1
|
Ivanov YD, Shumov ID, Kozlov AF, Valueva AA, Ershova MO, Ivanova IA, Ableev AN, Tatur VY, Lukyanitsa AA, Ivanova ND, Ziborov VS. Atomic Force Microscopy Study of the Long-Term Effect of the Glycerol Flow, Stopped in a Coiled Heat Exchanger, on Horseradish Peroxidase. Micromachines (Basel) 2024; 15:499. [PMID: 38675310 PMCID: PMC11052087 DOI: 10.3390/mi15040499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/19/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024]
Abstract
Glycerol is employed as a functional component of heat-transfer fluids, which are of use in both bioreactors and various biosensor devices. At the same time, flowing glycerol was reported to cause considerable triboelectric effects. Herein, by using atomic force microscopy (AFM), we have revealed the long-term effect of glycerol flow, stopped in a ground-shielded coiled heat exchanger, on horseradish peroxidase (HRP) adsorption on mica. Namely, the solution of HRP was incubated in the vicinity of the side of the cylindrical coil with stopped glycerol flow, and then HRP was adsorbed from this solution onto a mica substrate. This incubation has been found to markedly increase the content of aggregated enzyme on mica-as compared with the control enzyme sample. We explain the phenomenon observed by the influence of triboelectrically induced electromagnetic fields of non-trivial topology. The results reported should be further considered in the development of flow-based heat exchangers of biosensors and bioreactors intended for operation with enzymes.
Collapse
Affiliation(s)
- Yuri D. Ivanov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia; (I.D.S.); (A.F.K.); (A.A.V.); (M.O.E.); (I.A.I.); (A.N.A.); (V.S.Z.)
- Joint Institute for High Temperatures of the Russian Academy of Sciences, 125412 Moscow, Russia
| | - Ivan D. Shumov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia; (I.D.S.); (A.F.K.); (A.A.V.); (M.O.E.); (I.A.I.); (A.N.A.); (V.S.Z.)
| | - Andrey F. Kozlov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia; (I.D.S.); (A.F.K.); (A.A.V.); (M.O.E.); (I.A.I.); (A.N.A.); (V.S.Z.)
| | - Anastasia A. Valueva
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia; (I.D.S.); (A.F.K.); (A.A.V.); (M.O.E.); (I.A.I.); (A.N.A.); (V.S.Z.)
| | - Maria O. Ershova
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia; (I.D.S.); (A.F.K.); (A.A.V.); (M.O.E.); (I.A.I.); (A.N.A.); (V.S.Z.)
| | - Irina A. Ivanova
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia; (I.D.S.); (A.F.K.); (A.A.V.); (M.O.E.); (I.A.I.); (A.N.A.); (V.S.Z.)
| | - Alexander N. Ableev
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia; (I.D.S.); (A.F.K.); (A.A.V.); (M.O.E.); (I.A.I.); (A.N.A.); (V.S.Z.)
| | - Vadim Y. Tatur
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia; (V.Y.T.); (A.A.L.); (N.D.I.)
| | - Andrei A. Lukyanitsa
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia; (V.Y.T.); (A.A.L.); (N.D.I.)
- Faculty of Computational Mathematics and Cybernetics, Moscow State University, 119991 Moscow, Russia
| | - Nina D. Ivanova
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia; (V.Y.T.); (A.A.L.); (N.D.I.)
- Moscow State Academy of Veterinary Medicine and Biotechnology Named after Skryabin, 109472 Moscow, Russia
| | - Vadim S. Ziborov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia; (I.D.S.); (A.F.K.); (A.A.V.); (M.O.E.); (I.A.I.); (A.N.A.); (V.S.Z.)
- Joint Institute for High Temperatures of the Russian Academy of Sciences, 125412 Moscow, Russia
| |
Collapse
|
2
|
Gordeeva AI, Valueva AA, Rybakova EE, Ershova MO, Shumov ID, Kozlov AF, Ziborov VS, Kozlova AS, Zgoda VG, Ivanov YD, Ilgisonis EV, Kiseleva OI, Ponomarenko EA, Lisitsa AV, Archakov AI, Pleshakova TO. MS Identification of Blood Plasma Proteins Concentrated on a Photocrosslinker-Modified Surface. Int J Mol Sci 2023; 25:409. [PMID: 38203578 PMCID: PMC10778900 DOI: 10.3390/ijms25010409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/14/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
This work demonstrates the use of a modified mica to concentrate proteins, which is required for proteomic profiling of blood plasma by mass spectrometry (MS). The surface of mica substrates, which are routinely used in atomic force microscopy (AFM), was modified with a photocrosslinker to allow "irreversible" binding of proteins via covalent bond formation. This modified substrate was called the AFM chip. This study aimed to determine the role of the surface and crosslinker in the efficient concentration of various types of proteins in plasma over a wide concentration range. The substrate surface was modified with a 4-benzoylbenzoic acid N-succinimidyl ester (SuccBB) photocrosslinker, activated by UV irradiation. AFM chips were incubated with plasma samples from a healthy volunteer at various dilution ratios (102X, 104X, and 106X). Control experiments were performed without UV irradiation to evaluate the contribution of physical protein adsorption to the concentration efficiency. AFM imaging confirmed the presence of protein layers on the chip surface after incubation with the samples. MS analysis of different samples indicated that the proteomic profile of the AFM-visualized layers contained common and unique proteins. In the working series of experiments, 228 proteins were identified on the chip surface for all samples, and 21 proteins were not identified in the control series. In the control series, a total of 220 proteins were identified on the chip surface, seven of which were not found in the working series. In plasma samples at various dilution ratios, a total of 146 proteins were identified without the concentration step, while 17 proteins were not detected in the series using AFM chips. The introduction of a concentration step using AFM chips allowed us to identify more proteins than in plasma samples without this step. We found that AFM chips with a modified surface facilitate the efficient concentration of proteins owing to the adsorption factor and the formation of covalent bonds between the proteins and the chip surface. The results of our study can be applied in the development of highly sensitive analytical systems for determining the complete composition of the plasma proteome.
Collapse
Affiliation(s)
| | | | | | | | - Ivan D. Shumov
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia; (A.I.G.); (A.A.V.); (E.E.R.); (M.O.E.); (A.F.K.); (V.S.Z.); (A.S.K.); (V.G.Z.); (Y.D.I.); (E.V.I.); (O.I.K.); (E.A.P.); (A.V.L.); (A.I.A.); (T.O.P.)
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
3
|
Ershova MO, Taldaev A, Konarev PV, Peters GS, Valueva AA, Ivanova IA, Kraevsky SV, Kozlov AF, Ziborov VS, Ivanov YD, Archakov AI, Pleshakova TO. Selection of Aptamers for Use as Molecular Probes in AFM Detection of Proteins. Biomolecules 2023; 13:1776. [PMID: 38136647 PMCID: PMC10742151 DOI: 10.3390/biom13121776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/02/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Currently, there is great interest in the development of highly sensitive bioanalytical systems for diagnosing diseases at an early stage, when pathological biomarkers are present in biological fluids at low concentrations and there are no clinical manifestations. A promising direction is the use of molecular detectors-highly sensitive devices that detect signals from single biomacromolecules. A typical detector in this class is the atomic force microscope (AFM). The high sensitivity of an AFM-based bioanalysis system is determined by the size of the sensing element of an atomic force microscope-the cantilever-the radius of the curvature of which is comparable to that of a biomolecule. Biospecific molecular probe-target interactions are used to ensure detection system specificity. Antibodies, aptamers, synthetic antibodies, and peptides can be used as molecular probes. This study has demonstrated the possibility of using aptamers as molecular probes for AFM-based detection of the ovarian cancer biomarker CA125. Antigen detection in a nanomolar solution was carried out using AFM chips with immobilized aptamers, commercially available or synthesized based on sequences from open sources. Both aptamer types can be used for antigen detection, but the availability of sequence information enables additional modeling of the aptamer structure with allowance for modifications necessary for immobilization of the aptamer on an AFM chip surface. Information on the structure and oligomeric composition of aptamers in the solution was acquired by combining small-angle X-ray scattering and molecular modeling. Modeling enabled pre-selection, before the experimental stage, of aptamers for use as surface-immobilized molecular probes.
Collapse
Affiliation(s)
- Maria O. Ershova
- Institute of Biomedical Chemistry, Pogodinskaya Str. 10/8, 119121 Moscow, Russia; (M.O.E.); (A.A.V.)
| | - Amir Taldaev
- Institute of Biomedical Chemistry, Pogodinskaya Str. 10/8, 119121 Moscow, Russia; (M.O.E.); (A.A.V.)
| | - Petr V. Konarev
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninsky Ave. 59, 119333 Moscow, Russia
- National Research Centre “Kurchatov Institute”, Akademika Kurchatova Square 1, 123182 Moscow, Russia
| | - Georgy S. Peters
- National Research Centre “Kurchatov Institute”, Akademika Kurchatova Square 1, 123182 Moscow, Russia
| | - Anastasia A. Valueva
- Institute of Biomedical Chemistry, Pogodinskaya Str. 10/8, 119121 Moscow, Russia; (M.O.E.); (A.A.V.)
| | - Irina A. Ivanova
- Institute of Biomedical Chemistry, Pogodinskaya Str. 10/8, 119121 Moscow, Russia; (M.O.E.); (A.A.V.)
| | - Sergey V. Kraevsky
- Institute of Biomedical Chemistry, Pogodinskaya Str. 10/8, 119121 Moscow, Russia; (M.O.E.); (A.A.V.)
| | - Andrey F. Kozlov
- Institute of Biomedical Chemistry, Pogodinskaya Str. 10/8, 119121 Moscow, Russia; (M.O.E.); (A.A.V.)
| | - Vadim S. Ziborov
- Institute of Biomedical Chemistry, Pogodinskaya Str. 10/8, 119121 Moscow, Russia; (M.O.E.); (A.A.V.)
| | - Yuri D. Ivanov
- Institute of Biomedical Chemistry, Pogodinskaya Str. 10/8, 119121 Moscow, Russia; (M.O.E.); (A.A.V.)
| | - Alexander I. Archakov
- Institute of Biomedical Chemistry, Pogodinskaya Str. 10/8, 119121 Moscow, Russia; (M.O.E.); (A.A.V.)
| | - Tatyana O. Pleshakova
- Institute of Biomedical Chemistry, Pogodinskaya Str. 10/8, 119121 Moscow, Russia; (M.O.E.); (A.A.V.)
| |
Collapse
|
4
|
Ivanov YD, Ableev AN, Shumov ID, Ivanova IA, Vaulin NV, Lebedev DV, Bukatin AS, Mukhin IS, Archakov AI. Registration of Functioning of a Single Horseradish Peroxidase Macromolecule with a Solid-State Nanopore. Int J Mol Sci 2023; 24:15636. [PMID: 37958620 PMCID: PMC10647385 DOI: 10.3390/ijms242115636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 11/15/2023] Open
Abstract
Currently, nanopore-based technology for the determination of the functional activity of single enzyme molecules continues its development. The use of natural nanopores for studying single enzyme molecules is known. At that, the approach utilizing artificial solid-state nanopores is also promising but still understudied. Herein, we demonstrate the use of a nanotechnology-based approach for the investigation of the enzymatic activity of a single molecule of horseradish peroxidase with a solid-state nanopore. The artificial 5 nm solid-state nanopore has been formed in a 40 nm thick silicon nitride structure. A single molecule of HRP has been entrapped into the nanopore. The activity of the horseradish peroxidase (HRP) enzyme molecule inserted in the nanopore has been monitored by recording the time dependence of the ion current through the nanopore in the course of the reaction of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonate) (ABTS) oxidation reaction. We have found that in the process of ABTS oxidation in the presence of 2.5 mM hydrogen peroxide, individual HRP enzyme molecules are able to retain activity for approximately 700 s before a decrease in the ion current through the nanopore, which can be explained by structural changes of the enzyme.
Collapse
Affiliation(s)
- Yuri D. Ivanov
- Institute of Biomedical Chemistry, 10, Pogodinskaya St., Moscow 119121, Russia; (A.N.A.); (I.D.S.); (I.A.I.); (A.I.A.)
| | - Alexander N. Ableev
- Institute of Biomedical Chemistry, 10, Pogodinskaya St., Moscow 119121, Russia; (A.N.A.); (I.D.S.); (I.A.I.); (A.I.A.)
| | - Ivan D. Shumov
- Institute of Biomedical Chemistry, 10, Pogodinskaya St., Moscow 119121, Russia; (A.N.A.); (I.D.S.); (I.A.I.); (A.I.A.)
| | - Irina A. Ivanova
- Institute of Biomedical Chemistry, 10, Pogodinskaya St., Moscow 119121, Russia; (A.N.A.); (I.D.S.); (I.A.I.); (A.I.A.)
| | - Nikita V. Vaulin
- Laboratory of Renewable Energy Sources, St. Petersburg Academic University, 8/3, Khlopina st., St. Petersburg 194021, Russia; (N.V.V.); (D.V.L.); (A.S.B.); (I.S.M.)
- Institute for Analytical Instrumentation RAS, 31-33 Lit. A, Ivana Chernykh St., St. Petersburg 198095, Russia
| | - Denis V. Lebedev
- Laboratory of Renewable Energy Sources, St. Petersburg Academic University, 8/3, Khlopina st., St. Petersburg 194021, Russia; (N.V.V.); (D.V.L.); (A.S.B.); (I.S.M.)
- Institute for Analytical Instrumentation RAS, 31-33 Lit. A, Ivana Chernykh St., St. Petersburg 198095, Russia
- Institute of Chemistry, Saint Petersburg State University, 7/9, Universitetskaya Nab., St. Petersburg 199034, Russia
| | - Anton S. Bukatin
- Laboratory of Renewable Energy Sources, St. Petersburg Academic University, 8/3, Khlopina st., St. Petersburg 194021, Russia; (N.V.V.); (D.V.L.); (A.S.B.); (I.S.M.)
- Institute for Analytical Instrumentation RAS, 31-33 Lit. A, Ivana Chernykh St., St. Petersburg 198095, Russia
| | - Ivan S. Mukhin
- Laboratory of Renewable Energy Sources, St. Petersburg Academic University, 8/3, Khlopina st., St. Petersburg 194021, Russia; (N.V.V.); (D.V.L.); (A.S.B.); (I.S.M.)
- Higher School of Engineering Physics, Peter the Great Polytechnic University, 26, Polytehnicheskaya St., St. Petersburg 194021, Russia
| | - Alexander I. Archakov
- Institute of Biomedical Chemistry, 10, Pogodinskaya St., Moscow 119121, Russia; (A.N.A.); (I.D.S.); (I.A.I.); (A.I.A.)
| |
Collapse
|
5
|
Ivanov YD, Malsagova KA, Goldaeva KV, Pleshakova TO, Kozlov AF, Galiullin RA, Shumov ID, Popov VP, Abramova IK, Ziborov VS, Petrov OF, Dolgoborodov AY, Archakov AI. The Study of Performance of a Nanoribbon Biosensor, Sensitized with Aptamers and Antibodies, upon Detection of Core Antigen of Hepatitis C Virus. Micromachines (Basel) 2023; 14:1946. [PMID: 37893383 PMCID: PMC10609547 DOI: 10.3390/mi14101946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023]
Abstract
The development of highly sensitive diagnostic systems for the early revelation of diseases in humans is one of the most important tasks of modern biomedical research, and the detection of the core antigen of the hepatitis C virus (HCVcoreAg)-a protein marker of the hepatitis C virus-is just the case. Our study is aimed at testing the performance of the nanoribbon biosensor in the case of the use of two different types of molecular probes: the antibodies and the aptamers against HCVcoreAg. The nanoribbon sensor chips employed are based on "silicon-on-insulator structures" (SOI-NR). Two different HCVcoreAg preparations are tested: recombinant β-galactosidase-conjugated HCVcoreAg ("Virogen", Watertown, MA, USA) and recombinant HCVcoreAg ("Vector-Best", Novosibirsk, Russia). Upon the detection of either type of antigen preparation, the lowest concentration of the antigen detectable in buffer with pH 5.1 was found to be approximately equal, amounting to ~10-15 M. This value was similar upon the use of either type of molecular probes.
Collapse
Affiliation(s)
- Yuri D. Ivanov
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia; (Y.D.I.); (K.A.M.); (T.O.P.); (A.F.K.); (R.A.G.); (I.D.S.); (I.K.A.); (V.S.Z.); (A.I.A.)
