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11C-radiolabeled aptamer for imaging of tumors and metastases using positron emission tomography-computed tomography / A. V. Ozerskaya, T. N. Zamay, O. S. Kolovskaya [et al.] // Mol. Ther. Nucl. Acids. - 2021. - Vol. 26. - P. 1159-1172, DOI 10.1016/j.omtn.2021.10.020. - Cited References: 44 . - ISSN 2162-2531
Кл.слова (ненормированные):
11C radiolabeling -- radiopharmaceuticals -- PET/CT -- in vivo imaging -- DNA aptamers -- Ehrlich ascites carcinoma -- metastasis
Аннотация: Identification of primary tumors and metastasis sites is an essential step in cancer diagnostics and the following treatment. Positron emission tomography-computed tomography (PET/CT) is one of the most reliable methods for scanning the whole organism for malignancies. In this work, we synthesized an 11C-labeled oligonucleotide primer and hybridized it to an anti-cancer DNA aptamer. The 11C-aptamer was applied for in vivo imaging of Ehrlich ascites carcinoma and its metastases in mice using PET/CT. The imaging experiments with the 11C-aptamer determined very small primary and secondary tumors of 3 mm2 and less. We also compared 11C imaging with the standard radiotracer, 2-deoxy-2-[fluorine-18]fluoro-D-glucose (18F-FDG), and found better selectivity of the 11C-aptamer to metastatic lesions in the metabolically active organs than 18F-FDG. 11C radionuclide with an ultra-short (20.38 min) half-life is considered safest for PET/CT imaging and does not cause false-positive results in heart imaging. Its combination with aptamers gives us high-specificity and high-contrast imaging of cancer cells and can be applied for PET/CT-guided drug delivery in cancer therapies.

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Federal Siberian Research Clinical Centre Under the Federal Medical Biological Agency, Krasnoyarsk, Russian Federation
Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenetsky, Krasnoyarsk, Russian Federation
Federal Research Center Krasnoyarsk Science- Center SB RAS, Krasnoyarsk, Russian Federation
Kirensky Institute of Physics, Krasnoyarsk, Russian Federation
Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada
Krasnoyarsk Regional Pathology-Anatomic Bureau, Krasnoyarsk, Russian Federation

Доп.точки доступа:
Ozerskaya, A. V.; Zamay, T. N.; Kolovskaya, O. S.; Tokarev, N. A.; Belugin, K. V.; Chanchikova, N. G.; Badmaev, O. N.; Zamay, G. S.; Shchugoreva, I. A.; Moryachkov, R. V.; Морячков, Роман Владимирович; Zabluda, V. N.; Заблуда, Владимир Николаевич; Khorzhevskii, V. A.; Shepelevich, N.; Gappoev, S. V.; Karlova, E. A.; Saveleva, A. S.; Volzhentsev, A. A.; Blagodatova, A. N.; Lukyanenko, K. A.; Veprintsev, D. V.; Smolyarova, T. E.; Смолярова, Татьяна Евгеньевна; Tomilin, F. N.; Томилин, Феликс Николаевич; Zamay, S. S.; Silnikov, V. N.; Berezovski, M. V.; Kichkailo, A. S.
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Aptamer-conjugated superparamagnetic ferroarabinogalactan nanoparticles for targeted magnetodynamic therapy of cancer / O. S. Kolovskaya, T. N. Zamay, G. S. Zamay [et al.] // Cancers. - 2020. - Vol. 12, Is. 1. - Ст. 216, DOI 10.3390/cancers12010216. - Cited References: 46. - This research was funded by the Ministry of Science and Higher Education of the Russian Federation; project 0287-2019-0007 . - ISSN 2072-6694
Кл.слова (ненормированные):
aptamers -- arabinogalactan -- superparamagnetic ferroarabinogalactans -- drug delivery -- magnetodynamic therapy -- magnetically induced cell disruption -- magnetic resonance imaging
Аннотация: Nanotechnologies involving physical methods of tumor destruction using functional oligonucleotides are promising for targeted cancer therapy. Our study presents magnetodynamic therapy for selective elimination of tumor cells in vivo using DNA aptamer-functionalized magnetic nanoparticles exposed to a low frequency alternating magnetic field. We developed an enhanced targeting approach of cancer cells with aptamers and arabinogalactan. Aptamers to fibronectin (AS-14) and heat shock cognate 71 kDa protein (AS-42) facilitated the delivery of the nanoparticles to Ehrlich carcinoma cells, and arabinogalactan (AG) promoted internalization through asialoglycoprotein receptors. Specific delivery of the aptamer-modified FeAG nanoparticles to the tumor site was confirmed by magnetic resonance imaging (MRI). After the following treatment with a low frequency alternating magnetic field, AS-FeAG caused cancer cell death in vitro and tumor reduction in vivo. Histological analyses showed mechanical disruption of tumor tissues, total necrosis, cell lysis, and disruption of the extracellular matrix. The enhanced targeted magnetic theranostics with the aptamer conjugated superparamagnetic ferroarabinogalactans opens up a new venue for making biocompatible contrasting agents for MRI imaging and performing non-invasive anti-cancer therapies with a deep penetrated magnetic field.

