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The Use of Excess Electric Charge for Highly Sensitive Protein Detection: Proof of Concept. ELECTRONICS 2022. [DOI: 10.3390/electronics11131955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In highly sensitive bioanalytical systems intended for the detection of protein biomarkers at low and ultra-low concentrations, the efficiency of capturing target biomolecules from the volume of the analyzed sample onto the sensitive surface of the detection system is a crucial factor. Herein, the application of excess electric charge for the enhancement of transport of target biomolecules towards the sensitive surface of a detection system is considered. In our experiments, we demonstrate that an uncompensated electric charge is induced in droplets of protein-free water owing to the separation of charge in a part of the Kelvin dropper either with or without the use of an external electric field. The distribution of an excess electric charge within a protein-free water droplet is calculated. It is proposed that the efficiency of protein capturing onto the sensitive surface correlates with the sign and the amount of charge induced per every single protein biomolecule. The effect described herein can allow one to make the protein capturing controllable, enhancing the protein capturing in the desired (though small) sensitive area of a detector. This can be very useful in novel systems intended for highly sensitive detection of proteins at ultra-low (≤10−15 M) concentrations.
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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 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] [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.
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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.)
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Nanoribbon-Based Electronic Detection of a Glioma-Associated Circular miRNA. BIOSENSORS-BASEL 2021; 11:bios11070237. [PMID: 34356707 PMCID: PMC8301916 DOI: 10.3390/bios11070237] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 12/29/2022]
Abstract
Nanoribbon chips, based on “silicon-on-insulator” structures (SOI-NR chips), have been fabricated. These SOI-NR chips, whose surface was sensitized with covalently immobilized oligonucleotide molecular probes (oDNA probes), have been employed for the nanoribbon biosensor-based detection of a circular ribonucleic acid (circRNA) molecular marker of glioma in humans. The nucleotide sequence of the oDNA probes was complimentary to the sequence of the target oDNA. The latter represents a synthetic analogue of a glioma marker—NFIX circular RNA. In this way, the detection of target oDNA molecules in a pure buffer has been performed. The lowest concentration of the target biomolecules, detectable in our experiments, was of the order of ~10−17 M. The SOI-NR sensor chips proposed herein have allowed us to reveal an elevated level of the NFIX circular RNA in the blood of a glioma patient.
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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] [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.
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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
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Covalent Protein Immobilization onto Muscovite Mica Surface with a Photocrosslinker. MINERALS 2020. [DOI: 10.3390/min10050464] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Muscovite mica with an amino silane-modified surface is commonly used as a substrate in atomic force microscopy (AFM) studies of biological macromolecules. Herein, the efficiency of two different protein immobilization strategies employing either (N-hydroxysuccinimide ester)-based crosslinker (DSP) or benzophenone-based photoactivatable crosslinker (SuccBB) has been compared using AFM and mass spectrometry analysis. Two proteins with different physicochemical properties—human serum albumin (HSA) and horseradish peroxidase enzyme protein (HRP)—have been used as model objects in the study. In the case of HRP, both crosslinkers exhibited high immobilization efficiency—as opposed to the case with HSA, when sufficient capturing efficiency has only been observed with SuccBB photocrosslinker. The results obtained herein can find their application in commonly employed bioanalytical systems and in the development of novel highly sensitive chip-based diagnostic platforms employing immobilized proteins. The obtained data can also be of interest for other research areas in medicine and biotechnology employing immobilized biomolecules.
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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 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] [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.
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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.
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Abstract
The method for the detection of 2,4-dinitrophenol (DNP) in solution is proposed. This method employs the sensors based on silicon nanowire field-effect transistors with protective layers of high-k dielectrics, whose surface is functionalized with an amino silane. Direct highly sensitive detection of DNP has been demonstrated, and the lowest detectable concentration of DNP was determined to be 10−14 M. Silicon-on-insulator nanowire (SOI-NW) sensors can well be employed for the rapid detection of a wide range of toxic and explosive compounds by selection of sensor surface modification techniques.
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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: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [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.
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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.
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Ivanov YD, Kozlov AF, Galiullin RA, Kolesanova EF, Pleshakova TO. Spontaneous Charge Generation in Flowing Albumin Solutions at 35 °C and 38 °C. BIOSENSORS 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] [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.
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Affiliation(s)
- Yuri D Ivanov
- Institute of Biomedical Chemistry, 119121 Moscow, Russia.
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