- Joint Institute for High Temperatures of Russian Academy of Sciences, 125412 Moscow, Russia; (O.F.P.); (A.Y.D.)
| | - Kristina A. Malsagova
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia; (Y.D.I.); (K.A.M.); (T.O.P.); (A.F.K.); (R.A.G.); (I.D.S.); (I.K.A.); (V.S.Z.); (A.I.A.)
| | - Kristina V. Goldaeva
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia; (Y.D.I.); (K.A.M.); (T.O.P.); (A.F.K.); (R.A.G.); (I.D.S.); (I.K.A.); (V.S.Z.); (A.I.A.)
| | - Tatyana O. Pleshakova
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia; (Y.D.I.); (K.A.M.); (T.O.P.); (A.F.K.); (R.A.G.); (I.D.S.); (I.K.A.); (V.S.Z.); (A.I.A.)
| | - Andrey F. Kozlov
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia; (Y.D.I.); (K.A.M.); (T.O.P.); (A.F.K.); (R.A.G.); (I.D.S.); (I.K.A.); (V.S.Z.); (A.I.A.)
| | - Rafael A. Galiullin
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia; (Y.D.I.); (K.A.M.); (T.O.P.); (A.F.K.); (R.A.G.); (I.D.S.); (I.K.A.); (V.S.Z.); (A.I.A.)
| | - Ivan D. Shumov
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia; (Y.D.I.); (K.A.M.); (T.O.P.); (A.F.K.); (R.A.G.); (I.D.S.); (I.K.A.); (V.S.Z.); (A.I.A.)
| | - Vladimir P. Popov
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia;
| | - Irina K. Abramova
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia; (Y.D.I.); (K.A.M.); (T.O.P.); (A.F.K.); (R.A.G.); (I.D.S.); (I.K.A.); (V.S.Z.); (A.I.A.)
| | - Vadim S. Ziborov
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia; (Y.D.I.); (K.A.M.); (T.O.P.); (A.F.K.); (R.A.G.); (I.D.S.); (I.K.A.); (V.S.Z.); (A.I.A.)
- Joint Institute for High Temperatures of Russian Academy of Sciences, 125412 Moscow, Russia; (O.F.P.); (A.Y.D.)
| | - Oleg F. Petrov
- Joint Institute for High Temperatures of Russian Academy of Sciences, 125412 Moscow, Russia; (O.F.P.); (A.Y.D.)
| | - Alexander Yu. Dolgoborodov
- Joint Institute for High Temperatures of Russian Academy of Sciences, 125412 Moscow, Russia; (O.F.P.); (A.Y.D.)
| | - Alexander I. Archakov
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia; (Y.D.I.); (K.A.M.); (T.O.P.); (A.F.K.); (R.A.G.); (I.D.S.); (I.K.A.); (V.S.Z.); (A.I.A.)
| |
Collapse
|
6
|
Ivanov YD, Malsagova KA, Goldaeva KV, Kapustina SI, Pleshakova TO, Popov VP, Kozlov AF, Galiullin RA, Shumov ID, Enikeev DV, Potoldykova NV, Ziborov VS, Petrov OF, Dolgoborodov AY, Glukhov AV, Novikov SV, Grabezhova VK, Yushkov ES, Konev VA, Kovalev OB, Archakov AI. Nanoribbon Biosensor-Based Detection of microRNA Markers of Prostate Cancer. Sensors (Basel) 2023; 23:7527. [PMID: 37687982 PMCID: PMC10490786 DOI: 10.3390/s23177527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/19/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023]
Abstract
Prostate cancer (PC) is one of the major causes of death among elderly men. PC is often diagnosed later in progression due to asymptomatic early stages. Early detection of PC is thus crucial for effective PC treatment. The aim of this study is the simultaneous highly sensitive detection of a palette of PC-associated microRNAs (miRNAs) in human plasma samples. With this aim, a nanoribbon biosensor system based on "silicon-on-insulator" structures (SOI-NR biosensor) has been employed. In order to provide biospecific detection of the target miRNAs, the surface of individual nanoribbons has been sensitized with DNA oligonucleotide probes (oDNA probes) complementary to the target miRNAs. The lowest concentration of nucleic acids, detectable with our biosensor, has been found to be 1.1 × 10-17 M. The successful detection of target miRNAs, isolated from real plasma samples of PC patients, has also been demonstrated. We believe that the development of highly sensitive nanotechnology-based biosensors for the detection of PC markers is a step towards personalized medicine.
Collapse
Affiliation(s)
- Yuri D. Ivanov
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia; (Y.D.I.); (K.A.M.); (S.I.K.); (T.O.P.); (A.F.K.); (R.A.G.); (I.D.S.); (A.I.A.)
| | - Kristina A. Malsagova
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia; (Y.D.I.); (K.A.M.); (S.I.K.); (T.O.P.); (A.F.K.); (R.A.G.); (I.D.S.); (A.I.A.)
| | - Kristina V. Goldaeva
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia; (Y.D.I.); (K.A.M.); (S.I.K.); (T.O.P.); (A.F.K.); (R.A.G.); (I.D.S.); (A.I.A.)
| | - Svetlana I. Kapustina
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia; (Y.D.I.); (K.A.M.); (S.I.K.); (T.O.P.); (A.F.K.); (R.A.G.); (I.D.S.); (A.I.A.)
| | - Tatyana O. Pleshakova
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia; (Y.D.I.); (K.A.M.); (S.I.K.); (T.O.P.); (A.F.K.); (R.A.G.); (I.D.S.); (A.I.A.)
| | - Vladimir P. Popov
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia;
| | - Andrey F. Kozlov
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia; (Y.D.I.); (K.A.M.); (S.I.K.); (T.O.P.); (A.F.K.); (R.A.G.); (I.D.S.); (A.I.A.)
| | - Rafael A. Galiullin
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia; (Y.D.I.); (K.A.M.); (S.I.K.); (T.O.P.); (A.F.K.); (R.A.G.); (I.D.S.); (A.I.A.)
| | - Ivan D. Shumov
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia; (Y.D.I.); (K.A.M.); (S.I.K.); (T.O.P.); (A.F.K.); (R.A.G.); (I.D.S.); (A.I.A.)
| | - Dmitry V. Enikeev
- Institute for Urology and Reproductive Health, Sechenov University, 119992 Moscow, Russia; (D.V.E.); (N.V.P.)
| | - Natalia V. Potoldykova
- Institute for Urology and Reproductive Health, Sechenov University, 119992 Moscow, Russia; (D.V.E.); (N.V.P.)
| | - Vadim S. Ziborov
- Joint Institute for High Temperatures of Russian Academy of Sciences, 125412 Moscow, Russia; (V.S.Z.); (O.F.P.); (A.Y.D.)
| | - Oleg F. Petrov
- Joint Institute for High Temperatures of Russian Academy of Sciences, 125412 Moscow, Russia; (V.S.Z.); (O.F.P.); (A.Y.D.)
| | - Alexander Y. Dolgoborodov
- Joint Institute for High Temperatures of Russian Academy of Sciences, 125412 Moscow, Russia; (V.S.Z.); (O.F.P.); (A.Y.D.)
| | - Alexander V. Glukhov
- JSC “Novosibirsk Plant of Semiconductor Devices with OKB”, 630082 Novosibirsk, Russia;
| | - Sergey V. Novikov
- Associate Printing-and-Publication Centre Technosphera, 125319 Moscow, Russia;
| | - Victoria K. Grabezhova
- JSC “Design Center for Biomicroelectronic Technologies “Vega””, 630082 Novosibirsk, Russia;
| | - Evgeniy S. Yushkov
- Department for Business Project Management, National Research Nuclear University “MEPhI”, 115409 Moscow, Russia
| | - Vladimir A. Konev
- Department of Infectious Diseases in Children, Faculty of Pediatrics, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (V.A.K.); (O.B.K.)
| | - Oleg B. Kovalev
- Department of Infectious Diseases in Children, Faculty of Pediatrics, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (V.A.K.); (O.B.K.)
| | - Alexander I. Archakov
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia; (Y.D.I.); (K.A.M.); (S.I.K.); (T.O.P.); (A.F.K.); (R.A.G.); (I.D.S.); (A.I.A.)
| |
Collapse
|
7
|
Gordeeva AI, Valueva AA, Ershova MO, Rybakova EE, Shumov ID, Kozlov AF, Ziborov VS, Zavialova MG, Zgoda VG, Ivanov YD, Archakov AI, Pleshakova TO. Mass Spectrometric Identification of BSA Covalently Captured onto a Chip for Atomic Force Microscopy. Int J Mol Sci 2023; 24:ijms24108999. [PMID: 37240343 DOI: 10.3390/ijms24108999] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Mass spectrometry (MS) is one of the main techniques for protein identification. Herein, MS has been employed for the identification of bovine serum albumin (BSA), which was covalently immobilized on the surface of a mica chip intended for investigation by atomic force microscopy (AFM). For the immobilization, two different types of crosslinkers have been used: 4-benzoylbenzoic acid N-succinimidyl ester (SuccBB) and dithiobis(succinimidyl propionate) (DSP). According to the data obtained by using an AFM-based molecular detector, the SuccBB crosslinker was more efficient in BSA immobilization than the DSP. The type of crosslinker used for protein capturing has been found to affect the results of MS identification. The results obtained herein can be applied in the development of novel systems intended for the highly sensitive analysis of proteins with molecular detectors.
Collapse
Affiliation(s)
| | | | - Maria O Ershova
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia
| | | | - Ivan D Shumov
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia
| | - Andrey F Kozlov
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia
| | - Vadim S Ziborov
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia
| | | | - Victor G Zgoda
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia
| | - Yuri D Ivanov
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia
| | | | | |
Collapse
|
8
|
Ivanov YD, Shumov ID, Kozlov AF, Ershova MO, Valueva AA, Ivanova IA, Tatur VY, Lukyanitsa AA, Ivanova ND, Ziborov VS. Stopped Flow of Glycerol Induces the Enhancement of Adsorption and Aggregation of HRP on Mica. Micromachines (Basel) 2023; 14:mi14051024. [PMID: 37241647 DOI: 10.3390/mi14051024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/26/2023] [Accepted: 05/06/2023] [Indexed: 05/28/2023]
Abstract
Glycerol is a usable component of heat-transfer fluids, and is thus suitable for the use in microchannel-based heat exchangers in biosensors and microelectronic devices. The flow of a fluid can lead to the generation of electromagnetic fields, which can affect enzymes. Herein, by means of atomic force microscopy (AFM) and spectrophotometry, a long-term effect of stopped flow of glycerol through a coiled heat exchanger on horseradish peroxidase (HRP) has been revealed. Samples of buffered HRP solution were incubated near either the inlet or the outlet sections of the heat exchanger after stopping the flow. It has been found that both the enzyme aggregation state and the number of mica-adsorbed HRP particles increase after such an incubation for 40 min. Moreover, the enzymatic activity of the enzyme incubated near the inlet section has been found to increase in comparison with that of the control sample, while the activity of the enzyme incubated near the outlet section remained unaffected. Our results can find application in the development of biosensors and bioreactors, in which flow-based heat exchangers are employed.
Collapse
Affiliation(s)
- Yuri D Ivanov
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10 Build. 8, Moscow 119121, Russia
- Joint Institute for High Temperatures of the Russian Academy of Sciences, Moscow 125412, Russia
| | - Ivan D Shumov
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10 Build. 8, Moscow 119121, Russia
| | - Andrey F Kozlov
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10 Build. 8, Moscow 119121, Russia
| | - Maria O Ershova
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10 Build. 8, Moscow 119121, Russia
| | - Anastasia A Valueva
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10 Build. 8, Moscow 119121, Russia
| | - Irina A Ivanova
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10 Build. 8, Moscow 119121, Russia
| | - Vadim Y Tatur
- Foundation of Perspective Technologies and Novations, Moscow 115682, Russia
| | - Andrei A Lukyanitsa
- Foundation of Perspective Technologies and Novations, Moscow 115682, Russia
- Faculty of Computational Mathematics and Cybernetics, Moscow State University, Moscow 119991, Russia
| | - Nina D Ivanova
- Foundation of Perspective Technologies and Novations, Moscow 115682, Russia
- Moscow State Academy of Veterinary Medicine and Biotechnology Named after Skryabin, Moscow 109472, Russia
| | - Vadim S Ziborov
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10 Build. 8, Moscow 119121, Russia
- Joint Institute for High Temperatures of the Russian Academy of Sciences, Moscow 125412, Russia
| |
Collapse
|
9
|
Pleshakova TO, Ivanov YD, Valueva AA, Shumyantseva VV, Ilgisonis EV, Ponomarenko EA, Lisitsa AV, Chekhonin VP, Archakov AI. Analysis of Single Biomacromolecules and Viruses: Is It a Myth or Reality? Int J Mol Sci 2023; 24:ijms24031877. [PMID: 36768195 PMCID: PMC9915366 DOI: 10.3390/ijms24031877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/04/2023] [Accepted: 01/15/2023] [Indexed: 01/20/2023] Open
Abstract
The beginning of the twenty-first century witnessed novel breakthrough research directions in the life sciences, such as genomics, transcriptomics, translatomics, proteomics, metabolomics, and bioinformatics. A newly developed single-molecule approach addresses the physical and chemical properties and the functional activity of single (individual) biomacromolecules and viral particles. Within the alternative approach, the combination of "single-molecule approaches" is opposed to "omics approaches". This new approach is fundamentally unique in terms of its research object (a single biomacromolecule). Most studies are currently performed using postgenomic technologies that allow the properties of several hundreds of millions or even billions of biomacromolecules to be analyzed. This paper discusses the relevance and theoretical, methodological, and practical issues related to the development potential of a single-molecule approach using methods based on molecular detectors.
Collapse
|
10
|
Ivanov YD, Kapustina SI, Malsagova KA, Goldaeva KV, Pleshakova TO, Galiullin RA, Shumov ID, Kozlov AF, Glukhov AV, Grabezhova VK, Popov VP, Petrov OF, Ziborov VS, Kushlinskii NE, Alferov AA, Konev VA, Kovalev OB, Uchaikin VF, Archakov AI. "Silicon-On-Insulator"-Based Biosensor for the Detection of MicroRNA Markers of Ovarian Cancer. Micromachines (Basel) 2022; 14:70. [PMID: 36677130 PMCID: PMC9861449 DOI: 10.3390/mi14010070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/16/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Ovarian cancer is a gynecological cancer characterized by a high mortality rate and tumor heterogeneity. Its early detection and primary prophylaxis are difficult to perform. Detecting biomarkers for ovarian cancer plays a pivotal role in therapy effectiveness and affects patients' survival. This study demonstrates the detection of microRNAs (miRNAs), which were reported to be associated with ovarian cancer tumorigenesis, with a nanowire biosensor based on silicon-on-insulator structures (SOI-NW biosensor). The advantages of the method proposed for miRNA detection using the SOI-NW biosensor are as follows: (1) no need for additional labeling or amplification reaction during sample preparation, and (2) real-time detection of target biomolecules. The detecting component of the biosensor is a chip with an array of 3 µm wide, 10 µm long silicon nanowires on its surface. The SOI-NW chip was fabricated using the "top-down" method, which is compatible with large-scale CMOS technology. Oligonucleotide probes (oDNA probes) carrying sequences complementary to the target miRNAs were covalently immobilized on the nanowire surface to ensure high-sensitivity biospecific sensing of the target biomolecules. The study involved two experimental series. Detection of model DNA oligonucleotides being synthetic analogs of the target miRNAs was carried out to assess the method's sensitivity. The lowest concentration of the target oligonucleotides detectable in buffer solution was 1.1 × 10-16 M. In the second experimental series, detection of miRNAs (miRNA-21, miRNA-141, and miRNA-200a) isolated from blood plasma samples collected from patients having a verified diagnosis of ovarian cancer was performed. The results of our present study represent a step towards the development of novel highly sensitive diagnostic systems for the early revelation of ovarian cancer in women.
