Laboratory of Nucleic Acids Bioсhemistry

Marina A. Zenkova,
prof., D.Biol.Sci.
Phone: +7(383)363-51-60
Email

• Elaboration of new methods of gene expression regulation and novel therapeutic agents on the base of the oligonucleotides and their derivatives.
• Investigation of ways of the genetic material delivery into cells.
• Creation and study of artificial ribonucleases.

• Mechanism of hybridization of antisense oligonucleotides with RNA was defined. It was shown that antisense oligonucleotide hybridization with RNA as a target was a multistep process initiated by an intermediate oligonucleotide complex formation between oligonucleotide and partially complementary sequence localized in the loop or single-stranded region of RNA. [Serikov R. et al., J. Biomol. Strt. Dyn., 2011. 29(1), 27].
• A new class of conjugates of short oligonucleotides with [ArgLeu]4 peptide capable of cleaving the RNA phosphodiester bonds at GpX motives was synthetized. Such specificity was for the first time revealed for artificial ribonucleases. It was shown that the catalyst active conformation was formed due to specific interaction of peptide with oligonucleotide. These elaborated catalysts are interesting as tools for the study of RNA and RNA-protein complexes structure. [Mironova N.L. et al., Nucleic Acids Res. 2007. 35, 2356; Mironova N.L. et al., J. Biomol. Strt. Dyn. 2006. 23, 591].
• Formation of new molecules of RNA in the cleavage/ligation coupled reaction proceeding in the complex of partially complementary oligoribonucleotides in the presence of magnesium ions was shown for the first time. This reaction could proceed in the prebiotic conditions of RNA world providing both elongation of molecules and appearance of novel sequences. [Nechaev S.V. et al., Int. J. Molecular Sci. 2009. 10, 1788; Lutay A.V. et al., In book: Origin of life. Chemical Approach. 2008, 323; Lutay, A.V. et al., Chem. & Biodivers. 2007. 4, 762; Lutay A.V. et al., Biogeosciences. 2006. 3, 243].
• Series of novel low-molecular weight compounds capable of efficient cleavage of phosphodiester bonds within RNA were designed. The compounds - so called artificial ribonucleases (aRNases) - were shown to cleave RNA with specificity of RNase A. Designed aRNases display antiviral activity in respect to RNA containing viruses and can be applied for preparation of candidate vaccines. [Tamkovich N.V. et al., Bioorg. Chem. 2010. 36, 223; Kovalev N. et al., Bioorganic Chem. 2008 36, 33; Kovalev N. et al., Bioorg. Chem. 2006. 34, 274; Goncharova E.P. et al., Dokl. A.N. 2009. 427, 840].
• Based on the data of degradation of small interfering RNAs (siRNAs) and their modified analogs in the presence of serum the algorithm of addressed chemical modification of siRNA was created, which allows to prepare nuclease resistant siRNA analogs bearing minimal number of modifications. These siRNAs analogs provide a record of 12–15 days gene silencing after a single application. [Chernolovskaya E.L. et al., Curr. Opin. Mol. Ther. 2010. 12, 158; Kruglova N.S. et al., Mol Biol. 2010. 44, 284; Spirin P.V. et al., Mol Biol. 2010. 44, 876].
• Small interfering RNAs (siRNAs), targeted to mRNA of C- and N-MYC genes capable of effective gene silencing were developed. These siRNAs induce 10-15 fold retardation of human neuroblastoma cells proliferation. Prolonged inhibition of C-MYC gene expression gives opportunity to use the potential of siRNA (siRNA-I) to create drugs for cancer therapy. [Akimov I.A. et al., Mol Biol. 2010. 44, 98; Akimov I.A. et al., Oligonucleotides. 2009. 19, 31; Kabilova T.O. et al., Oligonucleotides. 2006. 16, 15; Kabilova Т.О. et al., Mol Biol. 2006. 40, 1037; Kabilova Т.О. et al., Ann. N.Y. Acad. Sci. 2006. 1091, 425].
• Nuclease resistant siRNAs, targeted different regions of MDR1 mRNA, which efficiently reverse multiple drug resistance phenotype of tumor cells and 10-times increase their sensitivity to cytostatic agents were developed. Combined therapy of tumor with multidrug resistance phenotype based on siRNA, targeted MDR1 gene, and pro-apoptotic cytostatic cyclophosphamide were applied to the model of tumor progression in vivo. Single administration of the developed siRNA increases the effectiveness of chemotherapy twice. [Patutina O.A. et al., BMC Cancer. 2010. 10, 1; Volkov A.A. et al., Oligonucleotides. 2009. 19, 191; Logashenko E.B. et al., RUSS CHEM B. 2006. 7, 1227].
• Using two murine tumor models with pulmonary or liver metastases allowed to show the antimetastatic potential of RNase A and DNase I for the first time. Daily administration of ultralow doses of RNase A and DNase I inhibits the development of metastasis to 60 – 90 % and exerts retardation of tumor growth. Simultaneous treatment of tumor-bearing animals with RNase A and DNase I leads to an additive effect and results in almost total absence of metastases. The search for possible molecular mechanism of antimetastatic effect of nucleases showed that the enzymes restored pathologically increased level of extracellular nucleic acids and reduced nuclease activity of the blood plasma of tumor-bearing mice in comparison with the level of healthy animals. [Patutina O.A. et al., Acta Naturae. 2010. 2, 95; Patutina O.A. et al., Acta Naturae. 2009. 2, 47; Shkliaeva (Patutina) O.A. et al., Dokl Biochem Biophys. 2008. 420, 134; Mironova N.L. et al., Ann. N.Y. Acad. Sci. 2006. 1091, 490].

