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

• Published in: Biochimica et biophysica acta. General subjects Vol. 1864; no. 9; p. 129651
• Main Authors: Školáková, Petra, Badri, Zahra, Foldynová-Trantírková, Silvie, Ryneš, Jan, Šponer, Jiří, Fojtová, Miloslava, Fajkus, Jiří, Marek, Radek, Vorlíčková, Michaela, Mergny, Jean-Louis, Trantírek, Lukáš
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.09.2020
• Subjects: Base Sequence; cytosine; Cytosine - metabolism; Cytosine methylation; denaturation; DNA; DNA Methylation; DNA nanotechnology; DNA, Plant - chemistry; DNA, Plant - genetics; Epigenesis, Genetic; Epigenetic modification; epigenetics; genes; i-motif; Models, Molecular; Nanotechnology; Nucleotide Motifs - genetics; Plant telomeric DNA; plants (botany); polyacrylamide gel electrophoresis; quantum mechanics; spectroscopy; Telomere - genetics; telomeres; Plant telomeric DNA; DNA nanotechnology; Cytosine methylation; Epigenetic modification; DNA; i-motif
• ISSN: 0304-4165; 1872-8006; 1872-8006
• DOI: 10.1016/j.bbagen.2020.129651

The i-motif is a tetrameric DNA structure based on the formation of hemiprotonated cytosine-cytosine (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. We employed CD and UV-absorption spectroscopies, native PAGE, thermal denaturation and quantum-chemical 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. CMPs have strong influence on i-motif stability and pKa and influence these parameters in sequence-specific 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. 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. 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. •Complex methylation patterns impact i-motif stability in sequence dependent manner•Complex methylation patterns do not invariably stabilize DNA i-motif•In i-motif, methylation has a larger influence on stacking than base-paring