Collapse
Affiliation(s)
- Yuri D. Ivanov
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia
- Joint Institute for High Temperatures of Russian Academy of Sciences, 125412 Moscow, Russia
| | - Svetlana I. Kapustina
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia
- Department of Cybernetics of Chemical and Technological Processes, Mendeleev University of Chemical Technology of Russia (MUCTR), 125047 Moscow, Russia
| | | | | | | | | | - Ivan D. Shumov
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia
| | | | - Alexander V. Glukhov
- JSC “Novosibirsk Plant of Semiconductor Devices with OKB”, 630082 Novosibirsk, Russia
| | - Victoria K. Grabezhova
- JSC “Design Center for Biomicroelectronic Technologies “Vega””, 630082 Novosibirsk, Russia
| | - Vladimir P. Popov
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Oleg F. Petrov
- Joint Institute for High Temperatures of Russian Academy of Sciences, 125412 Moscow, Russia
| | - Vadim S. Ziborov
- Institute of Biomedical Chemistry (IBMC), 119121 Moscow, Russia
- Joint Institute for High Temperatures of Russian Academy of Sciences, 125412 Moscow, Russia
| | | | - Alexander A. Alferov
- N.N. Blokhin National Medical Research Center of Oncology, 115478 Moscow, Russia
| | - Vladimir A. Konev
- Department of Infectious Diseases in Children, Faculty of Pediatrics, Pirogov Russian National Research Medical University (RNRMU), 117997 Moscow, Russia
| | - Oleg B. Kovalev
- Department of Infectious Diseases in Children, Faculty of Pediatrics, Pirogov Russian National Research Medical University (RNRMU), 117997 Moscow, Russia
| | - Vasiliy F. Uchaikin
- Department of Infectious Diseases in Children, Faculty of Pediatrics, Pirogov Russian National Research Medical University (RNRMU), 117997 Moscow, Russia
| | | |
Collapse
|
11
|
Ivanov YD, Shumov ID, Tatur VY, Valueva AA, Kozlov AF, Ivanova IA, Ershova MO, Ivanova ND, Stepanov IN, Lukyanitsa AA, Ziborov VS. AFM Investigation of the Influence of Steam Flow through a Conical Coil Heat Exchanger on Enzyme Properties. Micromachines (Basel) 2022; 13:2041. [PMID: 36557340 PMCID: PMC9784692 DOI: 10.3390/mi13122041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/15/2022] [Accepted: 11/19/2022] [Indexed: 06/17/2023]
Abstract
The present study is aimed at the revelation of subtle effects of steam flow through a conical coil heat exchanger on an enzyme, incubated near the heat exchanger, at the nanoscale. For this purpose, atomic force microscopy (AFM) has been employed. In our experiments, horseradish peroxidase (HRP) was used as a model enzyme. HRP is extensively employed as a model in food science in order to determine the influence of electromagnetic fields on enzymes. Adsorption properties of HRP on mica have been studied by AFM at the level of individual enzyme macromolecules, while the enzymatic activity of HRP has been studied by spectrophotometry. The solution of HRP was incubated either near the top or at the side of the conically wound aluminium pipe, through which steam flow passed. Our AFM data indicated an increase in the enzyme aggregation on mica after its incubation at either of the two points near the heat exchanger. At the same time, in the spectrophotometry experiments, a slight change in the shape of the curves, reflecting the HRP-catalyzed kinetics of ABTS oxidation by hydrogen peroxide, has also been observed after the incubation of the enzyme solution near the heat exchanger. These effects on the enzyme adsorption and kinetics can be explained by alterations in the enzyme hydration caused by the influence of the electromagnetic field, induced triboelectrically by the flow of steam through the heat exchanger. Our findings should thus be considered in the development of equipment involving conical heat exchangers, intended for either research or industrial use (including miniaturized bioreactors and biosensors). The increased aggregation of the HRP enzyme, observed after its incubation near the heat exchanger, should also be taken into account in analysis of possible adverse effects from steam-heated industrial equipment on the human body.
Collapse
Affiliation(s)
- Yuri D. Ivanov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, Moscow 119121, Russia
- Joint Institute for High Temperatures of the Russian Academy of Sciences, Moscow 125412, Russia
| | - Ivan D. Shumov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, Moscow 119121, Russia
| | - Vadim Y. Tatur
- Foundation of Perspective Technologies and Novations, Moscow 115682, Russia
| | - Anastasia A. Valueva
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, Moscow 119121, Russia
| | - Andrey F. Kozlov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, Moscow 119121, Russia
| | - Irina A. Ivanova
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, Moscow 119121, Russia
| | - Maria O. Ershova
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, Moscow 119121, Russia
| | - Nina D. Ivanova
- Foundation of Perspective Technologies and Novations, Moscow 115682, Russia
- Moscow State Academy of Veterinary Medicine and Biotechnology Named after Skryabin, Moscow 109472, Russia
| | - Igor N. Stepanov
- Foundation of Perspective Technologies and Novations, Moscow 115682, Russia
| | - Andrei A. Lukyanitsa
- Foundation of Perspective Technologies and Novations, Moscow 115682, Russia
- Faculty of Computational Mathematics and Cybernetics, Moscow State University, Moscow 119991, Russia
| | - Vadim S. Ziborov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, Moscow 119121, Russia
- Joint Institute for High Temperatures of the Russian Academy of Sciences, Moscow 125412, Russia
| |
Collapse
|
12
|
Ivanov YD, Tatur VY, Shumov ID, Kozlov AF, Valueva AA, Ivanova IA, Ershova MO, Ivanova ND, Stepanov IN, Lukyanitsa AA, Ziborov VS. The Effect of a Rotating Cone on Horseradish Peroxidase Aggregation on Mica Revealed by Atomic Force Microscopy. Micromachines (Basel) 2022; 13:1947. [PMID: 36363968 PMCID: PMC9697547 DOI: 10.3390/mi13111947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/03/2022] [Accepted: 11/08/2022] [Indexed: 06/16/2023]
Abstract
Our study reported herein aims to determine whether an electromagnetic field, induced triboelectrically by a metallic cone, rotating at a frequency of 167 Hz, has an effect on the properties of the horseradish peroxidase (HRP) enzyme. Atomic force microscopy (AFM) was employed to detect even the most subtle effects on single enzyme molecules. In parallel, a macroscopic method (spectrophotometry) was used to reveal whether the enzymatic activity of HRP in solution was affected. An aqueous solution of the enzyme was incubated at a distance of 2 cm from the rotating cone. The experiments were performed at various incubation times. The control experiments were performed with a non-rotating cone. The incubation of the HRP solution was found to cause the disaggregation of the enzyme. At longer incubation times, this disaggregation was found to be accompanied by the formation of higher-order aggregates; however, no change in the HRP enzymatic activity was observed. The results of our experiments could be of interest in the development of enzyme-based biosensors with rotating elements such as stirrers. Additionally, the results obtained herein are important for the correct interpretation of data obtained with such biosensors.
Collapse
Affiliation(s)
- Yuri D. Ivanov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia
- Joint Institute for High Temperatures of the Russian Academy of Sciences, 125412 Moscow, Russia
| | - Vadim Y. Tatur
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia
| | - Ivan D. Shumov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia
| | - Andrey F. Kozlov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia
| | - Anastasia A. Valueva
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia
| | - Irina A. Ivanova
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia
| | - Maria O. Ershova
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia
| | - Nina D. Ivanova
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia
- Moscow State Academy of Veterinary Medicine and Biotechnology Named after Skryabin, 109472 Moscow, Russia
| | - Igor N. Stepanov
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia
| | - Andrei A. Lukyanitsa
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia
- Faculty of Computational Mathematics and Cybernetics, Moscow State University, 119991 Moscow, Russia
| | - Vadim S. Ziborov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10 Build. 8, 119121 Moscow, Russia
- Joint Institute for High Temperatures of the Russian Academy of Sciences, 125412 Moscow, Russia
| |
Collapse
|
13
|
Ivanov YD, Tatur VY, Shumov ID, Kozlov AF, Valueva AA, Ivanova IA, Ershova MO, Ivanova ND, Stepanov IN, Lukyanitsa AA, Ziborov VS. Atomic Force Microscopy Study of the Effect of an Electric Field, Applied to a Pyramidal Structure, on Enzyme Biomolecules. J Funct Biomater 2022; 13:jfb13040234. [PMID: 36412875 PMCID: PMC9680214 DOI: 10.3390/jfb13040234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 10/31/2022] [Accepted: 11/08/2022] [Indexed: 11/11/2022] Open
Abstract
The influence of an external constant strong electric field, formed using a pyramidal structure under a high electric potential, on an enzyme located near its apex, is studied. Horseradish peroxidase (HRP) is used as a model. In our experiments, a 27 kV direct current (DC) voltage was applied to two electrodes with a conducting pyramidal structure attached to one of them. The enzyme particles were visualized by atomic force microscopy (AFM) after the adsorption of the enzyme from its 0.1 µM solution onto mica AFM substrates. It is demonstrated that after the 40 min exposure to the electric field, the enzyme forms extended structures on mica, while in control experiments compact HRP particles are observed. After the exposure to the electric field, the majority of mica-adsorbed HRP particles had a height of 1.2 nm (as opposed to 1.0 nm in the case of control experiments), and the contribution of higher (>2.0 nm) particles was also considerable. This indicates the formation of high-order HRP aggregates under the influence of an applied electric field. At that, the enzymatic activity of HRP against its substrate 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonate) (ABTS) remains unaffected. These results are important for studying macroscopic effects of strong electromagnetic fields on enzymes, as well as for the development of cellular structure models.
Collapse
Affiliation(s)
- Yuri D. Ivanov
- Institute of Biomedical Chemistry, 119121 Moscow, Russia
- Joint Institute for High Temperatures of the Russian Academy of Sciences, 125412 Moscow, Russia
- Correspondence:
| | - Vadim Y. Tatur
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia
| | - Ivan D. Shumov
- Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | | | | | | | | | - Nina D. Ivanova
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia
- Moscow State Academy of Veterinary Medicine and Biotechnology Named after Skryabin, 109472 Moscow, Russia
| | - Igor N. Stepanov
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia
| | - Andrei A. Lukyanitsa
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia
- Faculty of Computational Mathematics and Cybernetics, Moscow State University, 119991 Moscow, Russia
| | - Vadim S. Ziborov
- Institute of Biomedical Chemistry, 119121 Moscow, Russia
- Joint Institute for High Temperatures of the Russian Academy of Sciences, 125412 Moscow, Russia
| |
Collapse
|
14
|
Ivanova IA, Ershova MO, Shumov ID, Valueva AA, Ivanov YD, Pleshakova TO. Atomic Force Microscopy Study of the Temperature and Storage Duration Dependencies of Horseradish Peroxidase Oligomeric State. Biomedicines 2022; 10:biomedicines10102645. [PMID: 36289907 PMCID: PMC9599489 DOI: 10.3390/biomedicines10102645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
This paper presents an investigation of the temperature dependence of the oligomeric state of the horseradish peroxidase (HRP) enzyme on the temperature of its solution, and on the solution storage time, at the single-molecule level. Atomic force microscopy has been employed to determine how the temperature and the storage time of the HRP solution influence its aggregation upon direct adsorption of the enzyme from the solution onto bare mica substrates. In parallel, spectrophotometric measurements have been performed in order to estimate whether the HRP enzymatic activity changes over time upon the storage of the enzyme solution. The temperature dependence of the HRP oligomeric state has been studied within a broad (15–40 °C) temperature range. It has been demonstrated that the storage of the HRP solution for 14 days does not have any considerable effect on the oligomeric state of the enzyme, neither does it affect its activity. At longer storage times, AFM has allowed us to reveal a tendency of HRP to oligomerization during the storage of its buffered solution, while the enzymatic activity remains virtually unchanged even after a 1-month-long storage. By AFM, it has been revealed that after the incubation of a mica substrate in the HRP solution at various temperatures, the content of the mica-adsorbed oligomers increases insignificantly owing to a high-temperature stability of the enzyme.
Collapse
|
15
|
Ivanov YD, Malsagova KA, Bukharina NS, Vesnin SG, Usanov SA, Tatur VY, Lukyanitsa AA, Ivanova ND, Konev VA, Ziborov VS. Radiothermometric Study of the Effect of Amino Acid Mutation on the Characteristics of the Enzymatic System. Diagnostics (Basel) 2022; 12:diagnostics12040943. [PMID: 35453991 PMCID: PMC9024681 DOI: 10.3390/diagnostics12040943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/05/2022] [Accepted: 04/08/2022] [Indexed: 11/16/2022] Open
Abstract
The radiothermometry (RTM) study of a cytochrome-containing system (CYP102 A1) has been conducted in order to demonstrate the applicability of RTM for monitoring changes in the functional activity of an enzyme in case of its point mutation. The study has been performed with the example of the wild-type cytochrome (WT) and its mutant type A264K. CYP102 A1 is a nanoscale protein-enzymatic system of about 10 nm in size. RTM uses a radio detector and can record the corresponding brightness temperature (Tbr) of the nanoscale enzyme solution within the 3.4–4.2 GHz frequency range during enzyme functioning. It was found that the enzymatic reaction during the lauric acid hydroxylation at the wild-type CYP102 A1 (WT) concentration of ~10−9 M is accompanied by Tbr fluctuations of ~0.5–1 °C. At the same time, no Tbr fluctuations are observed for the mutated forms of the enzyme CYP102 A1 (A264K), where one amino acid was replaced. We know that the activity of CYP102 A1 (WT) is ~4 orders of magnitude higher than that of CYP102 A1 (A264K). We therefore concluded that the disappearance of the fluctuation of Tbr CYP102 A1 (A264K) is associated with a decrease in the activity of the enzyme. This effect can be used to develop new methods for testing the activity of the enzyme that do not require additional labels and expensive equipment, in comparison with calorimetry and spectral methods. The RTM is beginning to find application in the diagnosis of oncological diseases and for the analysis of biochemical processes.
Collapse
Affiliation(s)
- Yuri D. Ivanov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10 Build. 8, 119121 Moscow, Russia; (N.S.B.); (V.S.Z.)
- Laboratory of Shock Wave Impacts, Joint Institute for High Temperatures of Russian Academy of Sciences, Izhorskaya St. 13 Build. 2, 125412 Moscow, Russia
- Correspondence: (Y.D.I.); (K.A.M.); Tel.: +7-(499)-246-37-61 (Y.D.I.)
| | - Kristina A. Malsagova
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10 Build. 8, 119121 Moscow, Russia; (N.S.B.); (V.S.Z.)
- Correspondence: (Y.D.I.); (K.A.M.); Tel.: +7-(499)-246-37-61 (Y.D.I.)
| | - Natalia S. Bukharina
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10 Build. 8, 119121 Moscow, Russia; (N.S.B.); (V.S.Z.)
| | | | - Sergey A. Usanov
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Academician V.F. Kuprevich 5 Build. 2, 220141 Minsk, Belarus;
| | - Vadim Yu. Tatur
- Foundation of Perspective Technologies and Novations, Shipilovskaya St. 64, 115682 Moscow, Russia; (V.Y.T.); (A.A.L.)
| | - Andrei A. Lukyanitsa
- Foundation of Perspective Technologies and Novations, Shipilovskaya St. 64, 115682 Moscow, Russia; (V.Y.T.); (A.A.L.)
| | - Nina D. Ivanova
- Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Academician Skryabin St. 23, 109472 Moscow, Russia;
| | - Vladimir A. Konev
- Department of Infectious Diseases in Children, Faculty of Pediatrics, Pirogov Russian National Research Medical University, Ostrovityanov St. 1, 117997 Moscow, Russia;
| | - Vadim S. Ziborov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10 Build. 8, 119121 Moscow, Russia; (N.S.B.); (V.S.Z.)
- Laboratory of Shock Wave Impacts, Joint Institute for High Temperatures of Russian Academy of Sciences, Izhorskaya St. 13 Build. 2, 125412 Moscow, Russia
| |
Collapse
|
16
|
Ivanov YD, Goldaeva KV, Malsagova KA, Pleshakova TO, Galiullin RA, Popov VP, Kushlinskii NE, Alferov AA, Enikeev DV, Potoldykova NV, Archakov AI. Nanoribbon Biosensor in the Detection of miRNAs Associated with Colorectal Cancer. Micromachines (Basel) 2021; 12:1581. [PMID: 34945431 PMCID: PMC8705149 DOI: 10.3390/mi12121581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/10/2021] [Accepted: 12/17/2021] [Indexed: 02/07/2023]
Abstract
A nanoribbon biosensor (NRBS) was developed to register synthetic DNAs that simulate and are analogous to miRNA-17-3p associated with colorectal cancer. Using this nanoribbon biosensor, the ability to detect miRNA-17-3p in the blood plasma of a patient diagnosed with colorectal cancer has been demonstrated. The sensing element of the NRBS was a nanochip based on a silicon-on-insulator (SOI) nanostructure. The nanochip included an array of 10 nanoribbons and was designed with the implementation of top-down technology. For biospecific recognition of miRNA-17-3p, the nanochip was modified with DNA probes specific for miRNA-17-3p. The performance of the nanochip was preliminarily tested on model DNA oligonucleotides, which are synthetic analogues of miRNA-17-3p, and a detection limit of ~10-17 M was achieved. The results of this work can be used in the development of serological diagnostic systems for early detection of colorectal cancer.
