Laboratory of Bionanotechnology

Dmitrii Pyshnyi,
Corr.Member of RAS, D.Chem.Sci., Director of the Institute
Award of the European academy of Sciences (1999) Prize of International Publishing Company “Nauka/Interperiodika” (1998).
Phone: +7(383) 363-51-51, Email

• Study of fundamental aspects in DNA diagnostics and in mechanisms of action of gene directed biologically active substances: nucleic acids hybridization with oligonucleotides, their analogues and derivatives under various conditions.
• Thermodynamic description of the formation of composit complexes between nucleic acids (tandems of oligonucleotides, oligonucleotides bearing residues of organic ligands (intercalators, minor groove binders, fluorophores, non-nucleotide inserts).
• Development of bioanalytical systems on the basis of micro- and nano-structured materials including molecular imprinted polymers, aptamers and nanoparticles.
• DNA-nanoarchetictonics – studies of self-assembling supramolecular systems on the basis of nucleic acids.

• Physico-chemical features of the formation of tandem complexes DNA - oligonucleotides, concatemeric complexes of oligonucleotides, and complexes DNA - bridged oligonucleotides, containing oligomethylenediol or oligoethyleneglycol inserts, have been systematically studied. The obtained thermodynamic characteristics allow us to design oligonucleotide probes with rationally lowered hybridization ability, as well as precalculate the stability of perfect and imperfect tandem complexes at various buffer conditions. [Pyshnyi D.V. et al., J. Biomol. Struct. Dyn. 2003. 21, 459; Pyshnyi D.V. et al., J. Biomol. Struct. Dyn. 2006. 23(5), 567; Lomzov A.A., Dokl. Biochem. Biophys. 2006. 409(2), 266].
• A new highly selective approach to detection of point mutations in DNA has been developed using oligonucleotides bearing non-nucleotide incerts. [Dmitrienko E.V. et al., Bioorg. Khim. 2010. 36(6), 802; Vinogradova O.A. et al., Mol. Biol. (Mosk). 2007. 41(1), 163].
• Detailed characteristics of enzymatic ligation of oligonucleotides on DNA matrices as a function of nucleotide composition near the DNA-nicks have been studied. The results obtained allow us to make optimal choice between various probe structures for efficient detection of DNA point mutations via oligonucleotide ligation assay (OLA). [Skobeltsyna L.M. et al., Mol. Biotechnol. 2010. 45, 1].
• A new approach has been developed to obtain molecularly imprinted polymers (MIPs), which contain the replices of biomolecules in their structures, and are capable of their specific recognition. [Dmitrienko E.V., Mol. Recogn. 2013.].
• It has been approved, that the spatial organization of supramolecular concatemeric complexes of DNA can be regulated via correct arrangement of building blocks - modified DNA duplexes, bearing non-nucleotide inserts. [Vinogradova O.A., Pyshnyi D.V., Russian Chem. Rev. 2012; Kupryushkin M.S., Pyshnyi D.V., Bioorg. Khim. 2012].

