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Hussein Z, Nour MAY, Kozlova AV, Kolpashchikov DM, Komissarov AB, El-Deeb AA. DNAzyme Nanomachine with Fluorogenic Substrate Delivery Function: Advancing Sensitivity in Nucleic Acid Detection. Anal Chem 2023; 95:18667-18672. [PMID: 38079240 DOI: 10.1021/acs.analchem.3c04420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
We have developed a hook-equipped DNA nanomachine (HDNM) for the rapid detection of specific nucleic acid sequences without a preamplification step. HDNM efficiently unwinds RNA structures and improves the detection sensitivity. Compared to the hookless system, HDNM offers an 80-fold and 13-fold enhancement in DNA and RNA detection, respectively, reducing incubation time from 3 to 1 h.
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Affiliation(s)
- Zain Hussein
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova 9, Saint Petersburg, 191002, Russian Federation
- Advanced Engineering School, 423450 Almetyevsk, Russian Federation
| | - Moustapha A Y Nour
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova 9, Saint Petersburg, 191002, Russian Federation
- Advanced Engineering School, 423450 Almetyevsk, Russian Federation
| | - Anastasia V Kozlova
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova 9, Saint Petersburg, 191002, Russian Federation
- Advanced Engineering School, 423450 Almetyevsk, Russian Federation
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, 4000 Central Florida Blvd., Orlando, Florida 32816, United States
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32816, United States
- National Center for Forensic Science, University of Central Florida, Orlando, Florida 32816, United States
| | - Andrey B Komissarov
- Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russian Federation
| | - Ahmed A El-Deeb
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova 9, Saint Petersburg, 191002, Russian Federation
- Advanced Engineering School, 423450 Almetyevsk, Russian Federation
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Lavrentev FV, Shilovskikh VV, Alabusheva VS, Yurova VY, Nikitina AA, Ulasevich SA, Skorb EV. Diffusion-Limited Processes in Hydrogels with Chosen Applications from Drug Delivery to Electronic Components. Molecules 2023; 28:5931. [PMID: 37570901 PMCID: PMC10421015 DOI: 10.3390/molecules28155931] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/13/2023] Open
Abstract
Diffusion is one of the key nature processes which plays an important role in respiration, digestion, and nutrient transport in cells. In this regard, the present article aims to review various diffusion approaches used to fabricate different functional materials based on hydrogels, unique examples of materials that control diffusion. They have found applications in fields such as drug encapsulation and delivery, nutrient delivery in agriculture, developing materials for regenerative medicine, and creating stimuli-responsive materials in soft robotics and microrobotics. In addition, mechanisms of release and drug diffusion kinetics as key tools for material design are discussed.
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Affiliation(s)
- Filipp V. Lavrentev
- Infochemistry Scientific Center, ITMO University, 191002 Saint Petersburg, Russia; (V.S.A.); (V.Y.Y.); (A.A.N.); (S.A.U.)
| | - Vladimir V. Shilovskikh
- Laboratory of Polymer and Composite Materials “SmartTextiles”, IRC–X-ray Coherent Optics, Immanuel Kant Baltic Federal University, 236041 Kaliningrad, Russia;
| | - Varvara S. Alabusheva
- Infochemistry Scientific Center, ITMO University, 191002 Saint Petersburg, Russia; (V.S.A.); (V.Y.Y.); (A.A.N.); (S.A.U.)
| | - Veronika Yu. Yurova
- Infochemistry Scientific Center, ITMO University, 191002 Saint Petersburg, Russia; (V.S.A.); (V.Y.Y.); (A.A.N.); (S.A.U.)
| | - Anna A. Nikitina
- Infochemistry Scientific Center, ITMO University, 191002 Saint Petersburg, Russia; (V.S.A.); (V.Y.Y.); (A.A.N.); (S.A.U.)
| | - Sviatlana A. Ulasevich
- Infochemistry Scientific Center, ITMO University, 191002 Saint Petersburg, Russia; (V.S.A.); (V.Y.Y.); (A.A.N.); (S.A.U.)
| | - Ekaterina V. Skorb
- Infochemistry Scientific Center, ITMO University, 191002 Saint Petersburg, Russia; (V.S.A.); (V.Y.Y.); (A.A.N.); (S.A.U.)