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Держатели документа:
Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”, 660036 Krasnoyarsk, Russia
Laboratory for Biomolecular and Medical Technologies, Faculty of Medicine, Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecki, 660022 Krasnoyarsk, Russia
Irkutsk Institute of Chemistry named after A.E. Favorsky, the Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia
L.V. Kirensky Institute of Physics SB RAS—The Branch of Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences”, 660036 Krasnoyarsk, Russia
Laboratory of Advanced Materials and Technology, Tomsk State University, 634050 Tomsk, Russia
Institute of Chemistry and Chemical Technology SB RAS—The Branch of Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences”, 660036 Krasnoyarsk, Russia
School of Engineering Physics and Radio Electronics, Siberian Federal University, 660041 Krasnoyarsk, Russia
Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8568, Japan
School of Non-Ferrous Metals and Materials Science, Siberian Federal University, 660041 Krasnoyarsk, Russia
Faculty of Physics, Department of Magnetism, Lomonosov Moscow State University, 119991 Moscow, Russia
School of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia
Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada

Доп.точки доступа:
Kolovskaya, O. S.; Коловская, О. С.; Zamay, T. N.; Замай, Т. Н.; Zamay, G. S.; Замай, Галина Сергеевна; Babkin, V. A.; Medvedeva, E. N.; Neverova, N. A.; Kirichenko, A. K.; Zamay, S. S.; Замай, С. С.; Lapin, I. N.; Morozov, E. V.; Морозов, Евгений Владимирович; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Narodov, A. A.; Fedorov, D. G.; Tomilin, F. N.; Томилин, Феликс Николаевич; Zabluda, V. N.; Заблуда, Владимир Николаевич; Alekhina, Yu.; Lukyanenko, K. A.; Glazyrin, Yu. E.; Svetlichnyi, V. A.; Berezovski, M. V.; Kichkailo, A. S.
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Biocompatible nanostructures fabricated by Dip-Pen nanolithography / T. E. Smolyarova, A. S. Tarasov, A. V. Lukyanenko [et al.] // Molecular Therapy - Nucleic Acids : book of abstracts of the 1st Int. conf. "Aptamers in Russia 2019". - 2019. - Vol. 17, Suppl. 1. - P. 8-9