1. Sen'kova A.V., Kozlov V.A., Patutina O.A., Mitkevich V.A., Markov O.V., Petrushanko IY., Burnysheva K.M., Zenkova M.A., Makarov A.A. Ribonuclease binase decreases destructive changes of the liver and restores its regeneration potential in mouse lung carcinoma model. Biochimie. 2014. 101, 256-259.
2. Gvozdeva O.V., Dovydenko I.S., Venyaminova A.G., Zenkova M.A., Vlassov V.V., Chernolovskaya E.L. 42- and 63-bp anti-MDR1-siRNAs bearing 2'-OMe modifications in nuclease-sensitive sites induce specific and potent gene silencing. FEBS Lett. 2014. 588(6), 1037-1043.
3. Apartsin E.K., Buyanova M., Novopashina D.S., Ryabchikova E.I., Filatov A.V., Zenkova M.A., Venyaminova A.G. Novel Multifunctional Hybrids of Single-Walled Carbon Nanotubes with Nucleic Acids: Synthesis and Interactions with Living Cells. ACS Appl. Mater. Interfaces. 2014. 6(3), 1454-1461.
4. Salomatina O.V., Markov A.V., Logashenko E.B., Korchagina D.V., Zenkova M.A., Salakhutdinov N.F., Vlassov V.V., Tolstikov G.A. Synthesis of novel 2-cyano substituted glycyrrhetinic acid derivatives as inhibitors of cancer cells growth and NO production in LPS-sctivated J-774 cells. Bioorg. Med. Chem. 2014. 22(1), 585-593.
5. Petrova N.S., Zenkova M.A., Chernolovskaya E.L. Structure-Functions Relations in Small Interfering RNAs. Practical Applications in Biomedical Engineering. Ed.by Andrade A.O., Pereira A.A., Naves E.L.M., Soares A.B. Rijeka, Croatia: InTech. 2013, 187-228.
6. Chernolovskaya E.L., Zenkova M.A. Design of Nuclease-Resistant Fork-Like Small Interfering RNA (fsiRNA) siRNA Design: Methods and Protocols. Ed. by D.J. Taxman. Humana Press, NY. 2013, 153–168.
7. Gusachenko O.N., Zenkova M.A., Vlassov V.V. Nucleic acids in exosomes: disease markers and intercellular communication molecules. Biochemistry (Mosc). 2013. 78(1), 1-7.
8. Mironova N.L.,Petrushanko I.V., Patutina O.A., Sen,kova A.V., Simonenko O.V., Mitkevich V.A., Markov O.V., Zenkova M.A., Makarov A.A. Ribonuclease binase inhibits primary tumor growth and metastases via apoptosis inductionin tumor cells. Cell Cycle. 2013. 12(13), 2120 -2131.
9. Ivanova E.A., Maslov M.A., Kabilova T.O., Puchkov P.A., Alekseeva A.S., Boldyrev I.A., Vlassov V.V., Serebrennikova G.A., Morozova N.G., Zenkova M.A. Structure-transfection activity relationships in a series of novel cationic lipids with heterocyclic head-groups. Оrganic and Biomolecular Chemistry. 2013. 11, 7164 – 7178.
10. Mironova N., Patutina O., Brenner E., Kurilshikov A., Vlassov V., Zenkova M. MicroRNA Drop in the Bloodstream and MicroRNA Boost in the Tumor Caused by Treatment with Ribonuclease A Leads to an Attenuation of Tumour Malignancy. PLOS One. 2013. 8(12). e83482.
11. Kuzina E.S., Chernolovskaya E.L., Kudriaeva A.A., Zenkova M.A., Knorre V.D., Surina E.A., Ponomarenko N.A., Bobik T.V., Smirnov I.V., Bacheva A.V., Belogurov A.A., Gabibov A.G., Vlasov V.V. Immunoproteasome enhances intracellular proteolysis of myelin basic protein. Dokl Biochem Biophys. 2013. 453, 300-303.
