Biophysical Investigation of RNA ⋅ DNA : DNA Triple Helix and RNA : DNA Heteroduplex Formation by the lncRNAs MEG3 and Fendrr

Chembiochem. 2024 May 17;25(10):e202400049. doi: 10.1002/cbic.202400049. Epub 2024 Apr 29.

Abstract

Long non-coding RNAs (lncRNAs) are important regulators of gene expression and can associate with DNA as RNA : DNA heteroduplexes or RNA ⋅ DNA : DNA triple helix structures. Here, we review in vitro biochemical and biophysical experiments including electromobility shift assays (EMSA), circular dichroism (CD) spectroscopy, thermal melting analysis, microscale thermophoresis (MST), single-molecule Förster resonance energy transfer (smFRET) and nuclear magnetic resonance (NMR) spectroscopy to investigate RNA ⋅ DNA : DNA triple helix and RNA : DNA heteroduplex formation. We present the investigations of the antiparallel triplex-forming lncRNA MEG3 targeting the gene TGFB2 and the parallel triplex-forming lncRNA Fendrr with its target gene Emp2. The thermodynamic properties of these oligonucleotides lead to concentration-dependent heterogeneous mixtures, where a DNA duplex, an RNA : DNA heteroduplex and an RNA ⋅ DNA : DNA triplex coexist and their relative populations are modulated in a temperature-dependent manner. The in vitro data provide a reliable readout of triplex structures, as RNA ⋅ DNA : DNA triplexes show distinct features compared to DNA duplexes and RNA : DNA heteroduplexes. Our experimental results can be used to validate computationally predicted triple helix formation between novel disease-relevant lncRNAs and their DNA target genes.

Keywords: Biophysical characterization; RNA : DNA Heteroduplex; RNA ⋅ DNA : DNA Triplex; lncRNA.

Publication types

  • Review

MeSH terms

  • DNA* / chemistry
  • DNA* / genetics
  • Humans
  • Nucleic Acid Conformation*
  • Nucleic Acid Heteroduplexes / chemistry
  • RNA / chemistry
  • RNA / genetics
  • RNA / metabolism
  • RNA, Long Noncoding* / chemistry
  • RNA, Long Noncoding* / genetics
  • RNA, Long Noncoding* / metabolism
  • Thermodynamics

Substances

  • MEG3 non-coding RNA, human
  • triplex DNA