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Доп.точки доступа:
Smolyarova, T. E.; Смолярова, Татьяна Евгеньевна; Tarasov, A. S.; Тарасов, Антон Сергеевич; Lukyanenko, A. V.; Лукьяненко, Анна Витальевна; Shanidze, L. V.; Шанидзе, Лев Викторович; Yakovlev, I. A.; Яковлев, Иван Александрович; Volkov, N. V.; Волков, Никита Валентинович; Aptamers in Russia, international conference(1 ; 2019 ; Aug. 27-30 ; Krasnoyarsk)
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Computational approach to design of aptamers to the receptor binding domain of sars-cov-2 / P. V. Artyushenko, V. A. Mironov, D. I. Morozov [et al.] // Sib. Med. Rev. - 2021. - Vol. 2021, Is. 2. - P. 66-67 ; Сиб. мед. обозрение, DOI 10.20333/2500136-2021-2-66-67. - Cited References: 5 . - ISSN 1819-9496
Кл.слова (ненормированные):
selection -- aptamer -- receptor-binding domain -- SARS-CoV-2
Аннотация: The aim of the research. In this work, in silico selection of DNA-aptamers to the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein was performed using molecular modeling methods. Material and methods. A new computational approach to aptamer in silico selection is based on a cycle of simulations, including the stages of molecular modeling, molecular docking, molecular dynamic simulations, and quantum chemical calculations. To verify the obtained calculated results flow cytometry, fluorescence polarization, and small-angle X-ray scattering methods were applied. Results. An initial library consisted of 256 16-mer oligonucleotides was modeled. Based on molecular docking results, the only one aptamer (Apt16) was selected from the library as a starting aptamer to the RBD protein. For Apt16/RBD complex, molecular dynamic and quantum chemical calculations revealed the pairs of nucleotides and amino acids whose contribution to the binding between aptamer and RBD is the largest. Taking into account these data, Apt16 was subjected to the structure modifications in order to increase the binding with the RBD. Thus, a new aptamer Apt25 was designed. The procedure of 1) aptamer structure modeling/modification, 2) molecular docking, 3) molecular dynamic simulations, 4) quantum chemical calculations was performed sev-eral times. As a result, four aptamers (Apt16, Apt25, Apt27, Apt31) to the RBD were designed in silico without any preliminary experimental data. Binding of the each modeled aptamer to the RBD was studied in terms of interactions between residues in protein and nucleotides in the aptamers. Based on the simulation results, the strongest binding with the RBD was predicted for two Apt27 and Apt31aptamers. The calculated results are in good agreement with experimental data obtained by flow cytometry, fluorescence polarization, and small-angle X-ray scattering methods. Conclusion. The proposed computational approach to selection and refinement of aptamers is universal and can be used for wide range of molecular ligands and targets.

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Держатели документа:
Federal Research Center KSC SB RAS, Krasnoyarsk, 660036, Russian Federation
Siberian Federal University, Krasnoyarsk, 660041, Russian Federation
Lomonosov Moscow State University, Moscow, 119991, Russian Federation
University of Jyvaskyla, Jyvaskyla, 40014, Finland
University of Naples Federico II, Naples, 80138, Italy
Kirensky Institute of Physics KSC SB RAS, Krasnoyarsk, 660036, Russian Federation

Доп.точки доступа:
Artyushenko, P. V.; Mironov, V. A.; Morozov, D. I.; Shchugoreva, I. A.; Borbone, N.; Tomilin, F. N.; Томилин, Феликс Николаевич; Kichkailo, A. S.

}
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Conformational changes in DNA aptamers upon binding to Pb ions / R. V. Moryachkov, A. N. Berlina, P. V. Artyushenko [et al.] // The Fifth Asian School-Conference on Physics and Technology of Nanostructured Materials : Proceedings. - VLadivostok : Dalnauka Publishing, 2020. - Ст. VII.31.01p. - P. 193. - The reported study was funded by RFBR, project number 19-32-90266. . - ISBN 978-5-8044-1698-1