12. Petrova N.S., Chernikov I.V., Meschaninova M.I., Dovydenko I.S., Venyaminova A.G., Zenkova M.A., Vlassov V.V., Chernolovskaya E.L. Carrier-free cellular uptake and the gene-silencing activity of the lipophilic siRNAs is strongly affected by the length of the linker between siRNA and lipophilic group. Nucleic Acids Research. 2012. 40(5), 2330-2344.
13. Fedorova A.A., Goncharova E.P., Kovpak M.P., Vlassov V.V., Zenkova M.A. Influenza virus inactivated by artificial ribonucleases as a prospective killed virus vaccine. Vaccine. 2012. 30, 2973-2980.
14. Maslov M.A., Kabilova T.O., Petukhov I.A., Morozova N.G., Serebrennikova G.A., Vlassov V.V., Zenkova M.A. Novel cholesterol spermine conjugates profide efficient cellular delivery of plasmid DNA and small interfering RNA. Journal of Controlled Release. 2012. 160 (2), 182-193.
15. Markov O.V., Mironova N.L., Maslov M.A., Petukhov I.A., Morozova N.G., Vlassov V.V., Zenkova M.A. Novel cationic liposomes provided highly efficient delivery of DNA and RNA into dendritic cell progenitors and their immature offsets. Journal of Controlled Release. 2012. 160(2), 200–210.
16. Kabilova T,O., Meschaninova M.I., Venyaminova A.G., Nikolin V.P., Zenkova M.A., Vlassov V.V., Chernolovskaya E.L. Short Double-Stranded RNA with Immunostimulatory Activity: Sequence Dependence. Nucleic Acid Therapeutics. 2012. 22(3), 196-204.
17. Fedorova A.A., Goncharova E.P., Ryabchikova E.I., Vlasov V.V., Zenkova M.A. Novel amphiphilic compounds effectively inactivate the vaccinia virus. FEBS Letters. 2012. 586, Iss.11, 1669–1673.
18. Senkova A.V., Mironova N.I., Patutina O.A., Ageeva T.A., Zenkova M.A. The Toxic Effects of Polychemotherapy onto the Liver Are Accelerated by the Upregulated MDR of Lymphosarcoma. ISRN Oncology. 2012. Article ID 721612, 1-15.
19. Kabilova T.O., Vladimirova A.V., Zenkova M.A., Chernolovskaya E.L., Vlassov V.V. Antiproliferative and interferon-inducing activities of unique short double-stranded RNA. Dokl Biochem Biophys. 2011. 436(3), 412-416.
20. Petrova N.S., Meschaninova M.I., Venyaminova A.G., Zenkova M.A., Vlassov V.V., Chernolovskaya E.L. Silencing activity of 2-O-methyl modified anti-MDR1 siRNAs with mismatches in the central part of the duplex. FEBS Letters. 2011. 585, 2352-2356.
21. Maslov M.A., Medvedeva D.A., Rapoport D.A., Serikov R.N., Morozova N.G., Serebrennikova G.A., Vlassov V.V., Zenkova M.A. Synthesis and transfection activity of novel galactosylated polycationic lipid. Bioorganic and Medicinal Chemistry Letters. 2011. 21, 2937-2940.
22. Fedorova A.A., Azzami K., Ryabchikova E.I., Spitsyna Y.E., Silnikov V.N., Ritter V., Gross H.J., Tautz J., Vlassov V.V., Beier H., Zenkova M.A.. Inactivation of a non-enveloped RNA virus by artifical ribonucleases: Honey bees and Acute bee paralysis virus as a new experimental model for in vivo antiviral activity assessment. Antiviral Research. 2011. 91, 267–277.

