1
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Zareie AR, Verma SC. Nucleolin Regulates the Expression of Kaposi's Sarcoma-Associated Herpesvirus' Latency-Associated Nuclear Antigen through G-Quadruplexes in the mRNA. Viruses 2023; 15:2438. [PMID: 38140679 PMCID: PMC10747643 DOI: 10.3390/v15122438] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) establishes life-long latent infection and is linked to several human malignancies. Latency-associated nuclear antigen (LANA) is highly expressed during latency, and is responsible for the replication and maintenance of the viral genome. The expression of LANA is regulated at transcriptional/translational levels through multiple mechanisms, including the secondary structures in the mRNA sequence. LANA mRNA has multiple G-quadruplexes (G4s) that are bound by multiple proteins to stabilize/destabilize these secondary structures for regulating LANA. In this manuscript, we demonstrate the role of Nucleolin (NCL) in regulating LANA expression through its interaction with G-quadruplexes of LANA mRNA. This interaction reduced LANA's protein expression through the sequestration of mRNA into the nucleus, demonstrated by the colocalization of G4-carrying mRNA with NCL. Furthermore, the downregulation of NCL, by way of a short hairpin, showed an increase in LANA translation following an alteration in the levels of LANA mRNA in the cytoplasm. Overall, the data presented in this manuscript showed that G-quadruplexes-mediated translational control could be regulated by NCL, which can be exploited for controlling KSHV latency.
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Affiliation(s)
| | - Subhash C. Verma
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, 1664 N Virginia Street, Reno, NV 89557, USA;
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2
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Jakab K, Melios N, Tsekenis G, Shaban A, Horváth V, Keresztes Z. Comparative Analysis of pH and Target-Induced Conformational Changes of an Oxytetracycline Aptamer in Solution Phase and Surface-Immobilized Form. Biomolecules 2023; 13:1363. [PMID: 37759762 PMCID: PMC10526194 DOI: 10.3390/biom13091363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
To date, numerous aptamer-based biosensing platforms have been developed for sensitive and selective monitoring of target analytes, relying on analyte-induced conformational changes in the aptamer for the quantification of the analyte and the conversion of the binding event into a measurable signal. Despite the impact of these conformational rearrangements on sensor performance, the influence of the environment on the structural conformations of aptamers has rarely been investigated, so the link between parameters directly influencing aptamer folding and the ability of the aptamer to bind to the target analyte remains elusive. Herein, the effect a number of variables have on an aptamer's 3D structure was examined, including the pH of the buffering medium, as well as the anchoring of the aptamer on a solid support, with the use of two label-free techniques. Circular dichroism spectroscopy was utilized to study the conformation of an aptamer in solution along with any changes induced to it by the environment (analyte binding, pH, composition and ionic strength of the buffer solution), while quartz crystal microbalance with dissipation monitoring was employed to investigate the surface-bound aptamer's behavior and performance. Analysis was performed on an aptamer against oxytetracycline, serving as a model system, representative of aptamers selected against small molecule analytes. The obtained results highlight the influence of the environment on the folding and thus analyte-binding capacity of an aptamer and emphasize the need to deploy appropriate surface functionalization protocols in sensor development as a means to minimize the steric obstructions and undesirable interactions of an aptamer with a surface onto which it is tethered.
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Affiliation(s)
- Kristóf Jakab
- Functional Interfaces Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117 Budapest, Hungary;
- Department of Inorganic and Analytical Chemistry, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, 1111 Budapest, Hungary;
| | - Nikitas Melios
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou Street, 115 27 Athens, Greece; (N.M.); (G.T.)
| | - George Tsekenis
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou Street, 115 27 Athens, Greece; (N.M.); (G.T.)
