In-cell NMR spectroscopy as a tool for studying the influence of changing intracellular environment on non-B DNA structures

Maturova Eva^1,*, Viskova Pavlina¹, Krafcikova Michaela¹, Dzatko Simon¹, Loja Tomas¹, Rynes Jan¹, Foldynova-Trantirkova Silvie^1,2, Trantirek Lukas¹

¹Central European Institute of Technology, Masaryk University, Brno, Czech Republic
²Institute of Biophysics of the AS CR, v.v.i., Brno, Czech Republic
eva.maturova@ceitec.muni.cz

In-cell NMR spectroscopy is useful technique enabling structural characterization of macromolecules such as proteins or DNA inside the complex environment of living cell [1]. This is very important for molecules sensitive to the parameters of their environment such as pH, ionic strength and composition, or molecular crowding.

I-motifs represents one of these structures. DNA i-motif is a tetrameric DNA structure based on the formation of hemi-protonated cytosine-cytosine (C+.C) base pairs [2]. Under in vitro conditions, i-motif formation is favored by acidic pH and low ionic strength [3], [4]. However, the existence of i-motifs in living cells has remained unclear until recently [5], [6].

In eukaryotic genomes, i-motif-prone sequences are enriched in biologically important regions, such as gene promoters where they were proposed to play an active role in regulation of gene expression [7]. Parameters of the intracellular environment vary during different cellular events such as cell cycle, apoptosis or hypoxia [8], which can trigger changes of occurence of i-motifs in vivo, as was recently demonstrated by [6]. Here, we present possibility to investigate formation of i-motifs in separate phases of the cell cycle using in-cell NMR spectroscopy.

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Acknowledgement: This project was supported by the project SYMBIT reg. number: CZ.02.1.01/0.0/0.0/15_003/0000477 financed by the ERDF, by the Ministry of Education, Youth and Sports of the Czech Republic under the projects CEITEC 2020 (LQ1601); CIISB-LM2018127; Czech-BioImaging LM2018129; EATRIS-CZ LM2018133, and by the grant from Czech Science Foundation (19-26041X), and Ministry of Health of the Czech Republic (NV19-08-00450).