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bioRxiv · 10.1101/2024.08.18.608433

Kinetics of i-motif folding within the duplex context

Alieva, R.·Keshek, A.·Zatsepin, T.·Orlov, V.·Aralov, A.·Zavyalova, E.
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Abstract

Non-canonical nucleic acid structures possess an ability to interact selectively with proteins, thereby exerting influence over various intracellular processes. Numerous studies indicate that genomic G-quadruplexes and i-motifs are involved in the regulation of transcription. These structures are formed temporarily during the unwinding of the DNA double helix; and their direct determination is a rather difficult task. In addition, i-motif folding is pH-dependent, with most i-motifs having low stability at neutral pH. However, some genomic i-motifs with long cytosine repeats were shown to be stable at pH 7.3, suggesting their functionality within the nucleus. Here we studied pH-dependent behavior of a model i-motif with flanking sequences that forms a duplex motif. Kinetic studies on bimodular structures with cytosine residues replaced with an environment-sensitive fluorescent label reveal the stabilization of the i-motif structure near the i-motif-duplex junction. These results highlight the importance of the natural environment of i-motifs for the correct assessment of their stability.

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Alieva, R., Keshek, A., Zatsepin, T., Orlov, V., Aralov, A., Zavyalova, E.. 2024-08-18. Kinetics of i-motif folding within the duplex context. https://doi.org/10.1101/2024.08.18.608433

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