Laboratory of Nanobiotechnology

Yury D. Ivanov Head of Lab
D.Sc., professor

CONTACTS

+7 (499) 246-37-61

Vladimir P. Chekhonin D.Sc., academician RAS



 
Ivan D. Shumov Ph.D.

 
Ekaterina E. Vazhenkova






Angelina V. Vinogradova






Ekaterina D. Nevedrova






Irina T. Utkina






Aleksandr N. Ableev


 

 
Andrej F. Kozlov

 

 
Vadim S. Ziborov Ph.D.

 

 

RESEARCH

SCIENTIFIC INTERESTS

Atomic force microscopy
Nanowire detection
Mass-spectrometry
Molecular fishing
Highly sensitive biosensor analysis
Electron microscopy
Magnetron sputtering

The main direction of the laboratory's scientific activity is fundamental and applied research for proteomics and medical diagnostics with the use of nanotechnology-based devices. The research is carried out using high-tech equipment based on molecular detectors: atomic force microscopes and a nanowire biosensor. Electron microscopy, mass spectrometric analysis and magnetron sputtering are also employed.
Atomic force microscopy (AFM) provides a fundamental possibility to visualize and count single protein macromolecules and their complexes. By AFM, the following studies of biological objects are performed:

  • AFM visualization of single biological macromolecules and their complexes on an atomically smooth chip surface.

  • Development of fundamental principles of detection of single biomolecules in low-concentration solutions using a combination of AFM and biospecific fishing methods.

  • Development and fabrication of AFM nanobiochips with an array of sensor areas for medical proteomics.

  • Determination of physicochemical properties of single molecules of enzymes (single-molecule enzymology) by AFM.

  • Development of a combination of an atomic force microscope with a mass spectrometer for the identification of objects, adsorbed or immobilized on the chip surface.

APPLIED RESEARCH

  • Development of bioanalytical complexes on the basis of an atomic force microscope for the diagnosis of infectious and oncological diseases at early (asymptomatic) stage. The main units of the complex are represented by an automated atomic force microscope and AFM chips (the chips are fabricated in collaboration with JIHT RAS). On the surface of the chips, an array of sensor areas is formed by magnetron sputtering; each of these areas can contain various types of probe molecules (antibodies, aptamers) against the target molecules to be detected. To date, the efficient detection of biomarkers of diseases in serum using a laboratory prototype of such an AFM-based bioanalytical complex was demonstrated. For the identification of biomolecules on the surface of the AFM chips, a unique system, combining the AFM with mass spectrometry analysis was developed; this system allows one to significantly expand the amount of data obtained.

  • Development of bioanalytical complexes on the basis of highly sensitive nanowire molecular detectors for the diagnosis of infectious and oncological diseases at the level of single viral and microbial particles. The development is performed in collaboration with ISP SB RAS. The laboratory prototype of the complex is a completely Russian development. The efficiency of the detection of biomarkers of diseases in real-time with the use of the nanowire biosensor was demonstrated and confirmed. The prospects of applied research are determined, among other things, by the fact that the manufacturing of chips for the nanowire biosensor is carried out using standard CMOS technology, which is routinely used for the manufacture of microcircuits. Thus, this type of bioanalytical complex is oriented at a large-scale application in routine clinical medical diagnostics.

  • Prof. R. Bernhardt, Institute of Biochemistry Saarland University, Saarbrucken, Germany.
  • Prof. S.A. Usanov, Institute of Bioorganic Chemistry, Minsk, Belarus.

  • Rzhanov Institute of Semiconductor Physics, Siberian Branch of Russian Academy of Sciences (ISP SB RAS), Novosibirsk.
    ISP SB RAS is a research center with a wide range of activities in the field of modern semiconductor physics, condensed matter physics, in the development of scientific bases of technologies for semiconductor micro-, opto-, nano- and acoustoelectronics, for information technology and quantum electronics.

  • Joint Institute for High Temperatures of the Russian Academy of Sciences (JIHT RAS, Moscow).
    JIHT RAS is a the largest institution of the Department of Power Engineering, Mechanical Engineering, Mechanics and Control Processes of the Russian Academy of Sciences, representing the Russia's leading scientific center in the field of power engineering and thermal physics of extreme conditions. In JIHT RAS, the thermodynamic, transport and optical properties of real substances under intense pulsed impacts (in shock compression waves and upon adiabatic unloading, under the action of intense ultra-short laser pulses, upon heating of conductors by powerful current pulses, etc.) are actively studied. During recent years, in JIHT RAS, a new direction in physics the physics of dusty plasma has been formed; studies on plasma medicine, and methods of plasma generation for the disinfection and treatment of extensive infected wounds are being developed.

  • NT-MDT (Zelenograd, Russia, Prof. Victor A. Bykov). This company specializes in the development of precision nanotechnology-based devices, including the manufacturing of devices combining AFM with Raman spectrometers, with mass spectrometers, etc. The production base and engineering personnel of NT-MDT perform the company’s design developments at high level. NT-MDT is a leader in the Russian market for the production of scanning probe microscopes (SPM), including atomic force microscopes.