Collapse
Affiliation(s)
- Yuri D. Ivanov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (K.V.G.); (K.A.M.); (T.O.P.); (R.A.G.); (A.I.A.)
| | - Kristina V. Goldaeva
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (K.V.G.); (K.A.M.); (T.O.P.); (R.A.G.); (A.I.A.)
| | - Kristina A. Malsagova
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (K.V.G.); (K.A.M.); (T.O.P.); (R.A.G.); (A.I.A.)
| | - Tatyana O. Pleshakova
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (K.V.G.); (K.A.M.); (T.O.P.); (R.A.G.); (A.I.A.)
| | - Rafael A. Galiullin
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (K.V.G.); (K.A.M.); (T.O.P.); (R.A.G.); (A.I.A.)
| | - Vladimir P. Popov
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia;
| | - Nikolay E. Kushlinskii
- N.N. Blokhin National Medical Research Center of Oncology, 115478 Moscow, Russia; (N.E.K.); (A.A.A.)
| | - Alexander A. Alferov
- N.N. Blokhin National Medical Research Center of Oncology, 115478 Moscow, Russia; (N.E.K.); (A.A.A.)
| | - Dmitry V. Enikeev
- Institute of Urology and Reproductive Health, Sechenov University, 119992 Moscow, Russia; (D.V.E.); (N.V.P.)
| | - Natalia V. Potoldykova
- Institute of Urology and Reproductive Health, Sechenov University, 119992 Moscow, Russia; (D.V.E.); (N.V.P.)
| | - Alexander I. Archakov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (K.V.G.); (K.A.M.); (T.O.P.); (R.A.G.); (A.I.A.)
| |
Collapse
|
17
|
Kaysheva AL, Isaeva AI, Pleshakova TO, Shumov ID, Valueva AA, Ershova MO, Ivanova IA, Ziborov VS, Iourov IY, Vorsanova SG, Ryabtsev SV, Archakov AI, Ivanov YD. Detection of Circulating Serum microRNA/Protein Complexes in ASD Using Functionalized Chips for an Atomic Force Microscope. Molecules 2021; 26:5979. [PMID: 34641523 PMCID: PMC8512613 DOI: 10.3390/molecules26195979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/17/2021] [Accepted: 09/29/2021] [Indexed: 11/17/2022] Open
Abstract
MicroRNAs, which circulate in blood, are characterized by high diagnostic value; in biomedical research, they can be considered as candidate markers of various diseases. Mature microRNAs of glial cells and neurons can cross the blood-brain barrier and can be detected in the serum of patients with autism spectrum disorders (ASD) as components of macrovesicles, macromolecular protein and low-density lipoprotein particles. In our present study, we have proposed an approach, in which microRNAs in protein complexes can be concentrated on the surface of AFM chips with oligonucleotide molecular probes, specific against the target microRNAs. MicroRNAs, associated with the development of ASD in children, were selected as targets. The chips with immobilized molecular probes were incubated in serum samples of ASD patients and healthy volunteers. By atomic force microscopy (AFM), objects on the AFM chip surface have been revealed after incubation in the serum samples. The height of these objects amounted to 10 nm and 6 nm in the case of samples of ASD patients and healthy volunteers, respectively. MALDI-TOF-MS analysis of protein components on the chip surface allowed us to identify several cell proteins. These proteins are involved in the binding of nucleic acids (GBG10, RT24, RALYL), in the organization of proteasomes and nucleosomes (PSA4, NP1L4), and participate in the functioning of the channel of active potassium transport (KCNE5, KCNV2).
Collapse
Affiliation(s)
- Anna L. Kaysheva
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.L.K.); (T.O.P.); (I.D.S.); (A.A.V.); (M.O.E.); (I.A.I.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Arina I. Isaeva
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.L.K.); (T.O.P.); (I.D.S.); (A.A.V.); (M.O.E.); (I.A.I.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Tatyana O. Pleshakova
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.L.K.); (T.O.P.); (I.D.S.); (A.A.V.); (M.O.E.); (I.A.I.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Ivan D. Shumov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.L.K.); (T.O.P.); (I.D.S.); (A.A.V.); (M.O.E.); (I.A.I.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Anastasia A. Valueva
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.L.K.); (T.O.P.); (I.D.S.); (A.A.V.); (M.O.E.); (I.A.I.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Maria O. Ershova
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.L.K.); (T.O.P.); (I.D.S.); (A.A.V.); (M.O.E.); (I.A.I.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Irina A. Ivanova
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.L.K.); (T.O.P.); (I.D.S.); (A.A.V.); (M.O.E.); (I.A.I.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Vadim S. Ziborov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.L.K.); (T.O.P.); (I.D.S.); (A.A.V.); (M.O.E.); (I.A.I.); (V.S.Z.); (A.I.A.); (Y.D.I.)
- Laboratory of Shock Wave Impacts, Joint Institute for High Temperatures of the Russian Academy of Sciences, Izhorskaya St. 13 Bd.2, 125412 Moscow, Russia
| | | | - Svetlana G. Vorsanova
- Veltischev Research and Clinical Institute for Pediatrics, Pirogov Russian National Research Medical University, Ministry of Health of Russian Federation, Taldomskaya St. 2, 125412 Moscow, Russia;
| | | | - Alexander I. Archakov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.L.K.); (T.O.P.); (I.D.S.); (A.A.V.); (M.O.E.); (I.A.I.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Yuri D. Ivanov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (A.L.K.); (T.O.P.); (I.D.S.); (A.A.V.); (M.O.E.); (I.A.I.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| |
Collapse
|
18
|
Ivanov YD, Malsagova KA, Popov VP, Kupriyanov IN, Pleshakova TO, Galiullin RA, Ziborov VS, Dolgoborodov AY, Petrov OF, Miakonkikh AV, Rudenko KV, Glukhov AV, Smirnov AY, Usachev DY, Gadzhieva OA, Bashiryan BA, Shimansky VN, Enikeev DV, Potoldykova NV, Archakov AI. Micro-Raman Characterization of Structural Features of High-k Stack Layer of SOI Nanowire Chip, Designed to Detect Circular RNA Associated with the Development of Glioma. Molecules 2021; 26:molecules26123715. [PMID: 34207029 PMCID: PMC8234461 DOI: 10.3390/molecules26123715] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/08/2021] [Accepted: 06/14/2021] [Indexed: 02/08/2023] Open
Abstract
The application of micro-Raman spectroscopy was used for characterization of structural features of the high-k stack (h-k) layer of "silicon-on-insulator" (SOI) nanowire (NW) chip (h-k-SOI-NW chip), including Al2O3 and HfO2 in various combinations after heat treatment from 425 to 1000 °C. After that, the NW structures h-k-SOI-NW chip was created using gas plasma etching optical lithography. The stability of the signals from the monocrine phase of HfO2 was shown. Significant differences were found in the elastic stresses of the silicon layers for very thick (>200 nm) Al2O3 layers. In the UV spectra of SOI layers of a silicon substrate with HfO2, shoulders in the Raman spectrum were observed at 480-490 cm-1 of single-phonon scattering. The h-k-SOI-NW chip created in this way has been used for the detection of DNA-oligonucleotide sequences (oDNA), that became a synthetic analog of circular RNA-circ-SHKBP1 associated with the development of glioma at a concentration of 1.1 × 10-16 M. The possibility of using such h-k-SOI NW chips for the detection of circ-SHKBP1 in blood plasma of patients diagnosed with neoplasm of uncertain nature of the brain and central nervous system was shown.
Collapse
Affiliation(s)
- Yuri D. Ivanov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (Y.D.I.); (T.O.P.); (R.A.G.); (V.S.Z.); (A.I.A.)
| | - Kristina A. Malsagova
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (Y.D.I.); (T.O.P.); (R.A.G.); (V.S.Z.); (A.I.A.)
- Correspondence: ; Tel.: +7-(499)-246-37-61
| | - Vladimir P. Popov
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia;
| | - Igor N. Kupriyanov
- Laboratory of Experimental Mineralogy and Crystallogenesis, Sobolev Institute of Geology and Mineralogy, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia;
| | - Tatyana O. Pleshakova
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (Y.D.I.); (T.O.P.); (R.A.G.); (V.S.Z.); (A.I.A.)
| | - Rafael A. Galiullin
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (Y.D.I.); (T.O.P.); (R.A.G.); (V.S.Z.); (A.I.A.)
| | - Vadim S. Ziborov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (Y.D.I.); (T.O.P.); (R.A.G.); (V.S.Z.); (A.I.A.)
- Joint Institute for High Temperatures of Russian Academy of Sciences, 125412 Moscow, Russia; (A.Y.D.); (O.F.P.)
| | - Alexander Yu. Dolgoborodov
- Joint Institute for High Temperatures of Russian Academy of Sciences, 125412 Moscow, Russia; (A.Y.D.); (O.F.P.)
| | - Oleg F. Petrov
- Joint Institute for High Temperatures of Russian Academy of Sciences, 125412 Moscow, Russia; (A.Y.D.); (O.F.P.)
| | - Andrey V. Miakonkikh
- K. A. Valiev Institute of Physics and Technology of the Russian Academy of Sciences, 117218 Moscow, Russia; (A.V.M.); (K.V.R.)
| | - Konstantin V. Rudenko
- K. A. Valiev Institute of Physics and Technology of the Russian Academy of Sciences, 117218 Moscow, Russia; (A.V.M.); (K.V.R.)
| | - Alexander V. Glukhov
- JSC Novosibirsk Plant of Semiconductor Devices with OKB, 630082 Novosibirsk, Russia;
| | | | - Dmitry Yu. Usachev
- Federal State Autonomous Institution “N. N. Burdenko National Medical Research Center of Neurosurgery” of the Ministry of Health of the Russian Federation, 125047 Moscow, Russia; (D.Y.U.); (O.A.G.); (B.A.B.); (V.N.S.)
| | - Olga A. Gadzhieva
- Federal State Autonomous Institution “N. N. Burdenko National Medical Research Center of Neurosurgery” of the Ministry of Health of the Russian Federation, 125047 Moscow, Russia; (D.Y.U.); (O.A.G.); (B.A.B.); (V.N.S.)
| | - Boris A. Bashiryan
- Federal State Autonomous Institution “N. N. Burdenko National Medical Research Center of Neurosurgery” of the Ministry of Health of the Russian Federation, 125047 Moscow, Russia; (D.Y.U.); (O.A.G.); (B.A.B.); (V.N.S.)
| | - Vadim N. Shimansky
- Federal State Autonomous Institution “N. N. Burdenko National Medical Research Center of Neurosurgery” of the Ministry of Health of the Russian Federation, 125047 Moscow, Russia; (D.Y.U.); (O.A.G.); (B.A.B.); (V.N.S.)
| | - Dmitry V. Enikeev
- Institute for Urology and Reproductive Health, Sechenov University, 119992 Moscow, Russia; (D.V.E.); (N.V.P.)
| | - Natalia V. Potoldykova
- Institute for Urology and Reproductive Health, Sechenov University, 119992 Moscow, Russia; (D.V.E.); (N.V.P.)
| | - Alexander I. Archakov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (Y.D.I.); (T.O.P.); (R.A.G.); (V.S.Z.); (A.I.A.)
| |
Collapse
|
19
|
Ivanov YD, Romanova TS, Malsagova KA, Pleshakova TO, Archakov AI. Use of Silicon Nanowire Sensors for Early Cancer Diagnosis. Molecules 2021; 26:3734. [PMID: 34207397 PMCID: PMC8234636 DOI: 10.3390/molecules26123734] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/10/2021] [Accepted: 06/16/2021] [Indexed: 11/17/2022] Open
Abstract
The review covers some research conducted in the field of medical and biomedical application of devices based on silicon sensor elements (Si-NW-sensors). The use of Si-NW-sensors is one of the key methods used in a whole range of healthcare fields. Their biomedical use is among the most important ones as they offer opportunities for early diagnosis of oncological pathologies, for monitoring the prescribed therapy and for improving the people's quality of life.
Collapse
Affiliation(s)
| | | | - Kristina A. Malsagova
- Institute of Biomedical Chemistry, 119121 Moscow, Russia; (Y.D.I.); (T.S.R.); (T.O.P.); (A.I.A.)
| | | | | |
Collapse
|
20
|
Ivanov YD, Tatur VY, Pleshakova TO, Shumov ID, Kozlov AF, Valueva AA, Ivanova IA, Ershova MO, Ivanova ND, Repnikov VV, Stepanov IN, Ziborov VS. Effect of Spherical Elements of Biosensors and Bioreactors on the Physicochemical Properties of a Peroxidase Protein. Polymers (Basel) 2021; 13:1601. [PMID: 34063512 PMCID: PMC8155990 DOI: 10.3390/polym13101601] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 11/16/2022] Open
Abstract
External electromagnetic fields are known to be able to concentrate inside the construction elements of biosensors and bioreactors owing to reflection from their surface. This can lead to changes in the structure of biopolymers (such as proteins), incubated inside these elements, thus influencing their functional properties. Our present study concerned the revelation of the effect of spherical elements, commonly employed in biosensors and bioreactors, on the physicochemical properties of proteins with the example of the horseradish peroxidase (HRP) enzyme. In our experiments, a solution of HRP was incubated within a 30 cm-diameter titanium half-sphere, which was used as a model construction element. Atomic force microscopy (AFM) was employed for the single-molecule visualization of the HRP macromolecules, adsorbed from the test solution onto mica substrates in order to find out whether the incubation of the test HRP solution within the half-sphere influenced the HRP aggregation state. Attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) was employed in order to reveal whether the incubation of HRP solution within the half-sphere led to any changes in its secondary structure. In parallel, spectrophotometry-based estimation of the HRP enzymatic activity was performed in order to find out if the HRP active site was affected by the electromagnetic field under the conditions of our experiments. We revealed an increased aggregation of HRP after the incubation of its solution within the half-sphere in comparison with the control sample incubated far outside the half-sphere. ATR-FTIR allowed us to reveal alterations in HRP's secondary structure. Such changes in the protein structure did not affect its active site, as was confirmed by spectrophotometry. The effect of spherical elements on a protein solution should be taken into account in the development of the optimized design of biosensors and bioreactors, intended for performing processes involving proteins in biomedicine and biotechnology, including highly sensitive biosensors intended for the diagnosis of socially significant diseases in humans (including oncology, cardiovascular diseases, etc.) at early stages.
Collapse
Affiliation(s)
- Yuri D. Ivanov
- Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (V.S.Z.)
- Joint Institute for High Temperatures of the Russian Academy of Sciences, 125412 Moscow, Russia
| | - Vadim Yu. Tatur
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia; (V.Y.T.); (N.D.I.); (I.N.S.)
| | - Tatyana O. Pleshakova
- Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (V.S.Z.)
| | - Ivan D. Shumov
- Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (V.S.Z.)
| | - Andrey F. Kozlov
- Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (V.S.Z.)
| | - Anastasia A. Valueva
- Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (V.S.Z.)
| | - Irina A. Ivanova
- Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (V.S.Z.)
| | - Maria O. Ershova
- Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (V.S.Z.)
| | - Nina D. Ivanova
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia; (V.Y.T.); (N.D.I.); (I.N.S.)
- Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, 109472 Moscow, Russia
| | | | - Igor N. Stepanov
- Foundation of Perspective Technologies and Novations, 115682 Moscow, Russia; (V.Y.T.); (N.D.I.); (I.N.S.)
| | - Vadim S. Ziborov
- Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (V.S.Z.)