1. Tonin Y., Heckel A.M., Dovydenko I.S., Meshchaninova M.I., Comte C., Pyshnyi D.V., Tarassov I., Entelis N. Characterization of chemically modified oligonucleotides targeting a pathogenic mutation in human mitochondrial DNA. Biochimie. 2014. 100, 192–199. - Dultsev F.N., Kolosovsky E.A., Mik I.A., Lomzov A.A., Pyshnyi D.V. QCM-Based Measurement of Bond Rupture Forces in DNA Double Helices for Complementarity Sensing. Langmuir. 2014. 30(13), 3795-3801.
2. Kupryushkin M.S., Konevetz D.A., Vasilyeva S.V., Kuznetsova A.S., Stetsenko D.A., Pyshnyi D.V. Oligonucleotide Functionalization by a Novel Alkyne-Modified Nonnucleosidic Reagent Obtained by Versatile Building Block Chemistry. Nucleosides Nucleotides Nucleic Acids. 2013. 32(6), 306-319. - Dmitriyenko E.V., Bulushev R.D., Haupt K., Kosolobov S.S., Latyshev A.V., Pyshnaya I.A., Pyshnyi D.V. A simple approach to prepare molecularly imprinted polymers from nylon-6. J. Mol. Recognit. 2013. 26(8), 368-375.
3. Romanov S.I., Pyshnyi D.V., Laktionov P.P. Sensors and filters based on nano- and microchannel membranes for biomedical technologies. Journal of Physics: Conference Series. 2012. 345(1), 1-6. - Krasitskaia V.V., Burakova L.P., Pyshnaya I.A., Frank L.A. Bioluminescent reporters to identify gene allelic variants. Russ. J. of Bioorg. Chemistry. 2012. 38(3), 342.
4. Pyshnyi D.V., Vinogradova. O.A. Principles of DNA architectonics: design of DNA-based nanoobjects. Russ. Chem. Rev. 2012. 81(2), 130-157. - Lomzov A.A., Pyshnyi D.V. Considering the oligonucleotides secondary structures at thermodynamic and kinetic analysis of the DNA-duplexes formation Biophysics (Moscow). 2012. 57(1), 27–44.
5. Kupryushkin M.S., Pyshnyi D.V. Oligonucleotide derivatives in nucleic acid hybridization analysis. III. Synthesis and investigation of properties of oligonucleotides, bearing bifunctional non-nucleotide insertion. Russ. J. of Bioorg. Chemistry. 2012. 38(6), 706-720. - Kupryushkin M.S., Pyshnyi D.V. A convenient method for the synthesis of phosphoramidite non-nucleotide inserts for preparation of functionalized oligonucleotides. Russ. J. of Bioorg. Chemistry. 2012. 38(6), 745-749.
6. Zakabunin A.I., Kamynina T.P., Khodyreva S.N., Pyshnaya I.A., Pushnyi D.V., Khrapov E.A., Filipenko M.L. Cloning of genes, purification and properties investigation of recombinant DNA ligases from the thermophilic archaeon Pyrococcus abyssi and Methanobacterium thermoautotrophicum. J. of Mol. Biol. (Mosc). 2011. 45(2), 258–266. - Lomzov A.A., Khalo I.V., Pyshnyi D.V. The influence of aliphatic alcohols on oligonucleotide hybridization. J. Biomol. Struct. Dyn. 2011. 28(6), 1130.
7. Vlassov V.V., Sinyakov A.N., Pyshnyi D.V., et al. Ellipsometric monitoring in label-free microarray biotechnology. Avtometria. 2011. 7(5), 67-77. - Kabilov M., Pyshnyi D. Analytical consideration of the selectivity of oligonucleotide hybridization. J. Biophys. Chem. 2011. 2(2), 75-91.

1. Pyshnyi D.V., Kupryushkin M.S. Method of producing amidophosphite monomer of achiral non-nucleotide insert for modifying oligonucleotides. Patent RF N.2460721, 2012.
   
2. Dmitrienko E.V., Romanov S.I., Vlassov V.V. Method of selective recovery of viable cell population from biological fluids. Patent RF N.2423698, 2011.
   

• N.12-04-31776 «Molecular dynamics method as a tool of prognostic calculatins of enthalpy and enthropy for the formation of complexes of oligonucleotides and their derivatives» (2013-2015).

• N.86 «Bioanalytical platforms on the base of electrophysical and electrokinetic sensors».
• N.45 «Magnetotransfer systems in catalytic, biological and sorptional technologies. Synthesis and physico-chemical study of magneto-driven catalysts, sorbents and carriers».
• N.133 «Development and complex studies of solid-state low-dimention systems for nano- and bio-materials».

• State contract N.14B25.31.0028 “Oligonucleotide-based RNA-targeting antibacterial and antiviral therapeutics”

• DNA-synthesizer ASM-800 (BIOSSET, Russia);
• HPLC devices Аgilent 1200 (Аgilent Technology, USA) and Millichrome А4 (EcoNova, Russia); UV-Vis spectrometer Cary 300 Biomelt (Varian, Australia), with thermostated 6-quvette adapter; NIR-Fourier spectrometer MPA (Bruker Optics, Germany);
• Real-time PCR-machine IQ5 (Bio-Rad, USA);
• microscope Leica DM 5000 (Leica Microsystems, Germany);
• capillary electrophoresis system P/ACE MDQ (Becman Coulter, USA);
• spectrophotometer Nanoview (GE, USA); bioanalytical system Bio-Plex 200 (BioRad, USA);
• system for characterization of nanoparticles Malvern Zetasizer Nano (Malvern Instruments Ltd, UK), atomic force microscope Multimode 8 (Bruker).