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ElDeeb AA, Zablotskaya SS, Rubel MS, Nour MAY, Kozlovskaya LI, Shtro AA, Komissarov AB, Kolpashchikov DM. Toward a Home Test for COVID 19 Diagnosis: DNA Machine for Amplification-Free SARS-CoV-2 Detection in Clinical Samples. ChemMedChem 2022; 17:e202200382. [PMID: 36031581 PMCID: PMC9538286 DOI: 10.1002/cmdc.202200382] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/26/2022] [Indexed: 11/08/2022]
Abstract
Nucleic acid-based detection of RNA viruses requires annealing procedure to obtain RNA/probe or RNA/primer complexes for unwinding stable structure of folded viral RNA. In this study, we designed a protein enzymes-free nano-construction, names four-armed DNA machine (4DNM), that requires neither amplification stage nor high temperature annealing step for SARS-CoV-2 detection. It uses binary deoxyribozyme (BiDz) sensor incorporated in a DNA nanostructure equipped with total of four RNA-binding arms. Additional arms improved limit of detection at least 10 times. The sensor distinguished SARS-CoV-2 from other respiratory viruses and correctly identified five positive and six negative clinical samples verified by quantitative polymerase chain reaction (RT-qPCR). The strategy reported here can be used for detection of long natural RNA and can become a basis for a point-of-care or home diagnostic test.
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Affiliation(s)
- Ahmed A ElDeeb
- ITMO University: Nacional'nyj issledovatel'skij universitet ITMO, Chemistry and molecular biology, RUSSIAN FEDERATION
| | - Sofia S Zablotskaya
- ITMO University: Nacional'nyj issledovatel'skij universitet ITMO, Chemistry and Molecular Biology, RUSSIAN FEDERATION
| | - Maria S Rubel
- ITMO University: Nacional'nyj issledovatel'skij universitet ITMO, Chemistry and Molecular Biology, RUSSIAN FEDERATION
| | - Moustapha A Y Nour
- ITMO University: Nacional'nyj issledovatel'skij universitet ITMO, Chemistry and Molecular Biology, RUSSIAN FEDERATION
| | - Liubov I Kozlovskaya
- FSBSI Institute of Engineering Science Ural Branch of the Russian Academy of Sciences: FGBUN Institut masinovedenia Ural'skogo otdelenia Rossijskoj akademii nauk, Chemistry and Molecular Biology, RUSSIAN FEDERATION
| | - Anna A Shtro
- Research Institute of Influenza: Naucno-issledovatel'skij institut grippa, diagnostics, RUSSIAN FEDERATION
| | - Andrey B Komissarov
- Research Institute of Influenza: Naucno-issledovatel'skij institut grippa, diagnostics, RUSSIAN FEDERATION
| | - Dmitry M Kolpashchikov
- University of Central Florida, Chemistry, 4000 Central Florida Blvd, P.O. Box 162366, 32816-2366, Orlando, UNITED STATES
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Kovtunov EA, Shkodenko LA, Goncharova EA, Nedorezova DD, Sidorenko SV, Koshel EI, Kolpashchikov DM. Towards Point of Care Diagnostics: Visual Detection of Meningitis Pathogens Directly from Cerebrospinal Fluid. ChemistrySelect 2020. [DOI: 10.1002/slct.202003869] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Evgeny A. Kovtunov
- Laboratory of Molecular Robotics and Biosensor Materials Chemistry Department SCAMT Institute ITMO University 9 Lomonosova Str. Saint Petersburg 191002 Russian Federation
| | - Liubov A. Shkodenko
- Laboratory of Molecular Robotics and Biosensor Materials Chemistry Department SCAMT Institute ITMO University 9 Lomonosova Str. Saint Petersburg 191002 Russian Federation
| | - Ekaterina A. Goncharova
- Laboratory of Molecular Robotics and Biosensor Materials Chemistry Department SCAMT Institute ITMO University 9 Lomonosova Str. Saint Petersburg 191002 Russian Federation
- Saint-Petersburg Pasteur Institute Mira st.14, St. Petersburg 197101 Russian Federation
| | - Daria D. Nedorezova