RFBR (Grants of the Russian Foundation for Basic Research)

• N.11-04-01429a «Natural extracellular vesicles transporting nucleic acids: properties, biological functions and probable uses in diagnostics and medicine» (2011-2013)
• N.11-04-01012a «Identification of extracellular nucleic acids participating in metastasis process» (2011-2013)
• N.11-04-01017a «Determination of molecular mechanisms of action and antitumor potential of 22-linked double-stranded immunostimulating RNA (isRNA)» (2011-2013)
• N.12-04-31254 mol_a «Molecular mechanisms of action and antitumor potential in vivo of novel derivative of glycyrrhetinic acid soloxolon methyl» (2012-2013)

Interdisciplinary integration projects of the Presidium of SB RAS (2012-2014)

• N.55 «Development of panel of isogenic induced human pluripotential stem cells with mutations associated with different forms of amyotrophic lateral sclerosis»
• N.58 «Correction of mutant phenotype using pluripotential cells on Brattleboro rat model with hereditary diabetes insipidus»
• N.84 «Natural microvesicles and complexes transporting nucleic acids: properties, biological functions and perspectives of application in the diagnosis and therapy»
• N.85 «Chemical modified small interfering RNA for overcoming of tumor multiple drag resistance»

Partner integration project of the Presidium of SB RAS (2012-2014)

• N.86 «Cellular technologies for overcoming of immunodeficiency states during cancer diseases»

Programs of the Presidium of RAS
N5 «Basic Science for Medicine» (2013-2015)

• N.10 «The new anti-cancer agents based on natural compounds undergoing chemical modification»
• N.24 «Combination therapy of tumor diseases with natural proteins and therapeutic nucleic acids»
• N.44 «Innovative immunostimulatory agents for the treatment of viral and malignant diseases»

N.6 «Molecular and Cell Biology» (2013-2017)

• N.1 «Biochemistry of extracellular nucleic acids and development of new types of gene targeted biologically active compounds»

N.24 «Fundamental bases of nanostructure and nanomaterial technologies» (2013)

• N.55 «Synthesis of nanocomplexes containing short double-stranded RNA with immunomodulating, interferon-inducing and antiproliferative actions»

Grants of the Ministry of education and science of the Russian Federation

• State contract N.14.740.11.1058 «Development of immunostimulating preparations on the base of chemical modificated double-stranded RNA» (2011-2013)
• Grant Agreement N.8277 «Directed transport of supramolecular complexes comprising therapeutic nucleic acids into cells and tissues» (2012-2013)

Russian President’ grant for national support of leading scientific schools

• SS-2972.2012.4 «Therapeutic nucleic acids: natural and non-natural mechanisms of transport» (2012-2013) (coordinator academician Vlassov V.V.)

Russian President’ scholarship for young scientists and graduate students

• SP-3372.2013.4 «Defining the molecular mechanisms of action and anti-tumor potential of short immunostimulatory RNA» (2013-2015), Kabilova T.O.
• SP-1619.2013.4 «Medicinal preparations on the base of dendritic cells to overcome immunodeficiencies caused by cancer» (2013-2015), Markov O.V.
• SP-408.2012.4 «Soloksolon methyl, derivative of glycyrrhetinic acid, for antitumor treatment» (2012-2013), Markov A.V.
• SP-2307.2012.4. «Ribonuclease as a new generation of anti-cancer drug: identification of molecular targets» (2012-2013), Patutina O.A.

• Chromatograph Waters Alliance;
• real-time PCR machines (Bio-Rad);
• robotic system for sample preparation for real time PCR;
• full set of electrophoretic equipment;
• fluorescent microscopes equipped with CCD-cameras (Zeiss);
• flow cytometer Cytomics FC500 (Beckman Coulter);
• phosphor imager PharosFX Plus(Bio-Rad);
• gel documentation system Infinity-1500/36 m (Vilber Lormat).