| | - Abdul Shaban
- Functional Interfaces Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117 Budapest, Hungary;
| | - Viola Horváth
- Department of Inorganic and Analytical Chemistry, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, 1111 Budapest, Hungary;
- ELKH-BME Computation Driven Chemistry Research Group, Műegyetem rkp. 3, 1111 Budapest, Hungary
| | - Zsófia Keresztes
- Functional Interfaces Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117 Budapest, Hungary;
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3
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Kukushkin V, Ambartsumyan O, Subekin A, Astrakhantseva A, Gushchin V, Nikonova A, Dorofeeva A, Zverev V, Keshek A, Meshcheryakova N, Zaborova O, Gambaryan A, Zavyalova E. Multiplex Lithographic SERS Aptasensor for Detection of Several Respiratory Viruses in One Pot. Int J Mol Sci 2023; 24:ijms24098081. [PMID: 37175786 PMCID: PMC10178974 DOI: 10.3390/ijms24098081] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
Rapid and reliable techniques for virus identification are required in light of recurring epidemics and pandemics throughout the world. Several techniques have been distributed for testing the flow of patients. Polymerase chain reaction with reverse transcription is a reliable and sensitive, though not rapid, tool. The antibody-based strip is a rapid, though not reliable, and sensitive tool. A set of alternative tools is being developed to meet all the needs of the customer. Surface-enhanced Raman spectroscopy (SERS) provides the possibility of single molecule detection taking several minutes. Here, a multiplex lithographic SERS aptasensor was developed aiming at the detection of several respiratory viruses in one pot within 17 min. The four labeled aptamers were anchored onto the metal surface of four SERS zones; the caught viruses affect the SERS signals of the labels, providing changes in the analytical signals. The sensor was able to decode mixes of SARS-CoV-2 (severe acute respiratory syndrome coronavirus two), influenza A virus, respiratory syncytial virus, and adenovirus within a single experiment through a one-stage recognition process.
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Affiliation(s)
- Vladimir Kukushkin
- Osipyan Institute of Solid State Physics, Russian Academy of Science, 142432 Chernogolovka, Russia
| | | | - Alexei Subekin
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Anna Astrakhantseva
- Osipyan Institute of Solid State Physics, Russian Academy of Science, 142432 Chernogolovka, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Vladimir Gushchin
- N. F. Gamaleya Federal Research Center for Epidemiology & Microbiology, 123098 Moscow, Russia
| | - Alexandra Nikonova
- Mechnikov Research Institute of Vaccines and Sera, 105064 Moscow, Russia
| | | | - Vitaly Zverev
- Mechnikov Research Institute of Vaccines and Sera, 105064 Moscow, Russia
| | - Anna Keshek
- Chemistry Department of Lomonosov, Moscow State University, 119991 Moscow, Russia
| | | | - Olga Zaborova
- Chemistry Department of Lomonosov, Moscow State University, 119991 Moscow, Russia
| | - Alexandra Gambaryan
- Chumakov Federal Scientific Center for Research, Development of Immune and Biological Products RAS, 108819 Moscow, Russia
| | - Elena Zavyalova
- Chemistry Department of Lomonosov, Moscow State University, 119991 Moscow, Russia
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4
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Kukushkin V, Kristavchuk O, Andreev E, Meshcheryakova N, Zaborova O, Gambaryan A, Nechaev A, Zavyalova E. Aptamer-coated track-etched membranes with a nanostructured silver layer for single virus detection in biological fluids. Front Bioeng Biotechnol 2023; 10:1076749. [PMID: 36704305 PMCID: PMC9871243 DOI: 10.3389/fbioe.2022.1076749] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/28/2022] [Indexed: 01/11/2023] Open
Abstract
Aptasensors based on surface-enhanced Raman spectroscopy (SERS) are of high interest due to the superior specificity and low limit of detection. It is possible to produce stable and cheap SERS-active substrates and portable equipment meeting the requirements of point-of-care devices. Here we combine the membrane filtration and SERS-active substrate in the one pot. This approach allows efficient adsorption of the viruses from the solution onto aptamer-covered silver nanoparticles. Specific determination of the viruses was provided by the aptamer to influenza A virus labeled with the Raman-active label. The SERS-signal from the label was decreased with a descending concentration of the target virus. Even several virus particles in the sample provided an increase in SERS-spectra intensity, requiring only a few minutes for the interaction between the aptamer and the virus. The limit of detection of the aptasensor was as low as 10 viral particles per mL (VP/mL) of influenza A virus or 2 VP/mL per probe. This value overcomes the limit of detection of PCR techniques (∼103 VP/mL). The proposed biosensor is very convenient for point-of-care applications.
