Laboratory of Artificial Antibodygenesis

People

People

Head of Laboratory
Pozmogova G.E.
Professor, DSci
Позмогова Галина Евгеньевна

Chuvilin A.N., PhD, senior researcher
Smirnov I.P., PhD, senior researcher
Kirrilova Y.G., PhD, senior researcher
Karpov V.A., chief engineer, head of the Department of synthesis
Tatarinova O.N., PhD, researcher
Varizhuk A.M., PhD, researcher
Tsvetkov V.B., Ph.D., research assistant
Severov V.V. , junior researcher
Sekridova A.V., junior researcher
Tankevich M.V., junior researcher

Topics of scientific interest and lines of research

Topics of scientific interest and lines of research

The major goals of the laboratory are to develop artificial DNA-containing supramolecular complexes and synthetic nucleotide antibodies, and to investigate their assembly process and structural/functional properties, with the purpose of creating, on their basis, diagnostic means and medications.

One of the basic natural properties of polynucleotides is their ability to associate with different biopolymers and low-molecular compounds to form functional supramolecular complexes. Supramolecular polynucleotide complexes are a natural state in which DNA exists.
Construction of complex synthetic DNA assemblies and structural-functional investigation of such model systems is an efficient way to study natural processes as well to develop new approaches to solve a large spectrum of applied problems. The research work of the lab on supramolecular DNA complexes can be grouped in several lines.

Nucleoprotein complexes, which are most similar to natural analogs, for targeted delivery of foreign oligo-/polynucleotides to the body cells. (1-5). RF Patent # RF 2248983
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Complexes modeling the properties of a living system [a living cell – DNA fixed on the outer membrane – complementary nucleotide sequence] (6). RF Patent # RU 203940916 C2
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Artificial DNA complexes and nucleoprotein assemblies based on nanoparticles (7-9).
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Investigation of DNA tertiary structures and their complexes through MS and spectral methods (10-15). RF Patent # 2010121769
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In the frame of this project, noncanonical DNA structures are studied. A new type of stable DNA G-quadruplexes, quadruplexes with mismatches (ImGQ) has been described. A new program for searching putative quadruplex-forming sites in genomic sequences, ImGQfinder (RU registration number 2012619464), which takes into account possible defects in quadruplex cores ('bulging' nucleotides and mismatches in G-tetrads), has been developed in collaboration with the Laboratory of Bioinformatics..
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A large part of the lab’s work centers on the investigation and optimization of the methods for preparation of oligonucleotides (among them, modified oligonucleotides). The laboratory also takes part in developing analytical medical-biological methods and test-systems (1,16-21).
RF Patent # 2010121694
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Collaborators

Collaborators

  • Lomonosov Moscow State University,
  • Lomonosov Moscow State University of Fine Chemical Technology,
  • Engelhardt Institute of Molecular Biology,
  • D. Mendeleev University of Chemical Technology of Russia

