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Krause NM, Bains JK, Blechar J, Richter C, Bessi I, Grote P, Leisegang MS, Brandes RP, Schwalbe H. Biophysical Investigation of RNA ⋅ DNA : DNA Triple Helix and RNA : DNA Heteroduplex Formation by the lncRNAs MEG3 and Fendrr. Chembiochem 2024; 25:e202400049. [PMID: 38456652 DOI: 10.1002/cbic.202400049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 03/09/2024]
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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Affiliation(s)
- Nina M Krause
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue-Straße7, 60438, Frankfurt am Main, Germany
| | - Jasleen K Bains
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue-Straße7, 60438, Frankfurt am Main, Germany
| | - Julius Blechar
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue-Straße7, 60438, Frankfurt am Main, Germany
| | - Christian Richter
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue-Straße7, 60438, Frankfurt am Main, Germany
| | - Irene Bessi
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue-Straße7, 60438, Frankfurt am Main, Germany
- Institute for Organic Chemistry, Julius-Maximilians-University, Würzburg, Bavaria, 97074, Germany
| | - Phillip Grote
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Frankfurt am Main, Hesse, 60590, Germany
- Georg-Speyer-Haus, Frankfurt am Main, Hesse, 60590, Germany
| | - Matthias S Leisegang
- Institute for Cardiovascular Physiology, Johann Wolfgang Goethe University, Frankfurt, Hesse, 60596, Germany
- German Centre of Cardiovascular Research (DZHK), Partner site Rhine-Main, Frankfurt, Hesse, 60596, Germany
| | - Ralf P Brandes
- Institute for Cardiovascular Physiology, Johann Wolfgang Goethe University, Frankfurt, Hesse, 60596, Germany
- German Centre of Cardiovascular Research (DZHK), Partner site Rhine-Main, Frankfurt, Hesse, 60596, Germany
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue-Straße7, 60438, Frankfurt am Main, Germany
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