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Journal/Book: ChemBioChem
Published: 2024
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Biophysical Investigation of RNA•DNA:DNA triple helix and RNA:DNA heteroduplex formation by the lncRNAs MEG3 and Fendrr

Krause NM, Bains JK, Blechar J, Richter C, Bessi I, Grote P, Leisegang MS, Brandes RP, Schwalbe H
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.
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© Copyright 2024
Prof. Dr. Harald Schwalbe
Institut für Organische Chemie und Chemische Biologie
Johann Wolfgang Goethe Universität
Max-von-Laue-Str. 7
D-60438 Frankfurt am Main
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