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Доп.точки доступа:
Moryachkov, R. V.; Морячков, Роман Владимирович; Berlina, A. N.; Artyushenko, P. V.; Zabluda, V. N.; Заблуда, Владимир Николаевич; Peters, G. S.; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Asian School-Conference on Physics and Technology of Nanostructured Materials(5 ; 2020 ; 30 Jul - 3 Aug ; Vladivostok); Азиатская школа-конференция по физике и технологии наноструктурированных материалов(5 ; 2013 ; 30 июля - 3 авг. ; Владивосток)
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Core–shell Fe3O4@C nanoparticles for the organic dye adsorption and targeted magneto-mechanical destruction of Ehrlich ascites carcinoma cells / O. S. Ivanova, I. S. Edelman, Ch.-R. Lin [et al.] // Materials. - 2023. - Vol. 16, Is. 1. - Ст. 23, DOI 10.3390/ma16010023. - Cited References: 65. - This research was funded partly by the Ministry of Science and Higher Education of the Russian Federation, project FWES-2021-0035. C.-R.L., Y.-Z.C. and A.A.S. thank the National Science and Technology Council of Taiwan for the financial support, Grants NSTC № 108-2923-M-153-001-MY3 and № 110-2112-M-153-005-. Magnetic investigations were carried out in the Center for Collective Use of the Krasnoyarsk Regional Center of Research Equipment of Federal Research Center “Krasnoyarsk Science Center SB RAS” . - ISSN 1996-1944
Кл.слова (ненормированные):
magnetite nanoparticles -- adsorption -- organic dyes -- aptamers -- magnetically induced cell destruction
Аннотация: The morphology, structure, and magnetic properties of Fe3O4 and Fe3O4@C nanoparticles, as well their effectiveness for organic dye adsorption and targeted destruction of carcinoma cells, were studied. The nanoparticles exhibited a high magnetic saturation value (79.4 and 63.8 emu/g, correspondingly) to facilitate magnetic separation. It has been shown that surface properties play a key role in the adsorption process. Both types of organic dyes—cationic (Rhodomine C) and anionic (Congo Red and Eosine)—were well adsorbed by the Fe3O4 nanoparticles’ surface, and the adsorption process was described by the polymolecular adsorption model with a maximum adsorption capacity of 58, 22, and 14 mg/g for Congo Red, Eosine, and Rhodomine C, correspondingly. In this case, the kinetic data were described well by the pseudo-first-order model. Carbon-coated particles selectively adsorbed only cationic dyes, and the adsorption process for Methylene Blue was described by the Freundlich model, with a maximum adsorption capacity of 14 mg/g. For the case of Rhodomine C, the adsorption isotherm has a polymolecular character with a maximum adsorption capacity of 34 mg/g. To realize the targeted destruction of the carcinoma cells, the Fe3O4@C nanoparticles were functionalized with aptamers, and an experiment on the Ehrlich ascetic carcinoma cells’ destruction was carried out successively using a low-frequency alternating magnetic field. The number of cells destroyed as a result of their interaction with Fe3O4@C nanoparticles in an alternating magnetic field was 27%, compared with the number of naturally dead control cells of 6%.

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Держатели документа:
Kirensky Institute of Physics, Federal Research Center KSC Siberian Branch, Russian Academy of Sciences, Krasnoyarsk 660036, Russia
Institute of Engineering Physics and Radioelectronics, Siberian Federal University, Krasnoyarsk 660041, Russia
Department of Applied Physics, National Pingtung University, Pingtung City 90003, Taiwan
Laboratory of Biomolecular and Medical Technologies, Krasnoyarsk State Medical University Named after Prof. V.F. Voino-Yasenetsky, Krasnoyarsk 660022, Russia
Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center KSC Siberian Branch, Russian Academy of Sciences, Krasnoyarsk 660036, Russia