List of selected publications

List of selected publications

  1. Posypanova, G.A., Chuvilin, A.N., Kireeva, N.N., Severin, E.S. and Pozmogova, G.E. (2008) Complexes of telomeric oligonucleotides with the PGEk protein vector: Internalization by target cells and antiproliferative activity. Molecular Biology, 42, 253-260.
  2. Pozmogova, G.E. and Chuvilin, A.N. (2007) Principles of creation of protein carriers of DNA new derivatives of human epidermal growth factor for gene therapy. Bulletin of Experimental Biology and Medicine, 144, 457-463.
  3. Besschetnova, I.A., Pozmogova, G.E., Chuvilin, A.N., Shchyolkina, A.K. and Borisova, O.F. (2006) Complexes of telomeric oligonucleotide d(TTAGGG)4 with the new recombinant protein vector PGEk carrying nucleic acids into proliferating cells. Molecular Biology, 40, 433-439.
  4. Pozmogova, G.E. and Knorre, D.G. (1998) Protein and peptide constructions for DNA and oligonucleotide delivery in cell. Voprosy Meditsinskoj Khimii, 44, 335-337.
  5. Tatarinova, O.I., Gorokhovets, N.V., Makarov, V.A., Posypanova, G.A., Serebryakova, M.V. and Pozmogova, G.E. (2010) New protein vectors based on an alphafetoprotein fragment for targeted dna delivery into cancer cells. Vestnik Rossiiskoi Akademii Meditsinskikh Nauk, 3-8.
  6. Borisenko, G.G., Zaitseva, M.A., Chuvilin, A.N. and Pozmogova, G.E. (2009) DNA modification of live cell surface. Nucleic Acids Research, 37.
  7. Позмогова, Г.Е. (2012) Искусственные ДНК-содержащие супрамолекулярные комплексы. Palmarium Academic Publishing.
  8. Pozmogova, G.E., Chuvilin, A.N., Smirnov, I.P., Zaitseva, M.A., Tatarinova, O.N. and Govorun, V.M. (2008) Preparation and Properties of Associates of Nickel Nanoparticles with ss-DNA and Proteins. Nanotechnologies in Russia, 3, 391-396.
  9. Tatarinova, O.N., Smirnov, I.P., Safenkova, I.V., Varizhuk A.M. and G.E., P. (2012) DNA complexes with Ni nanoparticles: structural and functional properties. Jopurnal of Nanoparticle Research, 14.
  10. Zaitseva, M., Kaluzhny, D., Shchyolkina, A., Borisova, O., Smirnov, I. and Pozmogova, G. (2010) Conformation and thermostability of oligonucleotide d(GGTTGGTGTGGTTGG) containing thiophosphoryl internucleotide bonds at different positions. Biophysical Chemistry, 146, 1-6.
  11. Pozmogova, G.E., Zaitseva, M.A., Smirnov, I.P., Shvachko, A.G., Murina, M.A. and Sergeenko, V.I. (2010) Anticoagulant Effects of Thioanalogs of Thrombin-Binding DNA-Aptamer and Their Stability in the Plasma. Bulletin of Experimental Biology and Medicine, 1-5.
  12. Shchyolkina, A.K., Borisova, O.F., Livshits, M.A., Pozmogova, G.E., Chernov, B.K., Klement, R. and Jovin, T.M. (2000) Parallel-stranded DNA with mixed AT/GC composition: Role of trans GВ•C base pairs in sequence dependent helical stability. Biochemistry, 39, 10034-10044.
  13. Smirnov, I.P. (2011) UV MALDI for DNA Analysis and the Developments in Sample Preparation Methods. Springer Science.
  14. Borisova, O.F., Shchelkina, A.K., Il'icheva, I.A. and Pozmogova, G.E. (2001) [Conformational polymorphism and extensibility of DNA quadruplexes formed from d(GT)n repeats]. Mol Biol (Mosk), 35, 860-867.
  15. Varizhuk, A.M., Tsvetkov, V.B., Tatarinova, O.N., Kaluzhny, D.N., Florentiev, V.L., Timofeev, E.N., Shchyolkina, A.K., Borisova, O.F., Smirnov, I.P., Grokhovsky, S.L. et al. (2013) Synthesis, characterization and in vitro activity of thrombin-binding DNA aptamers with triazole internucleotide linkages. Eur J Med Chem, 67C, 90-97.
  16. Chuvilin, A.N., Serebryakova, M.V., Smirnov, I.P. and Pozmogova, G.E. (2009) Byproduct with altered fluorescent properties is formed during standard deprotection step of hexachlorofluorescein labeled oligonucleotides. Bioconjugate Chemistry, 20, 1441-1443.