  • Joint plant "Novosibirsk plant of semiconductor devices with OKB" ("NZPP with OKB") and "NPP" Vostok "(part of GK "Element") is one of the Russia's largest manufacturers of electronic components, integrated circuits and discrete semiconductor devices. The company specializes in the development and production of electronic components and complete devices.

  • Interlab, Inc. (”Agilent Technologies”). One of the most dynamic and fastest growing companies in the analytical equipment market, supporting major government health programs.

  • ”Bruker” LLC (a representative of Bruker Corporation in Russia). A world-class company producing high-end analytical instruments, including nanotechnology-based equipment for biomedical research. The company has been actively cooperating with leading Russian research organizations since 1970.

avatar none  Gordeeva A.I., Valueva A.A., Rybakova E.E., Ershova M.O., Shumov I.D., Kozlov A.F., Ziborov V.S., Kozlova A.S., Zgoda V.G., Ivanov Y.D., Ilgisonis E.V., Kiseleva O.I., Ponomarenko E.A., Lisitsa A.V., Archakov A.I., Pleshakova T.O. (2024) MS Identification of Blood Plasma Proteins Concentrated on a Photocrosslinker-Modified Surface, International Journal of Molecular Sciences, 25(1), 409. DOI:10.3390/ijms25010409

avatar none  Pleshakova T.O., Ivanov Y.D., Valueva A.A., Shumyantseva V.V., Ilgisonis E.V., Ponomarenko E.A., Lisitsa A.V., Chekhonin V.P., Archakov A.I. (2023) Analysis of Single Biomacromolecules and Viruses: Is It a Myth or Reality?, International Journal of Molecular Sciences, 24(3), 1877. DOI:10.3390/ijms24031877

avatar none  Filippova T.A., Masamrekh R.A., Shumyantseva V.V., Latsis I.A., Farafonova T.E., Ilina I.Y., Kanashenko S.L., Moshkovskii S.A., Kuzikov A.V. (2023) Electrochemical biosensor for trypsin activity assay based on cleavage of immobilized tyrosine-containing peptide, Talanta, 257, 124341. DOI:10.1016/j.talanta.2023.124341

avatar none  Gordeeva A.I., Valueva A.A., Ershova M.O., Rybakova E.E., Shumov I.D., Kozlov A.F., Ziborov V.S., Zavialova M.G., Zgoda V.G., Ivanov Y.D., Archakov A.I., Pleshakova T.O. (2023) Mass Spectrometric Identification of BSA Covalently Captured onto a Chip for Atomic Force Microscopy, International Journal of Molecular Sciences, 24(10), 8999. DOI:10.3390/ijms24108999

avatar none  Kraevsky S.V., Ivanova I.A., Kanashenko S.L., Shumov I.D., Ryazantsev I.A., Tereshkina Yu.A., Kostryukova L.V., Romashova Yu.A., Pleshakova T.O. (2023) Nanoform of Phospholipid Composition: Investigation of the Morphological Features by Atomic Force Microscopy, International Journal of Molecular Sciences, 24(20), 15338. DOI:10.3390/ijms242015338

avatar none  Ivanov Y.D., Ableev A.N., Shumov I.D., Ivanova I.A., Vaulin N.V., Lebedev D.V., Bukatin A.S., Mukhin I.S., Archakov A.I. (2023) Registration of Functioning of a Single Horseradish Peroxidase Macromolecule with a Solid-State Nanopore, International Journal of Molecular Sciences, 24(21), 15636. DOI:10.3390/ijms242115636

avatar none  Ershova M.O., Taldaev A., Konarev P.V., Peters G.S., Valueva A.A., Ivanova I.A., Kraevsky S.V., Kozlov A.F., Ziborov V.S., Ivanov Yu.D., Archakov A.I., Pleshakova T.O. (2023) Selection of Aptamers for Use as Molecular Probes in AFM Detection of Proteins, Biomolecules, 13(12), 1776. DOI:10.3390/biom13121776

avatar none  Kaysheva A.L., Frantsuzov P.A., Kopylov A.T., Pleshakova T.O., Stepanov A.A., Malsagova K.A., Archakov A.I., Ivanov Y.D. (2021) Mass Spectrometric Identification of Proteins Enhanced by the Atomic Force Microscopy Immobilization Surface, International Journal of Molecular Sciences, 22(1), 431. DOI:10.3390/ijms22010431

avatar none  Goryanin I., Karbainov S., Shevelev O., Tarakanov A., Redpath K., Vesnin S., Ivanov Yu. (2020) Passive microwave radiometry in biomedical studies, Drug Discovery Today, 25(4), 757-763. DOI:10.1016/j.drudis.2020.01.016

avatar none  Archakov A.I., Aseev A.L., Bykov V.A., Grigoriev A.I., Govorun V.M., Ilgisonis E.V., Ivanov Y.D., Ivanov V.T., Kiseleva O.I., Kopylov A.T., Lisitsa A.V., Mazurenko S.N., Makarov A.A., Naryzhny S.N., Pleshakova T.O., Ponomarenko E.A., Poverennaya E.V., Pyatnitskiy M.A., Sagdeev R.Z., Skryabin K.G., Zgoda V.G. (2019) Challenges of the Human Proteome Project: 10-year Experience of the Russian Consortium, Journal of Proteome Research, 18(12), 4206-4214. DOI:10.1021/acs.jproteome.9b00358