Доп.точки доступа:
Ivanova, O. S.; Иванова, Оксана Станиславовна; Edelman, I. S.; Эдельман, Ирина Самсоновна; Lin, Chun-Rong; Svetlitsky, E. S.; Светлицкий, Евгений Сергеевич; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Lukyanenko, Kirill A.; Sukhachev, A. L.; Сухачев, Александр Леонидович; Shestakov, N. P.; Шестаков, Николай Петрович; Chen, Ying-Zhen; Spivakov, Aleksandr A.
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Development of DNA aptamers for visualization of glial brain tumors and detection of circulating tumor cells / A. S. Kichkailo, A. A. Narodov, M. A. Komarova [et al.] // Mol. Ther. - Nucleic Acids. - 2023. - Vol. 32. - P. 267-288, DOI 10.1016/j.omtn.2023.03.015. - Cited References: 69. - The authors are grateful to all the patients and hospital staff participating in this research. We acknowledge the assistance of the AptamerLab LCC (www.aptamerlab.com) and personally Mr. Vasily Mezko for the aptamer 3D structure optimization and financial and technical support. The authors thank Mr. Alexey Kichkailo, Dr. Arkady B. Kogan, and Dr. Rinat G. Galeev for their general support. Mrs. Valentina L. Grigoreva, and Irina V. Gildebrand for the help with histological staining. Technical and instrumental support was provided by the Multiple-Access Center at Tomsk State University; the Krasnoyarsk Inter-District Ambulance Hospital, named after N.S. Karpovich; John L. Holmes Mass Spectrometry Facility at the University of Ottawa; Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency; Shared Core Facilities of Molecular and Cell Technologies at Krasnoyarsk State Medical University and Krasnoyarsk Regional Centre for Collective Use at the Federal Research Centre “KSC SB RAS”. The confocal fluorescence microscopy research was carried out with the equipment of the Tomsk Regional Core Shared Research Facilities Center of the National Research Tomsk State University. The Center was supported by the Ministry of Science and Higher Education of the Russian Federation, grant no. 075-15-2021-693 (no. 13.RFC.21.0012). Acute toxicity studies were performed in a laboratory certified for preclinical studies, Laboratory of Biological Testing, Institute of Bioorganic Chemistry named after academics M.M. Shemyakin and Y.A. Ovchinnikov Russian Academy of Sciences. The authors are grateful to the Joint Super Computer Center of the Russian Academy of Sciences for providing supercomputers for computer simulations. Development of the glioma tumor model in immunosuppressed mice was supported by the Russian Science Foundation grant No. 22-64-00041 (M.A.D.), https://rscf.ru/en/project/22-64-00041/. Synthesis of 11C-aptamer and PET/CT visualization was funded by the Federal Medical Biological Agency; project 122041800132-2 (A.V.O.). Aptamer selection and their clinical applications were funded by the Ministry of Healthcare of the Russian Federation; project АААА-Б19-219090690032-5 (T.N.Z.). The Ministry of Science and Higher Education of the Russian Federation project FWES-2022-0005 (A.S.K.) supported aptamer characterization, molecular modelling, and in vivo experiments. Mass spectrometry analyses, DNA sequencing, and synthesis were supported by NSERC Discovery Grant (M.V.B.). We acknowledge the European Synchrotron Radiation Facility for SAXS experiments and thank Dr. Bart Van Laer for assistance in using a beamline BM29. SAXS measurements were supported by RFBR № 18-32-00478 for young scientists (R.V.M.). The synchrotron SEC-SAXS data for Gli-55 aptamer were also collected at beamline P12 operated by EMBL Hamburg at the PETRA III storage ring (DESY, Hamburg, Germany) . - ISSN 2162-2531
Аннотация: Here, we present DNA aptamers capable of specific binding to glial tumor cells in vitro, ex vivo, and in vivo for visualization diagnostics of central nervous system tumors. We selected the aptamers binding specifically to the postoperative human glial primary tumors and not to the healthy brain cells and meningioma, using a modified process of systematic evolution of ligands by exponential enrichment to cells; sequenced and analyzed ssDNA pools using bioinformatic tools and identified the best aptamers by their binding abilities; determined three-dimensional structures of lead aptamers (Gli-55 and Gli-233) with small-angle X-ray scattering and molecular modeling; isolated and identified molecular target proteins of the aptamers by mass spectrometry; the potential binding sites of Gli-233 to the target protein and the role of post-translational modifications were verified by molecular dynamics simulations. The anti-glioma aptamers Gli-233 and Gli-55 were used to detect circulating tumor cells in liquid biopsies. These aptamers were used for in situ, ex vivo tissue staining, histopathological analyses, and fluorescence-guided tumor and PET/CT tumor visualization in mice with xenotransplanted human astrocytoma. The aptamers did not show in vivo toxicity in the preclinical animal study. This study demonstrates the potential applications of aptamers for precise diagnostics and fluorescence-guided surgery of brain tumors.