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Affiliation(s)
| | | | | | | | | | - Alexandra Gambaryan
- Chumakov Federal Scientific Centre for Research and Development of Immune and Biological Products RAS, Moscow, Russia
| | | | - Elena Zavyalova
- Lomonosov Moscow State University, Moscow, Russia,*Correspondence: Elena Zavyalova,
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5
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Gautam V, Kumar R, Jain VK, Nagpal S. An overview of advancement in aptasensors for influenza detection. Expert Rev Mol Diagn 2022; 22:705-724. [PMID: 35994712 DOI: 10.1080/14737159.2022.2116276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION The platforms for early identification of infectious diseases such as influenza has seen a surge in recent years as delayed diagnosis of such infections can lead to dreadful effects causing large numbers of deaths. The time taken in detection of an infectious disease may vary from a few days to a few weeks depending upon the choice of the techniques. So, there is an urgent need for advanced methodologies for early diagnosis of the influenza. AREAS COVERED The emergence of "Aptasensor" synergistically with biosensors for diagnosis has opened a new era for sensitive, selective and early detection approaches. This review described various conventional as well as advanced methods based on artificial immunogenic nucleotide sequences complementing a part of the virus, i.e., aptamers based aptasensors for influenza diagnosis and the challenges faced in their commercialization. EXPERT OPINION Although numerous traditional methods are available for influenza detection but mostly associated with low sensitivity, specificity, high cost, trained personnel, and animals required for virus culture/ antibody raising as the major drawbacks. Aptamers can be manufactured invitro as 'chemical antibodies' at commercial level, no animal required. Following these advantages, aptamers can pave the way for an efficient diagnostic technique as compared to other existing conventional methods..
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Affiliation(s)
- Varsha Gautam
- Amity Institute for Advanced Research and Studies (Materials & Devices), Amity University, Noida India, India
| | - Ramesh Kumar
- Department of Biotechnology, Indira Gandhi University, Meerpur, India
| | - Vinod Kumar Jain
- Amity Institute for Advanced Research and Studies (Materials & Devices), Amity University, Noida India, India
| | - Suman Nagpal
- Department of Environmental sciences, Indira Gandhi University, Meerpur, India
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6
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Zhdanov G, Nyhrikova E, Meshcheryakova N, Kristavchuk O, Akhmetova A, Andreev E, Rudakova E, Gambaryan A, Yaminsky I, Aralov A, Kukushkin V, Zavyalova E. A Combination of Membrane Filtration and Raman-Active DNA Ligand Greatly Enhances Sensitivity of SERS-Based Aptasensors for Influenza A Virus. Front Chem 2022; 10:937180. [PMID: 35844641 PMCID: PMC9279936 DOI: 10.3389/fchem.2022.937180] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 05/25/2022] [Indexed: 01/20/2023] Open
Abstract
Biosensors combining the ultrahigh sensitivity of surface-enhanced Raman scattering (SERS) and the specificity of nucleic acid aptamers have recently drawn attention in the detection of respiratory viruses. The most sensitive SERS-based aptasensors allow determining as low as 104 virus particles per mL that is 100-fold lower than any antibody-based lateral flow tests but 10–100-times higher than a routine polymerase chain reaction with reversed transcription (RT-PCR). Sensitivity of RT-PCR has not been achieved in SERS-based aptasensors despite the usage of sophisticated SERS-active substrates. Here, we proposed a novel design of a SERS-based aptasensor with the limit of detection of just 103 particles per ml of the influenza A virus that approaches closely to RT-PCR sensitivity. The sensor utilizes silver nanoparticles with the simplest preparation instead of sophisticated SERS-active surfaces. The analytical signal is provided by a unique Raman-active dye that competes with the virus for the binding to the G-quadruplex core of the aptamer. The aptasensor functions even with aliquots of the biological fluids due to separation of the off-target molecules by pre-filtration through a polymeric membrane. The aptasensor detects influenza viruses in the range of 1·103–5·1010 virus particles per ml.