- Joint Institute for High Temperatures of the Russian Academy of Sciences, 125412 Moscow, Russia
| |
Collapse
|
21
|
Ivanov YD, Pleshakova TO, Shumov ID, Kozlov AF, Ivanova IA, Valueva AA, Ershova MO, Tatur VY, Stepanov IN, Repnikov VV, Ziborov VS. AFM study of changes in properties of horseradish peroxidase after incubation of its solution near a pyramidal structure. Sci Rep 2021; 11:9907. [PMID: 33972657 PMCID: PMC8110588 DOI: 10.1038/s41598-021-89377-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/22/2021] [Indexed: 12/14/2022] Open
Abstract
In our present paper, the influence of a pyramidal structure on physicochemical properties of a protein in buffer solution has been studied. The pyramidal structure employed herein was similar to those produced industrially for anechoic chambers. Pyramidal structures are also used as elements of biosensors. Herein, horseradish peroxidase (HRP) enzyme was used as a model protein. HRP macromolecules were adsorbed from their solution onto an atomically smooth mica substrate, and then visualized by atomic force microscopy (AFM). In parallel, the enzymatic activity of HRP was estimated by conventional spectrophotometry. Additionally, attenuated total reflection Fourier-transform infrared spectroscopy (ATR-FTIR) has been employed in order to find out whether or not the protein secondary structure changes after the incubation of its solution either near the apex of a pyramid or in the center of its base. Using AFM, we have demonstrated that the incubation of the protein solution either in the vicinity of the pyramid’s apex or in the center of its base influences the physicochemical properties of the protein macromolecules. Namely, the incubation of the HRP solution in the vicinity of the top of the pyramidal structure has been shown to lead to an increase in the efficiency of the HRP adsorption onto mica. Moreover, after the incubation of the HRP solution either near the top of the pyramid or in the center of its base, the HRP macromolecules adsorb onto the mica surface predominantly in monomeric form. At that, the enzymatic activity of HRP does not change. The results of our present study are useful to be taken into account in the development of novel biosensor devices (including those for the diagnosis of cancer in humans), in which pyramidal structures are employed as sensor, noise suppression or construction elements.
Collapse
Affiliation(s)
- Yuri D Ivanov
- Institute of Biomedical Chemistry, Pogodinskaya str., 10, Moscow, 119121, Russia. .,Joint Institute for High Temperatures of the Russian Academy of Sciences, Izhorskaya st. 13 Bd.2, Moscow, 125412, Russia.
| | - Tatyana O Pleshakova
- Institute of Biomedical Chemistry, Pogodinskaya str., 10, Moscow, 119121, Russia
| | - Ivan D Shumov
- Institute of Biomedical Chemistry, Pogodinskaya str., 10, Moscow, 119121, Russia
| | - Andrey F Kozlov
- Institute of Biomedical Chemistry, Pogodinskaya str., 10, Moscow, 119121, Russia
| | - Irina A Ivanova
- Institute of Biomedical Chemistry, Pogodinskaya str., 10, Moscow, 119121, Russia
| | - Anastasia A Valueva
- Institute of Biomedical Chemistry, Pogodinskaya str., 10, Moscow, 119121, Russia
| | - Maria O Ershova
- Institute of Biomedical Chemistry, Pogodinskaya str., 10, Moscow, 119121, Russia
| | - Vadim Yu Tatur
- Foundation of Perspective Technologies and Novations, Moscow, 115682, Russia
| | - Igor N Stepanov
- Foundation of Perspective Technologies and Novations, Moscow, 115682, Russia
| | | | - Vadim S Ziborov
- Institute of Biomedical Chemistry, Pogodinskaya str., 10, Moscow, 119121, Russia.,Joint Institute for High Temperatures of the Russian Academy of Sciences, Izhorskaya st. 13 Bd.2, Moscow, 125412, Russia
| |
Collapse
|
22
|
Malsagova KA, Pleshakova TO, Kozlov AF, Galiullin RA, Popov VP, Tikhonenko FV, Glukhov AV, Ziborov VS, Shumov ID, Petrov OF, Generalov VM, Cheremiskina AA, Durumanov AG, Agafonov AP, Gavrilova EV, Maksyutov RA, Safatov AS, Nikitaev VG, Pronichev AN, Konev VA, Archakov AI, Ivanov YD. Detection of Influenza Virus Using a SOI-Nanoribbon Chip, Based on an N-Type Field-Effect Transistor. Biosensors (Basel) 2021; 11:bios11040119. [PMID: 33921281 PMCID: PMC8069153 DOI: 10.3390/bios11040119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/26/2021] [Accepted: 04/07/2021] [Indexed: 02/05/2023]
Abstract
The detection of influenza A virions with a nanoribbon detector (NR detector) has been demonstrated. Chips for the detector have been fabricated based on silicon-on-insulator nanoribbon structures (SOI nanoribbon chip), using a complementary metal-oxide-semiconductor (CMOS)-compatible technology—by means of gas-phase etching and standard optical photolithography. The surface of the SOI nanoribbon chip contains a matrix of 10 nanoribbon (NR) sensor elements. SOI nanoribbon chips of n-type conductance have been used for this study. For biospecific detection of target particles, antibodies against influenza virus have been covalently immobilized onto NRs. Influenza A virus detection was performed by real-time registration of the source-drain current through the NRs. The detection of the target viral particles was carried out in buffer solutions at the target particles concentration within the range from 107 to 103 viral particles per milliliter (VP/mL). The lowest detectable concentration of the target viral particles was 6 × 10−16 M (corresponding to 104 VP/mL). The use of solutions containing ~109 to 1010 VP/mL resulted in saturation of the sensor surface with the target virions. In the saturation mode, detection was impossible.
Collapse
Affiliation(s)
- Kristina A. Malsagova
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (A.F.K.); (R.A.G.); (V.S.Z.); (I.D.S.); (A.I.A.); (Y.D.I.)
- Correspondence: ; Tel.: +7-499-246-3761
| | - Tatyana O. Pleshakova
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (A.F.K.); (R.A.G.); (V.S.Z.); (I.D.S.); (A.I.A.); (Y.D.I.)
| | - Andrey F. Kozlov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (A.F.K.); (R.A.G.); (V.S.Z.); (I.D.S.); (A.I.A.); (Y.D.I.)
| | - Rafael A. Galiullin
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (A.F.K.); (R.A.G.); (V.S.Z.); (I.D.S.); (A.I.A.); (Y.D.I.)
| | - Vladimir P. Popov
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (V.P.P.); (F.V.T.)
| | - Fedor V. Tikhonenko
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (V.P.P.); (F.V.T.)
| | - Alexander V. Glukhov
- JSC Novosibirsk Plant of Semiconductor Devices with OKB, 630082 Novosibirsk, Russia;
| | - Vadim S. Ziborov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (A.F.K.); (R.A.G.); (V.S.Z.); (I.D.S.); (A.I.A.); (Y.D.I.)
- Joint Institute for High Temperatures of Russian Academy of Sciences, 125412 Moscow, Russia;
| | - Ivan D. Shumov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (A.F.K.); (R.A.G.); (V.S.Z.); (I.D.S.); (A.I.A.); (Y.D.I.)
| | - Oleg F. Petrov
- Joint Institute for High Temperatures of Russian Academy of Sciences, 125412 Moscow, Russia;
| | - Vladimir M. Generalov
- Federal Budgetary Research Institution—State Research Center of Virology and Biotechnology VECTOR, Federal Service for Surveillance on Consumer Rights Protection and Human Well-Being, 630559 Novosibirsk Region, Koltsovo, Russia; (V.M.G.); (A.A.C.); (A.G.D.); (A.P.A.); (E.V.G.); (R.A.M.); (A.S.S.)
| | - Anastasia A. Cheremiskina
- Federal Budgetary Research Institution—State Research Center of Virology and Biotechnology VECTOR, Federal Service for Surveillance on Consumer Rights Protection and Human Well-Being, 630559 Novosibirsk Region, Koltsovo, Russia; (V.M.G.); (A.A.C.); (A.G.D.); (A.P.A.); (E.V.G.); (R.A.M.); (A.S.S.)
| | - Alexander G. Durumanov
- Federal Budgetary Research Institution—State Research Center of Virology and Biotechnology VECTOR, Federal Service for Surveillance on Consumer Rights Protection and Human Well-Being, 630559 Novosibirsk Region, Koltsovo, Russia; (V.M.G.); (A.A.C.); (A.G.D.); (A.P.A.); (E.V.G.); (R.A.M.); (A.S.S.)
| | - Alexander P. Agafonov
- Federal Budgetary Research Institution—State Research Center of Virology and Biotechnology VECTOR, Federal Service for Surveillance on Consumer Rights Protection and Human Well-Being, 630559 Novosibirsk Region, Koltsovo, Russia; (V.M.G.); (A.A.C.); (A.G.D.); (A.P.A.); (E.V.G.); (R.A.M.); (A.S.S.)
| | - Elena V. Gavrilova
- Federal Budgetary Research Institution—State Research Center of Virology and Biotechnology VECTOR, Federal Service for Surveillance on Consumer Rights Protection and Human Well-Being, 630559 Novosibirsk Region, Koltsovo, Russia; (V.M.G.); (A.A.C.); (A.G.D.); (A.P.A.); (E.V.G.); (R.A.M.); (A.S.S.)
| | - Rinat A. Maksyutov
- Federal Budgetary Research Institution—State Research Center of Virology and Biotechnology VECTOR, Federal Service for Surveillance on Consumer Rights Protection and Human Well-Being, 630559 Novosibirsk Region, Koltsovo, Russia; (V.M.G.); (A.A.C.); (A.G.D.); (A.P.A.); (E.V.G.); (R.A.M.); (A.S.S.)
| | - Alexander S. Safatov
- Federal Budgetary Research Institution—State Research Center of Virology and Biotechnology VECTOR, Federal Service for Surveillance on Consumer Rights Protection and Human Well-Being, 630559 Novosibirsk Region, Koltsovo, Russia; (V.M.G.); (A.A.C.); (A.G.D.); (A.P.A.); (E.V.G.); (R.A.M.); (A.S.S.)
| | - Valentin G. Nikitaev
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 115409 Moscow, Russia; (V.G.N.); (A.N.P.)
| | - Alexander N. Pronichev
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 115409 Moscow, Russia; (V.G.N.); (A.N.P.)
| | - Vladimir A. Konev
- Department of Infectious Diseases in Children, Faculty of Pediatrics, Pirogov Russian National Research Medical University, 117997 Moscow, Russia;
| | - Alexander I. Archakov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (A.F.K.); (R.A.G.); (V.S.Z.); (I.D.S.); (A.I.A.); (Y.D.I.)
| | - Yuri D. Ivanov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (A.F.K.); (R.A.G.); (V.S.Z.); (I.D.S.); (A.I.A.); (Y.D.I.)
| |
Collapse
|
23
|
Malsagova KA, Popov VP, Kupriyanov IN, Pleshakova TO, Galiullin RA, Kozlov AF, Shumov ID, Larionov DI, Tikhonenko FV, Kapustina SI, Ziborov VS, Petrov OF, Gadzhieva OA, Bashiryan BA, Shimansky VN, Archakov AI, Ivanov YD. Raman Spectroscopy-Based Quality Control of "Silicon-On-Insulator" Nanowire Chips for the Detection of Brain Cancer-Associated MicroRNA in Plasma. Sensors (Basel) 2021; 21:1333. [PMID: 33668578 PMCID: PMC7918486 DOI: 10.3390/s21041333] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/09/2021] [Accepted: 02/11/2021] [Indexed: 12/21/2022]
Abstract
Application of micro-Raman spectroscopy for the monitoring of quality of nanowire sensor chips fabrication has been demonstrated. Nanowire chips have been fabricated on the basis of «silicon-on-insulator» (SOI) structures (SOI-NW chips). The fabrication of SOI-NW chips was performed by optical litography with gas-phase etching. The so-fabricated SOI-NW chips are intended for highly sensitive detection of brain cancer biomarkers in humans. In our present study, two series of experiments have been conducted. In the first experimental series, detection of a synthetic DNA oligonucleotide (oDNA) analogue of brain cancer-associated microRNA miRNA-363 in purified buffer solution has been performed in order to demonstrate the high detection sensitivity. The second experimental series has been performed in order to reveal miRNA-363 itself in real human plasma samples. To provide detection biospecificity, the SOI-NW chip surface was modified by covalent immobilization of probe oligonucleotides (oDNA probes) complementary to the target biomolecules. Using the SOI-NW sensor chips proposed herein, the concentration detection limit of the target biomolecules at the level of 3.3 × 10-17 M has been demonstrated. Thus, the approach employing the SOI-NW chips proposed herein represents an attractive tool in biomedical practice, aimed at the early revelation of oncological diseases in humans.
Collapse
Affiliation(s)
- Kristina A. Malsagova
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (D.I.L.); (S.I.K.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Vladimir P. Popov
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (V.P.P.); (F.V.T.)
| | - Igor N. Kupriyanov
- Sobolev Institute of Geology and Mineralogy, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia;
| | - Tatyana O. Pleshakova
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (D.I.L.); (S.I.K.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Rafael A. Galiullin
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (D.I.L.); (S.I.K.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Andrey F. Kozlov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (D.I.L.); (S.I.K.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Ivan D. Shumov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (D.I.L.); (S.I.K.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Dmitry I. Larionov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (D.I.L.); (S.I.K.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Fedor V. Tikhonenko
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (V.P.P.); (F.V.T.)
| | - Svetlana I. Kapustina
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (D.I.L.); (S.I.K.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Vadim S. Ziborov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (D.I.L.); (S.I.K.); (V.S.Z.); (A.I.A.); (Y.D.I.)
- Joint Institute for High Temperatures of Russian Academy of Sciences, 125412 Moscow, Russia;
| | - Oleg F. Petrov
- Joint Institute for High Temperatures of Russian Academy of Sciences, 125412 Moscow, Russia;
| | - Olga A. Gadzhieva
- Federal State Autonomous Institution “N. N. Burdenko National Medical Research Center of Neurosurgery” of the Ministry of Health of the Russian Federation, 125047 Moscow, Russia; (O.A.G.); (B.A.B.); (V.N.S.)
| | - Boris A. Bashiryan
- Federal State Autonomous Institution “N. N. Burdenko National Medical Research Center of Neurosurgery” of the Ministry of Health of the Russian Federation, 125047 Moscow, Russia; (O.A.G.); (B.A.B.); (V.N.S.)
| | - Vadim N. Shimansky
- Federal State Autonomous Institution “N. N. Burdenko National Medical Research Center of Neurosurgery” of the Ministry of Health of the Russian Federation, 125047 Moscow, Russia; (O.A.G.); (B.A.B.); (V.N.S.)
| | - Alexander I. Archakov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (D.I.L.); (S.I.K.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Yuri D. Ivanov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (D.I.L.); (S.I.K.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| |
Collapse
|
24
|
Malsagova KA, Pleshakova TO, Popov VP, Kupriyanov IN, Galiullin RA, Kozlov AF, Shumov ID, Kaysheva AL, Tikhonenko FV, Archakov AI, Ivanov YD. Optical Monitoring of the Production Quality of Si-Nanoribbon Chips Intended for the Detection of ASD-Associated Oligonucleotides. Micromachines (Basel) 2021; 12:mi12020147. [PMID: 33546438 PMCID: PMC7913754 DOI: 10.3390/mi12020147] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 01/25/2021] [Accepted: 01/29/2021] [Indexed: 02/07/2023]
Abstract
Gas-phase etching and optical lithography were employed for the fabrication of a silicon nanoribbon chip (Si-NR chip). The quality of the so-fabricated silicon nanoribbons (Si-NRs) was monitored by optical Raman scattering spectroscopy. It was demonstrated that the structures of the Si-NRs were virtually defect-free, meaning they could be used for highly sensitive detection of biological macromolecules. The Si-NR chips were then used for the highly sensitive nanoelectronics detection of DNA oligonucleotides (oDNAs), which represent synthetic analogs of 106a-5p microRNA (miR-106a-5p), associated with the development of autism spectrum disorders in children. The specificity of the analysis was attained by the sensitization of the Si-NR chip sur-face by covalent immobilization of oDNA probes, whose nucleotide sequence was complementary to the known sequence of miR-106a-5p. The use of the Si-NR chip was demonstrated to al-low for the rapid label-free real-time detection of oDNA at ultra-low (~10−17 M) concentrations.
Collapse
Affiliation(s)
- Kristina A. Malsagova
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (A.L.K.); (A.I.A.); (Y.D.I.)