- Laboratory of Molecular Robotics and Biosensor Materials Chemistry Department SCAMT Institute ITMO University 9 Lomonosova Str. Saint Petersburg 191002 Russian Federation
| | - Sergey V. Sidorenko
- Department of Medical Microbiology and Molecular Epidemiology Pediatric Research and Clinical Center for Infectious Diseases Saint Petersburg 197022 Russian Federation
- North Western State Medical University named after I.I. Mechnikov Kirochnaya Str. 41, St. Petersburg Russia 191015
| | - Elena I. Koshel
- Laboratory of Molecular Robotics and Biosensor Materials Chemistry Department SCAMT Institute ITMO University 9 Lomonosova Str. Saint Petersburg 191002 Russian Federation
| | - Dmitry M. Kolpashchikov
- Laboratory of Molecular Robotics and Biosensor Materials Chemistry Department SCAMT Institute ITMO University 9 Lomonosova Str. Saint Petersburg 191002 Russian Federation
- University of Central Florida Chemistry Department 4111 Libra Drive, Physical Sciences 255 Orlando FL USA 32816-2366
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Nanoparticles in Polyelectrolyte Multilayer Layer-by-Layer (LbL) Films and Capsules—Key Enabling Components of Hybrid Coatings. COATINGS 2020. [DOI: 10.3390/coatings10111131] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Originally regarded as auxiliary additives, nanoparticles have become important constituents of polyelectrolyte multilayers. They represent the key components to enhance mechanical properties, enable activation by laser light or ultrasound, construct anisotropic and multicompartment structures, and facilitate the development of novel sensors and movable particles. Here, we discuss an increasingly important role of inorganic nanoparticles in the layer-by-layer assembly—effectively leading to the construction of the so-called hybrid coatings. The principles of assembly are discussed together with the properties of nanoparticles and layer-by-layer polymeric assembly essential in building hybrid coatings. Applications and emerging trends in development of such novel materials are also identified.
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Ryzhkov NV, Andreeva DV, Skorb EV. Coupling pH-Regulated Multilayers with Inorganic Surfaces for Bionic Devices and Infochemistry. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:8543-8556. [PMID: 31018639 DOI: 10.1021/acs.langmuir.9b00633] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
This article summarizes more than 10 years of cooperation with Prof. Helmuth Möhwald. Here we describe how the research moved from light-regulated feedback sustainable systems and control biodevices to the current focus on infochemistry in aqueous solution. An important advanced characteristic of such materials and devices is the pH concentration gradient in aqueous solution. A major part of the article focuses on the use of localized illumination for proton generation as a reliable, minimal-reagent-consuming, stable light-promoted proton pump. The in situ scanning vibration electrode technique (SVET) and scanning ion-selective electrode technique (SIET) are efficient for the spatiotemporal evolution of ions on the surface. pH-sensitive polyelectrolyte (PEs) multilayers with different PE architectures are composed with a feedback loop for bionic devices. We show here that pH-regulated PE multilayers can change their properties-film thickness and stiffness, permeability, hydrophilicity, and/or fluorescence-in response to light or electrochemical or biological processes instead of classical acid/base titration.
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Affiliation(s)
| | - Daria V Andreeva
- Centre for Advanced 2D Materials and Graphene Research Centre , National University of Singapore , 117546 Singapore
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