Composite 5-methylations of cytosines modulate i-motif stability in a sequence-specific manner: Implications for DNA nanotechnology and epigenetic regulation of plant telomeric DNA

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Authors	ŠKOLÁKOVÁ Petra BADRI Zahra TRANTÍRKOVÁ Silvie RYNEŠ Jan ŠPONER Jiří FOJTOVÁ Miloslava FAJKUS Jiří MAREK Radek VORLÍČKOVÁ Michaela MERGNY Jean-Louis TRANTÍREK Lukáš
Year of publication	2020
Type	Article in Periodical
Magazine / Source	BBA - General Subjects
MU Faculty or unit	Central European Institute of Technology
Citation
Web	DOI: 10.1016/j.bbagen.2020.129651
Doi	http://dx.doi.org/10.1016/j.bbagen.2020.129651
Keywords	i-motif;DNA;Epigenetic modification;DNA nanotechnology;Plant telomeric DNA;Cytosine methylation
Attached files	BBAGEN20_1864_129651.pdf
Description	Background: The i-motif is a tetrameric DNA structure based on the formation of hemiprotonated cytosinecytosine (C+.C) base pairs. i-motifs are widely used in nanotechnology. In biological systems, i-motifs are involved in gene regulation and in control of genome integrity. In vivo, the i-motif forming sequences are subjects of epigenetic modifications, particularly 5-cytosine methylation. In plants, natively occurring methylation patterns lead to a complex network of C+.C, 5mC+.C and 5mC+.5mC base-pairs in the i-motif stem. The impact of complex methylation patterns (CMPs) on i-motif formation propensity is currently unknown. Methods: We employed CD and UV-absorption spectroscopies, native PAGE, thermal denaturation and quantumchemical calculations to analyse the effects of native, native-like, and non-native CMPs in the i-motif stem on the i-motif stability and pKa. Results: CMPs have strong influence on i-motif stability and pKa and influence these parameters in sequencespecific manner. In contrast to a general belief, i) CMPs do not invariably stabilize the i-motif, and ii) when the CMPs do stabilize the i-motif, the extent of the stabilization depends (in a complex manner) on the number and pattern of symmetric 5mC+.5mC or asymmetric 5mC+.C base pairs in the i-motif stem. Conclusions: CMPs can be effectively used to fine-tune i-motif properties. Our data support the notion of epigenetic modifications as a plausible control mechanism of i-motif formation in vivo. General Significance: Our results have implications in epigenetic regulation of telomeric DNA in plants and highlight the potential and limitations of engineered patterning of cytosine methylations on the i-motif scaffold in nanotechnological applications.
Related projects:	CEITEC 2020 Atomically resolved in vivo NMR spectroscopy as a novel tool for biological testing of therapeutically important genomic non-canonical DNA targets and their interactions with drugs in phenotypically diversified cancer cells.