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“Silicon-On-Insulator”-Based Nanosensor for the Revelation of MicroRNA Markers of Autism. Genes (Basel) 2022; 13:genes13020199. [PMID: 35205244 PMCID: PMC8872218 DOI: 10.3390/genes13020199] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/10/2022] [Accepted: 01/19/2022] [Indexed: 02/04/2023] Open
Abstract
MicroRNAs (miRNAs), which represent short (20 to 22 nt) non-coding RNAs, were found to play a direct role in the development of autism in children. Herein, a highly sensitive “silicon-on-insulator”-based nanosensor (SOI-NS) has been developed for the revelation of autism-associated miRNAs. This SOI-NS comprises an array of nanowire sensor structures fabricated by complementary metal–oxide–semiconductor (CMOS)-compatible technology, gas-phase etching, and nanolithography. In our experiments described herein, we demonstrate the revelation of ASD-associated miRNAs in human plasma with the SOI-NS, whose sensor elements were sensitized with oligonucleotide probes. In order to determine the concentration sensitivity of the SOI-NS, experiments on the detection of synthetic DNA analogues of autism-associated miRNAs in purified buffer were performed. The lower limit of miRNA detection attained in our experiments amounted to 10−17 M.
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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] [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).
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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.)
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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 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] [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.
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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.)
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Yee WLS, Drum CL. Increasing Complexity to Simplify Clinical Care: High Resolution Mass Spectrometry as an Enabler of AI Guided Clinical and Therapeutic Monitoring. ADVANCED THERAPEUTICS 2020. [DOI: 10.1002/adtp.201900163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Wei Loong Sherman Yee
- Yong Loo Lin School of MedicineDepartment of MedicineNational University of Singapore Singapore 119077 Singapore
- Cardiovascular Research Institute (CVRI)National University Health System Singapore 119228 Singapore
| | - Chester Lee Drum
- Yong Loo Lin School of MedicineDepartment of MedicineNational University of Singapore Singapore 119077 Singapore
- Cardiovascular Research Institute (CVRI)National University Health System Singapore 119228 Singapore
- Yong Loo Lin School of MedicineDepartment of BiochemistryNational University of Singapore Singapore 119077 Singapore
- The N.1 Institute for Health (N.1)National University of Singapore Singapore 119077 Singapore
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