Группа молекулярных инструментов для исследования живых систем

Отдел функционирования живых систем

Руководитель: Аралов Андрей Владимирович, к. х. н.

РНК, ДНК, G-квадруплекс, i-мотив, антисмысловые олигонуклеотиды, зонды, pH сенсоры, модификация, флуоресценция

Основные направления исследований группы включают:

-дизайн и синтез нуклеотидных модификаций для регулирования свойств канонических и неканонических вторичных структур нуклеиновых кислот;

- разработку нуклеотидных модификаций, пригодных в антисенс- и RNAi технологиях для регуляции экспрессии генов;

- синтез и скрининг зондов/лигандов для детекции и изменения физико-химических параметров неканонических вторичных структур нуклеиновых кислот;

- разработку и исследование свойств олигонуклеотидных модификаций, связывающихся с ионами металлов;

- исследование физико-химических свойств модификаций, возникающих в живых организмах под воздействием мутагенных факторов окружающей среды.

- дизайн и синтез противовирусных соединений.


Аралов Андрей Владимирович, к. х. н.рук. подр.Baruh238@mail.ru

Избранные публикации

  1. Tsvetkov V.B., Zatsepin T.S., Belyaev E.S., Kostyukevich Y.I., Shpakovski G.V., Podgorsky V.V., Pozmogova G.E., Varizhuk A.M., Aralov A.V. (2018). i-Clamp phenoxazine for the fine tuning of DNA i-motif stability. Nucleic Acids Res. 46 (6), 2751–2764 [+]

    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 is moderate, which in turn limits its in vivo applications. Here, we report the rational design of a new substituted phenoxazine 2'-deoxynucleotide (i-clamp) 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.

  2. Shpakovski G.V., Spivak S.G., Berdichevets I.N., Babak O.G., Kubrak S.V., Kilchevsky A.V., Aralov A.V., Slovokhotov I.Y., Shpakovski D.G., Baranova E.N., Khaliluev M.R., Shematorova E.K. (2017). A key enzyme of animal steroidogenesis can function in plants enhancing their immunity and accelerating the processes of growth and development. BMC Plant Biol. 17 (Suppl 1), 189 [+]

    The initial stage of the biosynthesis of steroid hormones in animals occurs in the mitochondria of steroidogenic tissues, where cytochrome P450SCC (CYP11A1) encoded by the CYP11A1 gene catalyzes the conversion of cholesterol into pregnenolone - the general precursor of all the steroid hormones, starting with progesterone. This stage is missing in plants where mitochondrial cytochromes P450 (the mito CYP clan) have not been found. Generating transgenic plants with a mitochondrial type P450 from animals would offer an interesting option to verify whether plant mitochondria could serve as another site of P450 monooxygenase reaction for the steroid hormones biosynthesis.

  3. Varizhuk A.M., Zatsepin T.S., Golovin A.V., Belyaev E.S., Kostyukevich Y.I., Dedkov V.G., Shipulin G.A., Shpakovski G.V., Aralov A.V. (2017). Synthesis of oligonucleotides containing novel G-clamp analogue with C8-tethered group in phenoxazine ring: Implication to qPCR detection of the low-copy Kemerovo virus dsRNA. Bioorg. Med. Chem. 25 (14), 3597–3605 [+]

    Nowadays modified oligonucleotides are widely used in diagnostics and as novel therapeutics. Introduction of modified or unnatural residues into oligonucleotides allows fine tuning of their binding properties to complementary nucleic acids and leads to improved stability both in vitro and in vivo. Previously it was demonstrated that insertion of phenoxazine nucleotides with various groups in C9-position into oligonucleotides leads to a significant increase of duplex stability with complementary DNA and RNA. Here the synthesis of a novel G-clamp nucleoside analogue (G(8AE)-clamp) bearing 2-aminoethyl tether at C8-atom is presented. Introduction of such modified residues into oligonucleotides lead to enhanced specificity of duplex formation towards complementary DNA and RNA targets with increased thermal and 3'-exonuclease stability. According to CD-spectroscopy studies G(8AE)-clamp does not substantially disrupt helix geometry. Primers containing G(8AE)-clamp demonstrated superior sensitivity in qPCR detection of dsRNA of Kemerovo virus in comparison to native oligonucleotides.


Аралов Андрей Владимирович