- Correspondence: ; Tel.: +7-499-246-3761
| | - Tatyana O. Pleshakova
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (A.L.K.); (A.I.A.); (Y.D.I.)
| | - Vladimir P. Popov
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of Russian Academy of Sciences, Laboratory of Silicon Material Science, 630090 Novosibirsk, Russia; (V.P.P.); (F.V.T.)
| | - Igor N. Kupriyanov
- Sobolev Institute of Geology and Mineralogy, Siberian Branch of Russian Academy of Sciences, Laboratory of Experimental Mineralogy and Crystallogenesis, 630090 Novosibirsk, Russia;
| | - Rafael A. Galiullin
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (A.L.K.); (A.I.A.); (Y.D.I.)
| | - Andrey F. Kozlov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (A.L.K.); (A.I.A.); (Y.D.I.)
| | - Ivan D. Shumov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (A.L.K.); (A.I.A.); (Y.D.I.)
| | - Anna L. Kaysheva
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (A.L.K.); (A.I.A.); (Y.D.I.)
| | - Fedor V. Tikhonenko
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of Russian Academy of Sciences, Laboratory of Silicon Material Science, 630090 Novosibirsk, Russia; (V.P.P.); (F.V.T.)
| | - Alexander I. Archakov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (A.L.K.); (A.I.A.); (Y.D.I.)
| | - Yuri D. Ivanov
- Laboratory of Nanobiotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (A.L.K.); (A.I.A.); (Y.D.I.)
| |
Collapse
|
25
|
Ivanov YD, Pleshakova TO, Shumov ID, Kozlov AF, Valueva AA, Ivanova IA, Ershova MO, Larionov DI, Repnikov VV, Ivanova ND, Tatur VY, Stepanov IN, Ziborov VS. AFM and FTIR Investigation of the Effect of Water Flow on Horseradish Peroxidase. Molecules 2021; 26:E306. [PMID: 33435278 PMCID: PMC7826892 DOI: 10.3390/molecules26020306] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 11/17/2022] Open
Abstract
Atomic force microscopy (AFM)-based fishing is a promising method for the detection of low-abundant proteins. This method is based on the capturing of the target proteins from the analyzed solution onto a solid substrate, with subsequent counting of the captured protein molecules on the substrate surface by AFM. Protein adsorption onto the substrate surface represents one of the key factors determining the capturing efficiency. Accordingly, studying the factors influencing the protein adsorbability onto the substrate surface represents an actual direction in biomedical research. Herein, the influence of water motion in a flow-based system on the protein adsorbability and on its enzymatic activity has been studied with an example of horseradish peroxidase (HRP) enzyme by AFM, attenuated total reflection Fourier-transform infrared spectroscopy (ATR-FTIR) and conventional spectrophotometry. In the experiments, HRP solution was incubated in a setup modeling the flow section of a biosensor communication. The measuring cell with the protein solution was placed near a coiled silicone pipe, through which water was pumped. The adsorbability of the protein onto the surface of the mica substrate has been studied by AFM. It has been demonstrated that incubation of the HRP solution near the coiled silicone pipe with flowing water leads to an increase in its adsorbability onto mica. This is accompanied by a change in the enzyme's secondary structure, as has been revealed by ATR-FTIR. At the same time, its enzymatic activity remains unchanged. The results reported herein can be useful in the development of models describing the influence of liquid flow on the properties of enzymes and other proteins. The latter is particularly important for the development of biosensors for biomedical applications-particularly for serological analysis, which is intended for the early diagnosis of various types of cancer and infectious diseases. Our results should also be taken into account in studies of the effects of protein aggregation on hemodynamics, which plays a key role in human body functioning.
Collapse
Affiliation(s)
- Yuri D. Ivanov
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (D.I.L.); (V.S.Z.)
| | - Tatyana O. Pleshakova
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (D.I.L.); (V.S.Z.)
| | - Ivan D. Shumov
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (D.I.L.); (V.S.Z.)
| | - Andrey F. Kozlov
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (D.I.L.); (V.S.Z.)
| | - Anastasia A. Valueva
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (D.I.L.); (V.S.Z.)
| | - Irina A. Ivanova
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (D.I.L.); (V.S.Z.)
| | - Maria O. Ershova
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (D.I.L.); (V.S.Z.)
| | - Dmitry I. Larionov
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (D.I.L.); (V.S.Z.)
| | | | - Nina D. Ivanova
- Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow 109472, Russia;
| | - Vadim Yu. Tatur
- Foundation of Perspective Technologies and Novations, Moscow 115682, Russia; (V.Y.T.); (I.N.S.)
| | - Igor N. Stepanov
- Foundation of Perspective Technologies and Novations, Moscow 115682, Russia; (V.Y.T.); (I.N.S.)
| | - Vadim S. Ziborov
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (T.O.P.); (I.D.S.); (A.F.K.); (A.A.V.); (I.A.I.); (M.O.E.); (D.I.L.); (V.S.Z.)
- Joint Institute for High Temperatures of the Russian Academy of Sciences, Moscow 125412, Russia
| |
Collapse
|
26
|
Malsagova KA, Pleshakova TO, Galiullin RA, Kozlov AF, Shumov ID, Popov VP, Tikhonenko FV, Glukhov AV, Ziborov VS, Petrov OF, Fortov VE, Archakov AI, Ivanov YD. Highly Sensitive Detection of CA 125 Protein with the Use of an n-Type Nanowire Biosensor. Biosensors (Basel) 2020; 10:bios10120210. [PMID: 33353197 PMCID: PMC7766891 DOI: 10.3390/bios10120210] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/17/2020] [Accepted: 12/17/2020] [Indexed: 12/18/2022]
Abstract
The detection of CA 125 protein in a solution using a silicon-on-insulator (SOI)-nanowire biosensor with n-type chip has been experimentally demonstrated. The surface of nanowires was modified by covalent immobilization of antibodies against CA 125 in order to provide the biospecificity of the target protein detection. We have demonstrated that the biosensor signal, which results from the biospecific interaction between CA 125 and the covalently immobilized antibodies, increases with the increase in the protein concentration. At that, the minimum concentration, at which the target protein was detectable with the SOI-nanowire biosensor, amounted to 1.5 × 10−16 M.
Collapse
Affiliation(s)
- Kristina A. Malsagova
- Laboratory of nanotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (V.S.Z.); (A.I.A.); (Y.D.I.)
- Correspondence: ; Tel.: +7-499-246-3761
| | - Tatyana O. Pleshakova
- Laboratory of nanotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Rafael A. Galiullin
- Laboratory of nanotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Andrey F. Kozlov
- Laboratory of nanotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Ivan D. Shumov
- Laboratory of nanotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Vladimir P. Popov
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (V.P.P.); (F.V.T.)
| | - Fedor V. Tikhonenko
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (V.P.P.); (F.V.T.)
| | - Alexander V. Glukhov
- JSC Novosibirsk Plant of Semiconductor Devices with OKB, 630082 Novosibirsk, Russia;
| | - Vadim S. Ziborov
- Laboratory of nanotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (V.S.Z.); (A.I.A.); (Y.D.I.)
- Joint Institute for High Temperatures of Russian Academy of Sciences, 125412 Moscow, Russia; (O.F.P.); (V.E.F.)
| | - Oleg F. Petrov
- Joint Institute for High Temperatures of Russian Academy of Sciences, 125412 Moscow, Russia; (O.F.P.); (V.E.F.)
| | - Vladimir E. Fortov
- Joint Institute for High Temperatures of Russian Academy of Sciences, 125412 Moscow, Russia; (O.F.P.); (V.E.F.)
| | - Alexander I. Archakov
- Laboratory of nanotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| | - Yuri D. Ivanov
- Laboratory of nanotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (T.O.P.); (R.A.G.); (A.F.K.); (I.D.S.); (V.S.Z.); (A.I.A.); (Y.D.I.)
| |
Collapse
|
27
|
Ivanov YD, Pleshakova TO, Shumov ID, Kozlov AF, Ivanova IA, Valueva AA, Tatur VY, Smelov MV, Ivanova ND, Ziborov VS. AFM Imaging of Protein Aggregation in Studying the Impact of Knotted Electromagnetic Field on A Peroxidase. Sci Rep 2020; 10:9022. [PMID: 32488177 PMCID: PMC7265551 DOI: 10.1038/s41598-020-65888-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 05/12/2020] [Indexed: 11/09/2022] Open
Abstract
The phenomenon of knotted electromagnetic field (KEMF) is now actively studied, as such fields are characterized by a nontrivial topology. The research in this field is mainly aimed at technical applications - for instance, the development of efficient communication systems. Until present, however, the influence of KEMF on biological objects (including enzyme systems) was not considered. Herein, we have studied the influence of KEMF on the aggregation and enzymatic activity of a protein with the example of horseradish peroxidase (HRP). The test HRP solution was irradiated in KEMF (the radiation power density was 10-12 W/cm2 at 2.3 GHz frequency) for 40 min. After the irradiation, the aggregation of HRP was examined by atomic force microscopy (AFM) at the single-molecule level. The enzymatic activity was monitored by conventional spectrophotometry. It has been demonstrated that an increased aggregation of HRP, adsorbed on the AFM substrate surface, was observed after irradiation of the protein sample in KEMF with low (10-12 W/cm2) radiation power density; at the same time, the enzymatic activity remained unchanged. The results obtained herein can be used in the development of models describing the interaction of enzymes with electromagnetic field. The obtained data can also be of importance considering possible pathological factors that can take place upon the influence of KEMF on biological objects- for instance, changes in hemodynamics due to increased protein aggregation are possible; the functionality of protein complexes can also be affected by aggregation of their protein subunits. These effects should also be taken into account in the development of novel highly sensitive systems for human serological diagnostics of breast cancer, prostate cancer, brain cancer and other oncological pathologies, and for diagnostics of diseases in animals, and crops.
Collapse
Affiliation(s)
- Yuri D Ivanov
- Institute of Biomedical Chemistry, Pogodinskaya str., 10, Moscow, 119121, Russia.
| | - Tatyana O Pleshakova
- Institute of Biomedical Chemistry, Pogodinskaya str., 10, Moscow, 119121, Russia
| | - Ivan D Shumov
- Institute of Biomedical Chemistry, Pogodinskaya str., 10, Moscow, 119121, Russia
| | - Andrey F Kozlov
- Institute of Biomedical Chemistry, Pogodinskaya str., 10, Moscow, 119121, Russia
| | - Irina A Ivanova
- Institute of Biomedical Chemistry, Pogodinskaya str., 10, Moscow, 119121, Russia
| | - Anastasia A Valueva
- Institute of Biomedical Chemistry, Pogodinskaya str., 10, Moscow, 119121, Russia
| | - Vadim Yu Tatur
- Foundation of Perspective Technologies and Novations, Moscow, 115682, Russia
| | - Mikhail V Smelov
- Foundation of Perspective Technologies and Novations, Moscow, 115682, Russia
| | - Nina D Ivanova
- Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow, 109472, Russia
| | - Vadim S Ziborov
- Institute of Biomedical Chemistry, Pogodinskaya str., 10, Moscow, 119121, Russia.,Joint Institute for High Temperatures of the Russian Academy of Sciences, Moscow, 125412, Russia
| |
Collapse
|
28
|
Kaysheva AL, Stepanov AA, Kopylov AT, Butkova TV, Pleshakova T, Ryabtsev VV, Iourov IY, Vorsanova SG, Ivanov YD. Pilot data of serum proteins from children with autism spectrum disorders. Data Brief 2019; 27:104558. [PMID: 31673578 PMCID: PMC6817683 DOI: 10.1016/j.dib.2019.104558] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/03/2019] [Accepted: 07/05/2019] [Indexed: 11/29/2022] Open
Abstract
Protein profiles of 13 serum samples from children with autism spectrum disorders (ASD) and 11 serum samples from healthy volunteers was obtained using panoramic ultra-high resolution mass spectrometry. The analysis of measurements was performed using the proteomics search engine. We identified a group of 74 proteins which we term a "protein fingerprint" specific for serum samples collected from children with autism. Components of the protein fingerprint are involved in hemostasis maintenance including biological regulation, the response to stimulus, regulation of metabolism, and proteins of the immune system.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Svetlana G Vorsanova
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow, Russia
| | | |
Collapse
|
29
|
Archakov AI, Aseev AL, Bykov VA, Grigoriev AI, Govorun VM, Ilgisonis EV, Ivanov YD, Ivanov VT, Kiseleva OI, Kopylov AT, Lisitsa AV, Mazurenko SN, Makarov AA, Naryzhny SN, Pleshakova TO, Ponomarenko EA, Poverennaya EV, Pyatnitskii MA, Sagdeev RZ, Skryabin KG, Zgoda VG. Challenges of the Human Proteome Project: 10-Year Experience of the Russian Consortium. J Proteome Res 2019; 18:4206-4214. [PMID: 31599598 DOI: 10.1021/acs.jproteome.9b00358] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This manuscript collects all the efforts of the Russian Consortium, bottlenecks revealed in the course of the C-HPP realization, and ways of their overcoming. One of the main bottlenecks in the C-HPP is the insufficient sensitivity of proteomic technologies, hampering the detection of low- and ultralow-copy number proteins forming the "dark part" of the human proteome. In the frame of MP-Challenge, to increase proteome coverage we suggest an experimental workflow based on a combination of shotgun technology and selected reaction monitoring with two-dimensional alkaline fractionation. Further, to detect proteins that cannot be identified by such technologies, nanotechnologies such as combined atomic force microscopy with molecular fishing and/or nanowire detection may be useful. These technologies provide a powerful tool for single molecule analysis, by analogy with nanopore sequencing during genome analysis. To systematically analyze the functional features of some proteins (CP50 Challenge), we created a mathematical model that predicts the number of proteins differing in amino acid sequence: proteoforms. According to our data, we should expect about 100 000 different proteoforms in the liver tissue and a little more in the HepG2 cell line. The variety of proteins forming the whole human proteome significantly exceeds these results due to post-translational modifications (PTMs). As PTMs determine the functional specificity of the protein, we propose using a combination of gene-centric transcriptome-proteomic analysis with preliminary fractionation by two-dimensional electrophoresis to identify chemically modified proteoforms. Despite the complexity of the proposed solutions, such integrative approaches could be fruitful for MP50 and CP50 Challenges in the framework of the C-HPP.
Collapse
Affiliation(s)
| | | | | | | | - Vadim M Govorun
- Federal Research and Clinical Center of Physical-Chemical Medicine , Moscow 119435 , Russia
| | | | - Yuri D Ivanov
- Institute of Biomedical Chemistry , Moscow 119435 , Russia
| | - Vadim T Ivanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow 117997 , Russia
| | | | | | | | - Sergey N Mazurenko
- Joint Institute for Nuclear Research , Dubna, Moscow region 141980 , Russia
| | | | | | | | | | | | | | - Renad Z Sagdeev
- International Tomography Center , Novosibirsk 630090 , Russia
| | - Konstantin G Skryabin
- The Federal Research Centre "Fundamentals of Biotechnology" , Moscow 119071 , Russia
| | - Victor G Zgoda
- Institute of Biomedical Chemistry , Moscow 119435 , Russia
| |
Collapse
|
30
|
Pleshakova TO, Kaysheva AL, Shumov ID, Ziborov VS, Bayzyanova JM, Konev VA, Uchaikin VF, Archakov AI, Ivanov YD. Detection of Hepatitis C Virus Core Protein in Serum Using Aptamer-Functionalized AFM Chips. Micromachines (Basel) 2019; 10:E129. [PMID: 30781415 PMCID: PMC6413090 DOI: 10.3390/mi10020129] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/08/2019] [Accepted: 02/11/2019] [Indexed: 12/24/2022]
Abstract
In the present study, we demonstrate atomic force microscopy (AFM)-based detection of hepatitis C virus (HCV) particles in serum samples using a chip with aptamer-functionalized surface (apta-based AFM chip). The target particles, containing core antigen of HCV (HCVcoreAg protein), were biospecifically captured onto the chip surface from 1 mL of test solution containing 10 µL of serum collected from a hepatitis C patient. The registration of aptamer/antigen complexes on the chip surface was performed by AFM. The aptamers used in the present study were initially developed for therapeutic purposes; herein, these aptamers have been successfully utilized as probe molecules for HCVcoreAg detection in the presence of a complex protein matrix (human serum). The results obtained herein can be used for the development of detection systems that employ affine enrichment for protein detection.
