Structure Validation of G-Rich RNAs in Noncoding Regions of the Human Genome

Chembiochem. 2020 Jun 2;21(11):1656-1663. doi: 10.1002/cbic.201900696. Epub 2020 Feb 26.

Abstract

We present the rapid biophysical characterization of six previously reported putative G-quadruplex-forming RNAs from the 5'-untranslated region (5'-UTR) of silvestrol-sensitive transcripts for investigation of their secondary structures. By NMR and CD spectroscopic analysis, we found that only a single sequence-[AGG]2 [CGG]2 C-folds into a single well-defined G-quadruplex structure. Sequences with longer poly-G strands form unspecific aggregates, whereas CGG-repeat-containing sequences exhibit a temperature-dependent equilibrium between a hairpin and a G-quadruplex structure. The applied experimental strategy is fast and provides robust readout for G-quadruplex-forming capacities of RNA oligomers.

Keywords: G-quadruplexes; NMR spectroscopy; RNA; biophysical investigation; circular dichroism.

Publication types

  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • ADAM10 Protein / genetics
  • ADAM10 Protein / metabolism
  • Amyloid Precursor Protein Secretases / genetics
  • Amyloid Precursor Protein Secretases / metabolism
  • E1A-Associated p300 Protein / genetics
  • E1A-Associated p300 Protein / metabolism
  • G-Quadruplexes*
  • Genome, Human
  • Histone Deacetylases / genetics
  • Histone Deacetylases / metabolism
  • Humans
  • Intracellular Signaling Peptides and Proteins / genetics
  • Intracellular Signaling Peptides and Proteins / metabolism
  • Membrane Proteins / genetics
  • Membrane Proteins / metabolism
  • Poly G / chemistry
  • Poly G / genetics*
  • Poly G / metabolism
  • Protein Serine-Threonine Kinases / genetics
  • Protein Serine-Threonine Kinases / metabolism
  • RNA Folding / drug effects
  • RNA, Messenger / chemistry
  • RNA, Messenger / genetics*
  • RNA, Messenger / metabolism
  • RNA, Untranslated / chemistry
  • RNA, Untranslated / genetics*
  • RNA, Untranslated / metabolism
  • Repressor Proteins / genetics
  • Repressor Proteins / metabolism
  • Transforming Growth Factor beta1 / genetics
  • Transforming Growth Factor beta1 / metabolism
  • Triterpenes / pharmacology

Substances

  • Intracellular Signaling Peptides and Proteins
  • Membrane Proteins
  • RNA, Messenger
  • RNA, Untranslated
  • Repressor Proteins
  • TGFB1 protein, human
  • Transforming Growth Factor beta1
  • Triterpenes
  • silvestrol
  • Poly G
  • E1A-Associated p300 Protein
  • EP300 protein, human
  • MAP-kinase-activated kinase 2
  • Protein Serine-Threonine Kinases
  • Amyloid Precursor Protein Secretases
  • ADAM10 Protein
  • ADAM10 protein, human
  • MTA2 protein, human
  • Histone Deacetylases