I-Clamp phenoxazine for the fine tuning of DNA i-motif stability

Vladimir B. Tsvetkov, Timofei S. Zatsepin, Evgeny S. Belyaev, Yury I. Kostyukevich, George V. Shpakovski, Victor V. Podgorsky, Galina E. Pozmogova, Anna M. Varizhuk, Andrey V. Aralov

    Research output: Contribution to journalArticlepeer-review

    19 Citations (Scopus)


    Non-canonical DNA structures are widely used for regulation of gene expression, in DNA nanotechnology and for the development of new DNA-based sensors. I-motifs (iMs) are two intercalated parallel duplexes that are held together by hemiprotonated C-C base pairs. Previously, iMs were used as an accurate sensor for intracellular pH measurements. However, iM stability ismoderate, which in turn limits its in vivo applications. Here, we report the rational design of a new substituted phenoxazine 2′-deoxynucleotide (iclamp) for iM stabilization. This residue contains a C8-aminopropyl tether that interacts with the phosphate group within the neighboring chain without compromising base pairing.We studied the influence of i-clamp on pH-dependent stability for intra- and intermolecular iM structures and found the optimal positions for modification. Two i-clamps on opposite strands provide thermal stabilization up to 10-11°C at a pH of 5.8. Thus, we developed a new modification that shows significant iM-stabilizing effect both at strongly and mildly acidic pH and increases iM transition pH values. i-Clamp can be used for tuning iM-based pH probes or assembling extra stable iM structures for various applications.

    Original languageEnglish
    Pages (from-to)2751-2764
    Number of pages14
    JournalNucleic Acids Research
    Issue number6
    Publication statusPublished - 2018


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