  17. Tatarinova, O.N., Lukyanova, T.N., Zaitseva, M.A., Veremeev, K.Y., Karpov, V.A., Chuvilin, A.N., Petrunin, D.D. and Pozmogova, G.E. (2008) Significance of methods for purification of oligodeoxyribonucleotide probes for the efficiency of gene diagnosis by real-time PCR. Bulletin of Experimental Biology and Medicine, 145, 312-316.
  18. Luk'ianova, T.A., Zaitseva, M.A., Karpov, V.A. and Pozmogova, G.E. (2008) The synthesis and mass spectrometry of oligonucleotides bearing thiophosphoryl modifications of the predetermined localization. Bioorganicheskaia khimiia, 34, 83-88.
  19. Северов, В.В., Варижук, А.М. and Позмогова, Г.Е. (2012) Перспективы использования методов клик-химии в медицине. Эфферентная и физико-химическая медицина, 1.
  20. Varizhuk, A., Chizhov, A., Smirnov, I., Kaluzhny, D. and Florentiev, V. (2012) Triazole-Linked Oligonucleotides with Mixed-Base Sequences: Synthesis and Hybridization Properties. European Journal of Organic Chemistry, 2173–2179.
  21. Varizhuk, A.M., Kaluzhny, D.N., Novikov, R.A., Chizhov, A.O., Smirnov, I.P., Chuvilin, A.N., Tatarinova, O.N., Fisunov, G.Y., Pozmogova, G.E. and Florentiev, V.L. (2013) Synthesis of triazole-linked oligonucleotides with high affinity to DNA complements and an analysis of their compatibility with biosystemsonucleotides with High Affinity to DNA Complements and an Analysis of Their Compatibility with Biosystems. J Org Chem, 78, 5964-5969.
  22. Kovaleva OA, Tsvetkov VB, Mamaeva OK, Ol'shevskaya VA, Makarenkov AV, Dezhenkova LG, Semeikin AS, Borisova OF, Shtil AA, Shchyolkina AK, Kaluzhny DN. Preferential DNA photocleavage potency of Zn(II) over Ni(II) derivatives of carboxymethyl tetracationic porphyrin: the role of the mode of binding to DNA. European Biophysics Journal. 2014 Aug 28
  23. Vladimir B. Tsvetkov, Alexander V. Serbin Molecular dynamics modeling the synthetic and biological polymers interactions pre-studied via docking: anchors modified polyanions interference with the HIV-1 fusion mediator. Journal of Computer-Aided Molecular Design 2014 June, Volume 28, Issue 6, pp 647-673.
  24. Tsvetkov VB, Solov'eva AB, Melik-Nubarov NS. Computer modeling of the complexes of Chlorin e6 with amphiphilic polymers. Physical Chemistry Chemical Physics. 2014 Jun 14;16(22):10903-13.
  25. O. Tatarinova, V. Tsvetkov, D. Basmanov, N. Barinov, I. Smirnov, E. Timofeev, D. Kaluzhny, A. Chuvilin, D. Klinov, A. Varizhuk, G. Pozmogova. Comparison of the 'chemical' and 'structural' approaches to the optimization of the thrombin-binding aptamer. PLoS One 9, e89383 (2014). http://www.ncbi.nlm.nih.gov/pubmed/24586736
  26. N.A. Kolganova, A.M. Varizhuk, R.A. Novikov, V.L. Florentiev, G.E. Pozmogova, O.F. Borisova, A.K. Shchyolkina, I.P. Smirnov, D.N. Kaluzhny, E.N. Timofeev. Anomeric DNA quadruplexes: Modified thrombin aptamers. Artif DNA PNA XNA 5(2014). http://www.ncbi.nlm.nih.gov/pubmed/24622343
  27. Galina Pozmogova, Vyacheslav Severov1, Anna Varizhuk, Igor Smirnov, Alexandra Sekridova, Vladimir Tsvetkov. Secondary DNA structures in G/С-rich microsatellites. Investigating the equilibrium between G-quadruplexes, Imotifs and duplexes. FEBS Journal Volume 281, Issue Supplement s1, Article first published online: 27 AUG 2014. P. 639-640.
  28. Galina Pozmogova, Maria Tankevich, Andrey Dezhenkov, Anna Varizhuk, Igor Smirnov, Yulia Kirillova Kirillova. A new type of peptide nucleic acids derived from L-Glu. FEBS Journal Volume 281, Issue Supplement s1, Article first published online: 27 AUG 2014. P. 632.
  29. Vladimir Tsvetkov, Anna Varizhuk, Galina Pozmogova New parameters for describing conformational rearrangements in G-quadruplexes. FEBS Journal Volume 281, Issue Supplement s1, Article first published online: 27 AUG 2014. P. 401.
  30. Anna Varizhuk, Maria Prokofjeva, Vladimir Tsvetkov, Vladimir Prassolov, Sergey Mikhailov, Galina Pozmogova. G4-DNA inhibitors of HIV entry. FEBS Journal Volume 281, Issue Supplement s1, Article first published online: 27 AUG 2014. P. 743.

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