Collapse
Affiliation(s)
| | | | - Ivan D Shumov
- Institute of Biomedical Chemistry, Moscow 119121, Russia.
| | - Vadim S Ziborov
- Institute of Biomedical Chemistry, Moscow 119121, Russia.
- Joint Institute for High Temperatures of Russian Academy of Sciences, Moscow 125412, Russia.
| | - Jana M Bayzyanova
- Pirogov Russian National Research Medical University (RNRMU), Moscow 117997, Russia.
| | - Vladimir A Konev
- Pirogov Russian National Research Medical University (RNRMU), Moscow 117997, Russia.
| | - Vasiliy F Uchaikin
- Pirogov Russian National Research Medical University (RNRMU), Moscow 117997, Russia.
| | | | - Yuri D Ivanov
- Institute of Biomedical Chemistry, Moscow 119121, Russia.
| |
Collapse
|
31
|
Malsagova KA, Pleshakova TO, Kozlov AF, Shumov ID, Ilnitskii MA, Miakonkikh AV, Popov VP, Rudenko KV, Glukhov AV, Kupriyanov IN, Ivanova ND, Rogozhin AE, Archakov AI, Ivanov YD. Micro-Raman Spectroscopy for Monitoring of Deposition Quality of High-k Stack Protective Layer onto Nanowire FET Chips for Highly Sensitive miRNA Detection. Biosensors (Basel) 2018; 8:bios8030072. [PMID: 30060476 PMCID: PMC6164057 DOI: 10.3390/bios8030072] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 07/23/2018] [Accepted: 07/25/2018] [Indexed: 12/18/2022]
Abstract
Application of micro-Raman spectroscopy for the monitoring of quality of high-k (h-k) dielectric protective layer deposition onto the surface of a nanowire (NW) chip has been demonstrated. A NW chip based on silicon-on-insulator (SOI) structures, protected with a layer of high-k dielectric ((h-k)-SOI-NW chip), has been employed for highly sensitive detection of microRNA (miRNA) associated with oncological diseases. The protective dielectric included a 2-nm-thick Al2O3 surface layer and a 8-nm-thick HfO2 layer, deposited onto a silicon SOI-NW chip. Such a chip had increased time stability upon operation in solution, as compared with an unprotected SOI-NW chip with native oxide. The (h-k)-SOI-NW biosensor has been employed for the detection of DNA oligonucleotide (oDNA), which is a synthetic analogue of miRNA-21 associated with oncological diseases. To provide biospecificity of the detection, the surface of (h-k)-SOI-NW chip was modified with oligonucleotide probe molecules (oDVA probes) complementary to the sequence of the target biomolecule. Concentration sensitivity of the (h-k)-SOI-NW biosensor at the level of DL~10−16 M has been demonstrated.
Collapse
Affiliation(s)
| | | | - Andrey F Kozlov
- Institute of Biomedical Chemistry (IBMC), Moscow 119121, Russia.
| | - Ivan D Shumov
- Institute of Biomedical Chemistry (IBMC), Moscow 119121, Russia.
| | - Mikhail A Ilnitskii
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.
| | - Andrew V Miakonkikh
- Institute of Physics and Technology of Russian Academy of Sciences, Moscow 117218, Russia.
| | - Vladimir P Popov
- Rzhanov Institute of Semiconductor Physics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.
| | - Konstantin V Rudenko
- Institute of Physics and Technology of Russian Academy of Sciences, Moscow 117218, Russia.
| | - Alexander V Glukhov
- Joint-Stock Company "Novosibirsk Plant of Semiconductor Devices & DC", Novosibirsk 630082, Russia.
| | - Igor N Kupriyanov
- Sobolev Institute of Geology and Mineralogy, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.
| | - Nina D Ivanova
- Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow 109472, Russia.
| | - Alexander E Rogozhin
- Institute of Physics and Technology of Russian Academy of Sciences, Moscow 117218, Russia.
| | | | - Yuri D Ivanov
- Institute of Biomedical Chemistry (IBMC), Moscow 119121, Russia.
| |
Collapse
|
32
|
Pleshakova TO, Bukharina NS, Archakov AI, Ivanov YD. Atomic Force Microscopy for Protein Detection and Their Physicoсhemical Characterization. Int J Mol Sci 2018; 19:E1142. [PMID: 29642632 PMCID: PMC5979402 DOI: 10.3390/ijms19041142] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 03/30/2018] [Accepted: 04/05/2018] [Indexed: 11/18/2022] Open
Abstract
This review is focused on the atomic force microscopy (AFM) capabilities to study the properties of protein biomolecules and to detect the proteins in solution. The possibilities of application of a wide range of measuring techniques and modes for visualization of proteins, determination of their stoichiometric characteristics and physicochemical properties, are analyzed. Particular attention is paid to the use of AFM as a molecular detector for detection of proteins in solutions at low concentrations, and also for determination of functional properties of single biomolecules, including the activity of individual molecules of enzymes. Prospects for the development of AFM in combination with other methods for studying biomacromolecules are discussed.
Collapse
Affiliation(s)
| | - Natalia S Bukharina
- Institute of Biomedical Chemistry, 10, Pogodinskaya St., 119121 Moscow, Russia.
| | | | - Yuri D Ivanov
- Institute of Biomedical Chemistry, 10, Pogodinskaya St., 119121 Moscow, Russia.
| |
Collapse
|
33
|
Ivanov YD, Kozlov AF, Galiullin RA, Kolesanova EF, Pleshakova TO. Spontaneous Charge Generation in Flowing Albumin Solutions at 35 °C and 38 °C. Biosensors (Basel) 2017; 7:E60. [PMID: 29232911 PMCID: PMC5746783 DOI: 10.3390/bios7040060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Revised: 12/01/2017] [Accepted: 12/04/2017] [Indexed: 11/17/2022]
Abstract
The time dependence of a charge accumulation in a 10-15 M albumin solution, flowing through a measuring cell of an analytical flow system injector, had a nonlinear character under certain conditions, within a human physiological temperature range. Sharp charge increases depended on albumin concentration. This effect must be taken into consideration when generating models that describe electrokinetic phenomena in flowing protein solutions and when developing analytical flow systems for the registration of biomolecules in low concentration ranges.
Collapse
Affiliation(s)
- Yuri D Ivanov
- Institute of Biomedical Chemistry, 119121 Moscow, Russia.
| | | | | | | | | |
Collapse
|
34
|
Pleshakova TO, Kaysheva AL, Bayzyanova JМ, Anashkina АS, Uchaikin VF, Ziborov VS, Konev VA, Archakov AI, Ivanov YD. The detection of hepatitis c virus core antigen using afm chips with immobolized aptamers. J Virol Methods 2017; 251:99-105. [PMID: 29042217 DOI: 10.1016/j.jviromet.2017.10.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 10/09/2017] [Accepted: 10/14/2017] [Indexed: 10/18/2022]
Abstract
In the present study, the possibility of hepatitis C virus core antigen (HCVcoreAg) detection in buffer solution, using atomic force microscope chip (AFM-chip) with immobilized aptamers, has been demonstrated. The target protein was detected in 1mL of solution at concentrations from 10-10М to 10-13М. The registration of aptamer/antigen complexes on the chip surface was carried out by atomic force microscopy (AFM). The further mass-spectrometric (MS) identification of AFM-registered objects on the chip surface allowed reliable identification of HCVcoreAg target protein in the complexes. Aptamers, which were designed for therapeutic purposes, have been shown to be effective in HCVcoreAg detection as probe molecules.
Collapse
Affiliation(s)
- T O Pleshakova
- Institute of Biomedical Chemistry, Pogodinskaya St. 10, Moscow, 119121, Russia
| | - A L Kaysheva
- Institute of Biomedical Chemistry, Pogodinskaya St. 10, Moscow, 119121, Russia.
| | - J М Bayzyanova
- Institute of Biomedical Chemistry, Pogodinskaya St. 10, Moscow, 119121, Russia
| | - А S Anashkina
- Institute of Biomedical Chemistry, Pogodinskaya St. 10, Moscow, 119121, Russia
| | - V F Uchaikin
- Institute of Biomedical Chemistry, Pogodinskaya St. 10, Moscow, 119121, Russia
| | - V S Ziborov
- Joint Institute for High Temperatures RAS, Izhorskaya St. 13/19, Moscow, 125412, Russia
| | - V A Konev
- Pirogov Russian National Research Medical University (RNRMU), Ostrovitianov str. 1, Moscow, 117997, Russia
| | - A I Archakov
- Institute of Biomedical Chemistry, Pogodinskaya St. 10, Moscow, 119121, Russia
| | - Y D Ivanov
- Institute of Biomedical Chemistry, Pogodinskaya St. 10, Moscow, 119121, Russia
| |
Collapse
|
35
|
Pleshakova TO, Malsagova KA, Kaysheva AL, Kopylov AT, Tatur VY, Ziborov VS, Kanashenko SL, Galiullin RA, Ivanov YD. Highly sensitive protein detection by biospecific AFM-based fishing with pulsed electrical stimulation. FEBS Open Bio 2017; 7:1186-1195. [PMID: 28781958 PMCID: PMC5537060 DOI: 10.1002/2211-5463.12253] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 05/25/2017] [Accepted: 05/31/2017] [Indexed: 12/31/2022] Open
Abstract
We report here the highly sensitive detection of protein in solution at concentrations from 10-15 to 10-18 m using the combination of atomic force microscopy (AFM) and mass spectrometry. Biospecific detection of biotinylated bovine serum albumin was carried out by fishing out the protein onto the surface of AFM chips with immobilized avidin, which determined the specificity of the analysis. Electrical stimulation was applied to enhance the fishing efficiency. A high sensitivity of detection was achieved by application of nanosecond electric pulses to highly oriented pyrolytic graphite placed under the AFM chip. A peristaltic pump-based flow system, which is widely used in routine bioanalytical assays, was employed throughout the analysis. These results hold promise for the development of highly sensitive protein detection methods using nanosensor devices.
Collapse
Affiliation(s)
| | | | | | | | - Vadim Yu. Tatur
- Foundation of Perspective Technologies and NovationsMoscowRussia
| | | | | | | | | |
Collapse
|
36
|
Ivanov YD, Kaysheva AL, Frantsuzov PA, Pleshakova TO, Krohin NV, Izotov AA, Shumov ID, Uchaikin VF, Konev VA, Ziborov VS, Archakov AI. Detection of hepatitis C virus core protein in serum by atomic force microscopy combined with mass spectrometry. Int J Nanomedicine 2015; 10:1597-608. [PMID: 25759582 PMCID: PMC4346358 DOI: 10.2147/ijn.s71776] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A method for detection and identification of core antigen of hepatitis C virus (HCVcoreAg)-containing particles in the serum was proposed, with due account taken of the interactions of proteotypic peptides with Na(+), K(+), and Cl(-) ions. The method is based on a combination of reversible biospecific atomic force microscopy (AFM)-fishing and mass spectrometry (MS). AFM-fishing enables concentration, detection, and counting of protein complexes captured on the AFM chip surface, with their subsequent MS identification. Biospecific AFM-fishing of HCVcoreAg-containing particles from serum samples was carried out using AFM chips with immobilized antibodies against HCVcoreAg (HCVcoreAgim). Formation of complexes between anti-HCVcoreAgim and HCVcoreAg-containing particles on the AFM chip surface during the fishing process was demonstrated. These complexes were registered and counted by AFM. Further MS analysis allowed reliable identification of HCVcoreAg within the complexes formed on the AFM chip surface. It was shown that MS data processing, with account taken of the interactions between HCVcoreAg peptides and Na(+), K(+) cations, and Cl(-) anions, allows an increase in the number of peptides identified.
Collapse
Affiliation(s)
| | - Anna L Kaysheva
- Institute of Biomedical Chemistry, Moscow, Russia
- PostgenTech Ltd, Moscow, Russia
| | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Ivanov YD, Pleshakova T, Malsagova K, Kozlov A, Kaysheva A, Kopylov A, Izotov A, Andreeva E, Kanashenko S, Usanov S, Archakov A. Highly sensitive protein detection by combination of atomic force microscopy fishing with charge generation and mass spectrometry analysis. FEBS J 2014; 281:4705-17. [PMID: 25145394 DOI: 10.1111/febs.13011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 07/10/2014] [Accepted: 08/19/2014] [Indexed: 11/26/2022]
Abstract
An approach combining atomic force microscopy (AFM) fishing and mass spectrometry (MS) analysis to detect proteins at ultra-low concentrations is proposed. Fishing out protein molecules onto a highly oriented pyrolytic graphite surface coated with polytetrafluoroethylene film was carried out with and without application of an external electric field. After that they were visualized by AFM and identified by MS. It was found that injection of solution leads to charge generation in the solution, and an electric potential within the measuring cell is induced. It was demonstrated that without an external electric field in the rapid injection input of diluted protein solution the fishing is efficient, as opposed to slow fluid input. The high sensitivity of this method was demonstrated by detection of human serum albumin and human cytochrome b5 in 10(-17) -10(-18) m water solutions. It was shown that an external negative voltage applied to highly oriented pyrolytic graphite hinders the protein fishing. The efficiency of fishing with an external positive voltage was similar to that obtained without applying any voltage.
Collapse
Affiliation(s)
- Yuri D Ivanov
- Institute of Biomedical Chemistry RAMS, Moscow, Russia
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Ivanov YD, Bukharina NS, Pleshakova TO, Frantsuzov PA, Andreeva EY, Kaysheva AL, Zgoda VG, Izotov AA, Pavlova TI, Ziborov VS, Radko SP, Moshkovskii SA, Archakov AI. Atomic force microscopy fishing and mass spectrometry identification of gp120 on immobilized aptamers. Int J Nanomedicine 2014; 9:4659-70. [PMID: 25336946 PMCID: PMC4200055 DOI: 10.2147/ijn.s66946] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Atomic force microscopy (AFM) was applied to carry out direct and label-free detection of gp120 human immunodeficiency virus type 1 envelope glycoprotein as a target protein. This approach was based on the AFM fishing of gp120 from the analyte solution using anti-gp120 aptamers immobilized on the AFM chip to count gp120/aptamer complexes that were formed on the chip surface. The comparison of image contrasts of fished gp120 against the background of immobilized aptamers and anti-gp120 antibodies on the AFM images was conducted. It was shown that an image contrast of the protein/aptamer complexes was two-fold higher than the contrast of the protein/antibody complexes. Mass spectrometry identification provided an additional confirmation of the target protein presence on the AFM chips after biospecific fishing to avoid any artifacts.
Collapse
Affiliation(s)
- Yuri D Ivanov
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Natalia S Bukharina
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Tatyana O Pleshakova
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Pavel A Frantsuzov
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Elena Yu Andreeva
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Anna L Kaysheva
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
- PostgenTech Ltd., Moscow, Russia
| | - Victor G Zgoda
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Alexander A Izotov
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Tatyana I Pavlova
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Vadim S Ziborov
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Sergey P Radko
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Sergei A Moshkovskii
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Alexander I Archakov
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| |
Collapse
|
39
|
Ivanov YD, Pleshakova TO, Kozlov AF, Malsagova KA, Krohin NV, Shumyantseva VV, Shumov ID, Popov VP, Naumova OV, Fomin BI, Nasimov DA, Aseev AL, Archakov AI. SOI nanowire for the high-sensitive detection of HBsAg and α-fetoprotein. Lab Chip 2012; 12:5104-5111. [PMID: 23090136 DOI: 10.1039/c2lc40555e] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Silicon-on-isolator-nanowires (SOI-NWs) were used for the label-free, real-time biospecific detection of the hepatitis B marker HBsAg and cancer marker α-fetoprotein (AFP). Specific protein-protein recognition was carried out using individual NWs that were functionalized with antibodies. To solve the problem of non-specific binding of target protein molecules to the sensor element the use of a reference NW with immobilized antibodies against non-target proteins was proposed. Using individual SOI-NW surface functionalization allowed the fabrication of a NW array, containing working NWs and reference NWs within one chip. It was shown that this approach allows us to reach a detection limit up to 10(-14) and 10(-15) M for HBsAg and AFP, respectively. Our investigations also allowed us to reveal the influence of the charged state of the target protein molecules and antibodies in solutions with various pH values on the target protein detection limit. A high sensitivity NW-detector is of interest for the creation of diagnosticums for hepatitis B and for the early stages of cancer diseases.