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Affiliation(s)
- Gleb Zhdanov
- Chemistry Department, Lomonosov Moscow State University, Moscow, Russia
| | | | | | | | - Assel Akhmetova
- Belozersky Research Institute of Physical Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Elena Rudakova
- Institute of Physiologically Active Compounds of Russian Academy of Science, Chernogolovka, Russia
| | - Alexandra Gambaryan
- Chumakov Federal Scientific Centre for Research and Development of Immune and Biological Products RAS, Moscow, Russia
| | - Igor Yaminsky
- Chemistry Department, Lomonosov Moscow State University, Moscow, Russia
- Physical Department, Lomonosov Moscow State University, Moscow, Russia
| | - Andrey Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir Kukushkin
- Institute of Solid State Physics, Russian Academy of Science, Chernogolovka, Russia
| | - Elena Zavyalova
- Chemistry Department, Lomonosov Moscow State University, Moscow, Russia
- Belozersky Research Institute of Physical Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- *Correspondence: Elena Zavyalova,
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7
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Poimanova EY, Shaposhnik PA, Anisimov DS, Zavyalova EG, Trul AA, Skorotetcky MS, Borshchev OV, Vinnitskiy DZ, Polinskaya MS, Krylov VB, Nifantiev NE, Agina EV, Ponomarenko SA. Biorecognition Layer Based On Biotin-Containing [1]Benzothieno[3,2- b][1]benzothiophene Derivative for Biosensing by Electrolyte-Gated Organic Field-Effect Transistors. ACS APPLIED MATERIALS & INTERFACES 2022; 14:16462-16476. [PMID: 35357127 DOI: 10.1021/acsami.1c24109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Requirements of speed and simplicity in testing stimulate the development of modern biosensors. Electrolyte-gated organic field-effect transistors (EGOFETs) are a promising platform for ultrasensitive, fast, and reliable detection of biological molecules for low-cost, point-of-care bioelectronic sensing. Biosensitivity of the EGOFET devices can be achieved by modification with receptors of one of the electronic active interfaces of the transistor gate or organic semiconductor surface. Functionalization of the latter gives the advantage in the creation of a planar architecture and compact devices for lab-on-chip design. Herein, we propose a universal, fast, and simple technique based on doctor blading and Langmuir-Schaefer methods for functionalization of the semiconducting surface of C8-BTBT-C8, allowing the fabrication of a large-scale biorecognition layer based on the novel functional derivative of BTBT-containing biotin fragments as a foundation for further biomodification. The fabricated devices are very efficient and operate stably in phosphate-buffered saline solution with high reproducibility of electrical properties in the EGOFET regime. The development of biorecognition properties of the proposed biolayer is based on the streptavidin-biotin interactions between the consecutive layers and can be used for a wide variety of receptors. As a proof-of-concept, we demonstrate the specific response of the BTBT-based biorecognition layer in EGOFETs to influenza A virus (H7N1 strain). The elaborated approach to biorecognition layer formation is appropriate but not limited to aptamer-based receptor molecules and can be further applied for fabricating several biosensors for various analytes on one substrate and paves the way for "electronic tongue" creation.
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Affiliation(s)
- Elena Yu Poimanova
- Enikolopov Institute of Synthetic Polymeric Materials of Russian Academy of Sciences, Profsoyuznaya Str. 70, 117393 Moscow, Russian Federation
| | - Polina A Shaposhnik
- Enikolopov Institute of Synthetic Polymeric Materials of Russian Academy of Sciences, Profsoyuznaya Str. 70, 117393 Moscow, Russian Federation
- Chemistry Department, Lomonosov Moscow State University, Leninskiye Gory 1/3, 119991 Moscow, Russian Federation
| | - Daniil S Anisimov
- Enikolopov Institute of Synthetic Polymeric Materials of Russian Academy of Sciences, Profsoyuznaya Str. 70, 117393 Moscow, Russian Federation
| | - Elena G Zavyalova
- Chemistry Department, Lomonosov Moscow State University, Leninskiye Gory 1/3, 119991 Moscow, Russian Federation
| | - Askold A Trul
- Enikolopov Institute of Synthetic Polymeric Materials of Russian Academy of Sciences, Profsoyuznaya Str. 70, 117393 Moscow, Russian Federation
| | - Maxim S Skorotetcky
- Enikolopov Institute of Synthetic Polymeric Materials of Russian Academy of Sciences, Profsoyuznaya Str. 70, 117393 Moscow, Russian Federation
| | - Oleg V Borshchev
- Enikolopov Institute of Synthetic Polymeric Materials of Russian Academy of Sciences, Profsoyuznaya Str. 70, 117393 Moscow, Russian Federation
| | - Dmitry Z Vinnitskiy
- Enikolopov Institute of Synthetic Polymeric Materials of Russian Academy of Sciences, Profsoyuznaya Str. 70, 117393 Moscow, Russian Federation
| | - Marina S Polinskaya
- Zelinsky Institute of Organic Chemistry of Russian Academy of Sciences, Leninskiy pr. 47, 119991 Moscow, Russian Federation
| | - Vadim B Krylov
- Zelinsky Institute of Organic Chemistry of Russian Academy of Sciences, Leninskiy pr. 47, 119991 Moscow, Russian Federation
| | - Nikolay E Nifantiev
- Zelinsky Institute of Organic Chemistry of Russian Academy of Sciences, Leninskiy pr. 47, 119991 Moscow, Russian Federation
| | - Elena V Agina
- Enikolopov Institute of Synthetic Polymeric Materials of Russian Academy of Sciences, Profsoyuznaya Str. 70, 117393 Moscow, Russian Federation
| | - Sergey A Ponomarenko
- Enikolopov Institute of Synthetic Polymeric Materials of Russian Academy of Sciences, Profsoyuznaya Str. 70, 117393 Moscow, Russian Federation
- Chemistry Department, Lomonosov Moscow State University, Leninskiye Gory 1/3, 119991 Moscow, Russian Federation
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8
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Zhdanov GA, Gribanyov DA, Gambaryan AS, Kukushkin VI, Zavyalova EG. Using a Biosensor Based on Surface-Enhanced Raman Scattering to Identify Influenza Viruses in Biological Fluids. BULLETIN OF THE RUSSIAN ACADEMY OF SCIENCES: PHYSICS 2022. [PMCID: PMC9109670 DOI: 10.3103/s1062873822040293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Biosensors based on the effect of surface-enhanced Raman scattering obtained on silver nanoclusters modified with DNA aptamers allow viruses to be detected with high sensitivity. However, measurements in biological media are complicated by the nonspecific sorption of biomolecules on silver. Conditions for preparing samples of biological fluids that allow the nonspecific sorption of biomolecules to be nullified are studied.
