, although these genes were not affected by RNA quadruplex transfection, and their function remains unknown. Overall, transfecting RNA quadruplexes results in relatively few alterations in gene expression.

Keywords: 3′-UTR; EGR1; G-quartet; RNA quadruplex; quadruplex.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 3' Untranslated Regions
  • Cell Survival
  • Circular Dichroism
  • Codon, Terminator / genetics
  • Codon, Terminator / metabolism
  • Computational Biology
  • Early Growth Response Protein 1 / genetics
  • Early Growth Response Protein 1 / metabolism
  • G-Quadruplexes*
  • Gene Expression Profiling
  • Gene Expression Regulation, Neoplastic*
  • HEK293 Cells
  • Humans
  • Nucleotide Motifs
  • Oligonucleotides, Antisense / genetics
  • Oligonucleotides, Antisense / metabolism
  • RNA Folding*
  • Telomere / genetics
  • Telomere / metabolism
  • Transcriptome*
  • Transfection*


  • 3' Untranslated Regions
  • Codon, Terminator
  • EGR1 protein, human
  • Early Growth Response Protein 1
  • Oligonucleotides, Antisense