Collapse
Affiliation(s)
- Yuri D Ivanov
- Institute of Biomedical Chemistry RAMS, Russia, Moscow
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Ivanov YD, Frantsuzov PA, Zöllner A, Medvedeva NV, Archakov AI, Reinle W, Bernhardt R. Atomic Force Microscopy Study of Protein-Protein Interactions in the Cytochrome CYP11A1 (P450scc)-Containing Steroid Hydroxylase System. Nanoscale Res Lett 2011; 6:54. [PMID: 27502676 PMCID: PMC3212078 DOI: 10.1007/s11671-010-9809-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Accepted: 09/15/2010] [Indexed: 05/31/2023]
Abstract
Atomic force microscopy (AFM) and photon correlation spectroscopy (PCS) were used for monitoring of the procedure for cytochrome CYP11A1 monomerization in solution without phospholipids. It was shown that the incubation of 100 μM CYP11A1 with 12% Emulgen 913 in 50 mM KP, pH 7.4, for 10 min at T = 22°C leads to dissociation of hemoprotein aggregates to monomers with the monomerization degree of (82 ± 4)%. Following the monomerization procedure, CYP11A1 remained functionally active. AFM was employed to detect and visualize the isolated proteins as well as complexes formed between the components of the cytochrome CYP11A1-dependent steroid hydroxylase system. Both Ad and AdR were present in solution as monomers. The typical heights of the monomeric AdR, Ad and CYP11A1 images were measured by AFM and were found to correspond to the sizes 1.6 ± 0.2 nm, 1.0 ± 0.2 nm and 1.8 ± 0.2 nm, respectively. The binary Ad/AdR and AdR/CYP11A1mon complexes with the heights 2.2 ± 0.2 nm and 2.8 ± 0.2 nm, respectively, were registered by use of AFM. The Ad/CYP11A1mon complex formation reaction was kinetically characterized based on optical biosensor data. In addition, the ternary AdR/Ad/CYP11A1 complexes with a typical height of 4 ± 1 nm were AFM registered.
Collapse
Affiliation(s)
- Y D Ivanov
- Institute of Biomedical Chemistry RAMS, Pogodinskaya st. 10, 119121, Moscow, Russia.
| | - P A Frantsuzov
- Institute of Biomedical Chemistry RAMS, Pogodinskaya st. 10, 119121, Moscow, Russia
| | - A Zöllner
- Saarland University, Saarbrücken, Germany
| | - N V Medvedeva
- Institute of Biomedical Chemistry RAMS, Pogodinskaya st. 10, 119121, Moscow, Russia
| | - A I Archakov
- Institute of Biomedical Chemistry RAMS, Pogodinskaya st. 10, 119121, Moscow, Russia
| | - W Reinle
- Saarland University, Saarbrücken, Germany
| | | |
Collapse
|
41
|
Ivanov YD, Kanaeva IP, Eldarov MA, Sklyabin KG, Lehnerer M, Schulze J, Hlavica P, Archakov AI. An optical biosensor study of the interaction parameters and role of hydrophobic tails of cytochrome P450 2B4, b5 and NADPH-flavoprotein in complex formation. IUBMB Life 2011; 42:731-7. [PMID: 19856290 DOI: 10.1080/15216549700203161] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The real-time interactions of membrane proteins - cytochrome P450 2B4, NADPH cytochrome P450 reductase and cytochrome b5 - were studied by use of an optical biosensor system. The association and dissociation rate constants for the individual complexes were measured and the affinities of the redox partners for each other were estimated. The association rate constants of these complexes were found to be close to the diffusion limit and their dissociation rate constants were in the order of 1s-1. A dominant role of the interaction of the membraneous hydrophobic fragments in the formation of productive electron transferring complexes between the proteins was demonstrated.
Collapse
Affiliation(s)
- Y D Ivanov
- Institute of Biomedical Chemistry RAMS, Moscow, Russia
| | | | | | | | | | | | | | | |
Collapse
|
42
|
Abstract
Progress in proteomic researches is largely determined by development and implementation of new methods for the revelation and identification of proteins in biological material in a wide concentration range (from 10(-3) M to single molecules). The most perspective approaches to address this problem involve (i) nanotechnological physicochemical procedures for the separation of multicomponent protein mixtures; among these of particular interest are biospecific nanotechnological procedures for selection of proteins from multicomponent protein mixtures with their subsequent concentration on solid support; (ii) identification and counting of single molecules by use of molecular detectors. The prototypes of biospecific nanotechnological procedures, based on the capture of ligand biomolecules by biomolecules of immobilized ligate and the concentration of the captured ligands on appropriate surfaces, are well known; these are affinity chromatography, magnetic biobeads technology, different biosensor methods, etc. Here, we review the most promising nanotechnological approaches for selection of proteins and kinetic characterization of their complexes based on these biospecific methods with subsequent MS/MS identification of proteins and protein complexes. Two major groups of methods for the analysis and identification of individual molecules and their complexes by use of molecular detectors will be reviewed: scanning probe microscopy (SPM) (including atomic-force microscopy) and cryomassdetector technology.
Collapse
|
43
|
Shumyantseva VV, Ivanov YD, Bistolas N, Scheller FW, Archakov AI, Wollenberger U. Direct electron transfer of cytochrome P450 2B4 at electrodes modified with nonionic detergent and colloidal clay nanoparticles. Anal Chem 2005; 76:6046-52. [PMID: 15481952 DOI: 10.1021/ac049927y] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A method for construction of biosensors with membranous cytochrome P450 isoenzymes was developed based on clay/detergent/protein mixed films. Thin films of sodium montmorillonite colloid with incorporated cytochrome P450 2B4 (CYP2B4) with nonionic detergent were prepared on glassy carbon electrodes. The modified electrodes were electrochemically characterized, and bioelectrocatalytic reactions were followed. CYP2B4 can be reduced fast on clay-modified glassy carbon electrodes in the presence of the nonionic detergent Tween 80. In anaerobic solutions, reversible oxidation and reduction is obtained with a formal potential between -0.292 and -0.305 V vs Ag/AgCl 1 M KCl depending on the preparation of the biosensor. In air-saturated solution, bioelectrocatalytic reduction currents can be obtained with the CYP2B4-modified electrode on addition of typical substrates such as aminopyrine and benzphetamine. This reaction was suppressed when methyrapone, an inhibitor of P450 reactions, was present. Measurement of product formation also indicates the bioelectrocatalysis by CYP2B4.
Collapse
Affiliation(s)
- Victoria V Shumyantseva
- Department of Analytical Biochemistry, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Golm, Germany
| | | | | | | | | | | |
Collapse
|
44
|
Kuznetsov VY, Ivanov YD, Archakov AI. Atomic force microscopy revelation of molecular complexes in the multiprotein cytochrome P450 2B4-containing system. Proteomics 2004; 4:2390-6. [PMID: 15274134 DOI: 10.1002/pmic.200300751] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The application of atomic force microscopy (AFM) to the identification and visualization of individual molecules and their complexes in a reconstituted monooxygenase P450 2B4 system without the phospholipid was demonstrated. The method employed in this study distinguishes the monomeric proteins from their binary complexes and, also, the binary from the ternary complexes. The AFM images of the full-length P450 2B4 system's constituent components - cytochrome P450 2B4 (2B4), NADPH-cytochrome P450 reductase and cytochrome b5 (b5), were obtained on highly-oriented pyrolitic graphite. The typical heights of the d-2B4, d-flavoprotein (Fp) and d-b5 molecules were measured and found to be 2.2 +/- 0.2, 2.3 +/- 0.2 and 1.8 +/- 0.1 nm, respectively. The measured heights of the binary d-Fp/d-2B4 and d-2B4/d-b5 complexes were estimated to be 3.4 +/- 0.2 and 2.8 +/- 0.2 nm, respectively. No formation of d-Fp/d-b5 complexes was registered. The ternary d-Fp/d-2B4/d-b5 complexes were visualized and their heights were found to be roughly equal to 4.3 +/- 0.3 nm and 6.2 +/- 0.3 nm.
Collapse
|
45
|
Abstract
Protein-protein interactions play a central role in numerous processes in the cell and are one of the main fields of functional proteomics. This review highlights the methods of bioinformatics and functional proteomics of protein-protein interaction investigation. The structures and properties of contact surfaces, forces involved in protein-protein interactions, kinetic and thermodynamic parameters of these reactions were considered. The properties of protein contact surfaces depend on their functions. The contact surfaces of permanent complexes resemble domain contacts or the protein core and it is reasonable to consider such complex formation as a continuation of protein folding. Characteristics of contact surfaces of temporary protein complexes share some similarities with active sites of enzymes. The contact surfaces of the temporary protein complexes have unique structure and properties and they are more conservative in comparison with active site of enzymes. So they represent prospective targets for a new generation of drugs. During the last decade, numerous investigations were undertaken to find or design small molecules that block protein dimerization or protein(peptide)-receptor interaction, or, on the contrary, to induce protein dimerization.
Collapse
|
46
|
Archakov AI, Ivanov YD. Optical biosensor and scanning probe microscopy studies of cytochrome P450 interactions with redox partners and phospholipid layers. Methods Enzymol 2003; 357:94-103. [PMID: 12424901 DOI: 10.1016/s0076-6879(02)57669-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Affiliation(s)
- Alexander I Archakov
- Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Moscow 119992, Russia
| | | |
Collapse
|
47
|
Dmitriev DA, Massino YS, Segal OL, Smirnova MB, Pavlova EV, Kolyaskina GI, Gurevich KG, Gnedenko OV, Ivanov YD, Archakov AI, Osipov AP, Dmitriev AD, Egorov AM. Analysis of bispecific monoclonal antibody binding to immobilized antigens using an optical biosensor. Biochemistry (Mosc) 2002; 67:1356-65. [PMID: 12600264 DOI: 10.1023/a:1021805909314] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The interaction between two different monoclonal antibodies (Mabs) and their corresponding bispecific antibodies (Babs) with immobilized antigens was investigated using an optical biosensor (IAsys). The analyzed panel of affinity-purified antibodies included two parental Mabs (one of which was specific to human IgG (hIgG), and another one to horseradish peroxidase (HRP)), as well as Babs derived thereof (anti-hIgG/HRP). Babs resulting from the fusion of parental hybridomas bear two antigen-binding sites toward two different antigens and thus may interact with immobilized antigen through only one antigen-binding site (monovalently). Using an IAsys biosensor this study shows that the bivalent binding of Mabs predominates over the monovalent binding with immobilized HRP, whereas anti-hIgG parental Mabs were bound monovalently to the immobilized hIgG. The observed equilibrium association constant (K(ass)) values obtained in our last work [1] by solid-phase radioimmunoassay are consistent with those constants obtained by IAsys. The K(ass) of anti-HRP Mabs was about 50 times higher than that of anti-HRP shoulder of Babs. The dissociation rate constant (k(diss)) for anti-HRP shoulder of Babs was 21 times higher than k(diss) for anti-HRP Mabs. The comparison of the kinetic parameters for bivalent anti-HRP Mabs and Babs derived from anti-Mb/HRP and anti-hIgG/HRP, allowed to calculate that 95% of bound anti-HRP Mabs are bivalently linked with immobilized HRP, whereas only 5% of bound anti-HRP Mabs are monovalently linked. In general, the data obtained indicate that Babs bearing an enzyme-binding site may not be efficiently used instead of traditional antibody-enzyme conjugates in the case of binding of bivalent Mabs.
Collapse
Affiliation(s)
- D A Dmitriev
- Department of Chemical Enzymology, School of Chemistry, Lomonosov Moscow State University, Moscow, 119992 Russia.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Kuznetsov VY, Ivanov YD, Bykov VA, Saunin SA, Fedorov IA, Lemeshko SV, Hoa HB, Archakov AI. Atomic force microscopy detection of molecular complexes in multiprotein P450cam containing monooxygenase system. Proteomics 2002; 2:1699-705. [PMID: 12469339 DOI: 10.1002/1615-9861(200212)2:12<1699::aid-prot1699>3.0.co;2-r] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The application of atomic force microscopy (AFM) technique in proteomic research, identification and visualization of individual molecules and molecular complexes within the P450cam containing monooxygenase system was demonstrated. The method distinguishes between the binary protein complexes and appropriate monomeric proteins and, also, between the binary and ternary complexes. The AFM images of the components of a cytochrome P450cam containing monooxygenase system - cytochrome P450cam (P450cam), putidaredoxin (Pd) and putidaredoxin reductase (PdR) - were obtained on a mica support. The molecules of P450cam, Pd and PdR were found to have typical heights of 2.6 +/- 0.3 nm, 2.0 +/- 0.3 and 2.8 +/- 0.3 nm, respectively. The measured heights of the binary Pd/PdR and P450cam/PdR complexes were 4.9 +/- 0.3 nm and 5.1 +/- 0.3 nm, respectively. The binary P450cam/Pd complexes were found to have a typical height of about (3.9 / 5.7 nm) and the ternary PdR/Pd/P450cam complexes, a typical height of about 9.1 +/- 0.3 nm.
Collapse
|
49
|
Ivanov YD, Kanaeva IP, Karuzina II, Usanov SA, Hui Bon Hoa G, Sligar SG, Archakov AI. Revelation of ternary complexes between redox partners in cytochrome P450-containing monooxygenase systems by the optical biosensor method. J Inorg Biochem 2001; 87:175-84. [PMID: 11744054 DOI: 10.1016/s0162-0134(01)00332-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Formation of binary and ternary complexes in the water-soluble cytochrome P450cam (P450cam)-containing as well as in the membrane P4502B4(2B4)- and the mixed P450scc-containing monooxygenase systems was investigated in real time by the 'resonant mirror' optical biosensor method. It was shown that the inter-protein electron transfer occurs not only during complex formation but also upon random collision--as was the case with the d-Fp/d-b5 pair (2B4 system). Binary complexes may be either facilitative to electron transfer (electron-transfer complexes) or prohibitive to it (non-productive complexes). Although the binary PdR/Pd and P450cam/Pd complex formation (within the P450cam-system) as well as the binary AdR/Ad and P450scc/Ad complex formation (within the P450scc-system) does occur, the lifetimes of these complexes formed are several orders of magnitude higher than the time required for realization of a complete hydroxylation cycle. At the same time, the lifetimes of the ternary PdR/Pd/P450cam and AdR/Ad/P450scc complexes are sufficient to permit the realization of a complete hydroxylation cycle in either of these systems. For the membrane P450 2B4 system, the formation of both the binary (Fp/2B4 and 2B4/b5) and ternary (Fp/2B4/b5) complexes was registered. The lifetimes of the binary Fp/2B4 and the ternary Fp/2B4/b5 complexes are sufficient for realization of a complete hydroxylation cycle in each of them.
Collapse
Affiliation(s)
- Y D Ivanov
- Institute of Biomedical Chemistry RAMS, Pogodinskaya St. 10, 119832, Moscow, Russia.
| | | | | | | | | | | | | |
Collapse
|
50
|
Ivanov YD, Kanaeva IP, Karuzina II, Archakov AI, Hoa GH, Sligar SG. Molecular recognition in the p450cam monooxygenase system: direct monitoring of protein-protein interactions by using optical biosensor. Arch Biochem Biophys 2001; 391:255-64. [PMID: 11437357 DOI: 10.1006/abbi.2001.2405] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A real-time optical biosensor study on the interactions between putidaredoxin reductase (PdR), putidaredoxin (Pd), and cytochrome P450cam (P450cam) within the P450cam system was conducted. The binary Pd/P450cam and Pd/PdR complexes were revealed and kinetically characterized. The dominant role of electrostatic interactions in formation of productive electron transfer complexes was demonstrated. It was found that Pd/P450cam complex formation and decay obeys biphasic kinetics in contrast to the monophasic one for complexes formed by other redox partners within the system. Evidence for PdR/P450cam complex formation was obtained. It was found that, in contrast to Pd, which binds only to its redox partners, PdR and P450cam were able to form PdR/PdR and P450cam/P450cam complexes. A ternary PdR/Pd/P450cam complex was also registered. Its lifetime was sufficient to permit up to 60 turnovers to occur. The binding of Pd to P450cam and to PdR within the ternary complex occurred at distinct sites, with Pd serving as a bridge between the two proteins.
Collapse
Affiliation(s)
- Y D Ivanov
- Institute of Biomedical Chemistry RAMS, Moscow, 119832, Russia.
| | | | | | | | | | | |
Collapse
|