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9
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Bizyaeva AA, Bunin DA, Moiseenko VL, Gambaryan AS, Balk S, Tashlitsky VN, Arutyunyan AM, Kopylov AM, Zavyalova EG. The Functional Role of Loops and Flanking Sequences of G-Quadruplex Aptamer to the Hemagglutinin of Influenza a Virus. Int J Mol Sci 2021; 22:2409. [PMID: 33673708 PMCID: PMC7957560 DOI: 10.3390/ijms22052409] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/21/2021] [Accepted: 02/24/2021] [Indexed: 12/22/2022] Open
Abstract
Nucleic acid aptamers are generally accepted as promising elements for the specific and high-affinity binding of various biomolecules. It has been shown for a number of aptamers that the complexes with several related proteins may possess a similar affinity. An outstanding example is the G-quadruplex DNA aptamer RHA0385, which binds to the hemagglutinins of various influenza A virus strains. These hemagglutinins have homologous tertiary structures but moderate-to-low amino acid sequence identities. Here, the experiment was inverted, targeting the same protein using a set of related, parallel G-quadruplexes. The 5'- and 3'-flanking sequences of RHA0385 were truncated to yield parallel G-quadruplex with three propeller loops that were 7, 1, and 1 nucleotides in length. Next, a set of minimal, parallel G-quadruplexes with three single-nucleotide loops was tested. These G-quadruplexes were characterized both structurally and functionally. All parallel G-quadruplexes had affinities for both recombinant hemagglutinin and influenza virions. In summary, the parallel G-quadruplex represents a minimal core structure with functional activity that binds influenza A hemagglutinin. The flanking sequences and loops represent additional features that can be used to modulate the affinity. Thus, the RHA0385-hemagglutinin complex serves as an excellent example of the hypothesis of a core structure that is decorated with additional recognizing elements capable of improving the binding properties of the aptamer.
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Affiliation(s)
- Anastasia A. Bizyaeva
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia; (D.A.B.); (V.L.M.); (V.N.T.); (A.M.K.)
| | - Dmitry A. Bunin
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia; (D.A.B.); (V.L.M.); (V.N.T.); (A.M.K.)
| | - Valeria L. Moiseenko
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia; (D.A.B.); (V.L.M.); (V.N.T.); (A.M.K.)
| | - Alexandra S. Gambaryan
- Chumakov Federal Scientific Centre for Research and Development of Immune and Biological Products RAS, 108819 Moscow, Russia;
| | | | - Vadim N. Tashlitsky
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia; (D.A.B.); (V.L.M.); (V.N.T.); (A.M.K.)
| | - Alexander M. Arutyunyan
- Belozersky Research Institute of Physical Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Alexey M. Kopylov
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia; (D.A.B.); (V.L.M.); (V.N.T.); (A.M.K.)
| | - Elena G. Zavyalova
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia; (D.A.B.); (V.L.M.); (V.N.T.); (A.M.K.)
