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

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.