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10
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Gribanyov D, Zhdanov G, Olenin A, Lisichkin G, Gambaryan A, Kukushkin V, Zavyalova E. SERS-Based Colloidal Aptasensors for Quantitative Determination of Influenza Virus. Int J Mol Sci 2021; 22:1842. [PMID: 33673314 PMCID: PMC7918581 DOI: 10.3390/ijms22041842] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 02/06/2023] Open
Abstract
Development of sensitive techniques for rapid detection of viruses is on a high demand. Surface-enhanced Raman spectroscopy (SERS) is an appropriate tool for new techniques due to its high sensitivity. DNA aptamers are short structured oligonucleotides that can provide specificity for SERS biosensors. Existing SERS-based aptasensors for rapid virus detection had several disadvantages. Some of them lacked possibility of quantitative determination, while others had sophisticated and expensive implementation. In this paper, we provide a new approach that combines rapid specific detection and the possibility of quantitative determination of viruses using the example of influenza A virus.
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Affiliation(s)
- Dmitry Gribanyov
- Institute of Solid State Physics of Russian Academy of Science, 142432 Chernogolovka, Russia;
| | - Gleb Zhdanov
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia; (G.Z.); (A.O.); (G.L.)
| | - Andrei Olenin
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia; (G.Z.); (A.O.); (G.L.)
| | - Georgii Lisichkin
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia; (G.Z.); (A.O.); (G.L.)
| | - Alexandra Gambaryan
- Chumakov Federal Scientific Center for Research and Development of Immune and Biological Products RAS, 108819 Moscow, Russia;
| | - Vladimir Kukushkin
- Institute of Solid State Physics of Russian Academy of Science, 142432 Chernogolovka, Russia;
| | - Elena Zavyalova
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia; (G.Z.); (A.O.); (G.L.)
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11
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O’ Sullivan CK, Mairal T, Jauset-Rubio M, Svobodova M, Skouridou V, Esposito V, Virgilio A, Galeone A. Aptamers against the β-Conglutin Allergen: Insights into the Behavior of the Shortest Multimeric (Intra)Molecular DNA G-Quadruplex. Int J Mol Sci 2021; 22:ijms22031150. [PMID: 33498970 PMCID: PMC7865891 DOI: 10.3390/ijms22031150] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/13/2021] [Accepted: 01/19/2021] [Indexed: 01/25/2023] Open
Abstract
In previous work, a 93-mer aptamer was selected against the anaphylactic allergen, β-conglutin and truncated to an 11-mer, improving the affinity by two orders of magnitude, whilst maintaining the specificity. This 11-mer was observed to fold in a G-quadruplex, and preliminary results indicated the existence of a combination of monomeric and higher-order structures. Building on this previous work, in the current study, we aimed to elucidate a deeper understanding of the structural forms of this 11-mer and the effect of the structure on its binding ability. A battery of techniques including polyacrylamide gel electrophoresis, high-performance liquid chromatography in combination with electrospray ionization time-of-flight mass spectrometry, matrix-assisted laser desorption/ionization time-of-flight, thermal binding analysis, circular dichroism and nuclear magnetic resonance were used to probe the structure of both the 11-mer and the 11-mer flanked with TT- at either the 5′ or 3′ end or at both ends. The TT-tail at the 5′ end hinders stacking effects and effectively enforces the 11-mer to maintain a monomeric form. The 11-mer and the TT- derivatives of the 11-mer were also evaluated for their ability to bind its cognate target using microscale thermophoresis and surface plasmon resonance, and biolayer interferometry confirmed the nanomolar affinity of the 11-mer. All the techniques utilized confirmed that the 11-mer was found to exist in a combination of monomeric and higher-order structures, and that independent of the structural form present, nanomolar affinity was observed.
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Affiliation(s)
- Ciara K. O’ Sullivan
- INTERFIBIO Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain; (T.M.); (M.J.-R.); (M.S.); (V.S.)
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
- Correspondence:
| | - Teresa Mairal
- INTERFIBIO Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain; (T.M.); (M.J.-R.); (M.S.); (V.S.)
| | - Miriam Jauset-Rubio
- INTERFIBIO Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain; (T.M.); (M.J.-R.); (M.S.); (V.S.)
| | - Marketa Svobodova
- INTERFIBIO Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain; (T.M.); (M.J.-R.); (M.S.); (V.S.)
| | - Vasso Skouridou
- INTERFIBIO Research Group, Departament d’Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain; (T.M.); (M.J.-R.); (M.S.); (V.S.)
| | - Veronica Esposito
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy; (V.E.); (A.V.); (A.G.)
| | - Antonella Virgilio
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy; (V.E.); (A.V.); (A.G.)
| | - Aldo Galeone
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy; (V.E.); (A.V.); (A.G.)
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