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Держатели документа:
Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
Krasnoyarsk Inter-District Ambulance Hospital named after N.S. Karpovich, 17 Kurchatova, Krasnoyarsk 660062, Russia
Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia
Department of Molecular Electronics, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences”, 50 Akademgorodok, Krasnoyarsk 660036, Russia
National Research Center Kurchatov Institute, 1 Akademika Kurchatova, Moscow 123182, Russia
Laboratory of Advanced Materials and Technology, Siberian Physical-Technical Institute of Tomsk State University, 36 Lenina, Tomsk 634050, Russia
Krasnoyarsk Regional Pathology-Anatomic Bureau, 3d Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninskie gory, Moscow 119991, Russia
Department of Chemistry, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, 702-701, South Korea
Nanoscience Center and Department of Chemistry, University of Jyväskylä, P.O. Box 35, Jyväskylä 40014, Finland
A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” RAS, 59 Leninsky pr., Moscow, 119333, Russia
Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency, Krasnoyarsk, Russia
Krasnoyarsk Regional Clinical Cancer Center, 16 1-ya Smolenskaya, Krasnoyarsk 660133, Russia
Institute of Chemistry and Chemical Technology SB RAS – The Branch of Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences”, 660036 Krasnoyarsk, Russia
Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, Ontario K1N6N5, Canada
Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 8 Lavrentyev Avenue, 630090 Novosibirsk, Russia

Доп.точки доступа:
Kichkailo, A. S.; Narodov, A. A.; Komarova, M. A.; Zamay, T. N.; Zamay, G. S.; Kolovskaya, O. S.; Erakhtin, E. E.; Glazyrin, Y. E.; Veprintsev, D. V.; Moryachkov, R. V.; Zabluda, V. N.; Заблуда, Владимир Николаевич; Shchugoreva, I.; Artyushenko, P.; Mironov, V. A.; Morozov, D. I.; Gorbushin, A. V.; Khorzhevskii, V. A.; Koshmanova, A. A.; Nikolaeva, E. D.; Grinev, I. P.; Voronkovskii, I. I.; Grek, D. S.; Belugin, K. V.; Volzhentsev, A. A.; Badmaev, O. N.; Luzan, N.; Lukyanenko, K. A.; Peters, G.; Lapin, I. N.; Лапин, И. Н.; Kirichenko, A. K.; Konarev, P. V.; Morozov, E. V; Mironov, G. G.; Gargaun, A.; Muharemagic, D.; Zamay, S. S.; Kochkina, E. V.; Dymova, M. A.; Smolyarova, T. E.; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Modestov, A. A.; Tokarev, N. A.; Shepelevich, N.; Ozerskaya, A. V.; Chanchikova, N. G.; Krat, A. V.; Zukov, R. A.; Bakhtina, V. I.; Shnyakin, P. G.; Shesternya, P. A.; Svetlichnyi, V. A.; Petrova, M. M.; Artyukhov, I. P.; Tomilin, F. N.; Томилин, Феликс Николаевич; Berezovski, Maxim V.
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Discovery of DNA aptamers targeting SARS-CoV-2 nucleocapsid protein and protein-binding epitopes for label-free COVID-19 diagnostics / S. Poolsup, E. Zaripov, N. Huttmann [et al.] // Mol. Ther. Nucleic Acids. - 2023. - Vol. 31. - P. 731-743, DOI 10.1016/j.omtn.2023.02.010. - Cited References: 74. - M.V.B. thanks the Canadian Institutes of Health Research grant OV1-170353 for providing financial support. Molecular modeling and docking were supported by a grant from the Russian Science Foundation (project number 21-73-20240) for A.S.K. S.P. is thankful to Dr. Bob Dass, Dylan Tanner, and Dr. Degang Liu, Sartorius for generously providing excellent technical training and consumable support for binding assay on BLI, and Aldo Jordan for assisting with creating the figures. The authors also thank John L. Holmes’s mass spectrometry facility for providing access to perform nLC-MS/MS. Lastly, the authors thank the JCSS Joint Super Computer Center of the Russian Academy of Sciences for providing supercomputers for computer simulations . - ISSN 2162-2531
Кл.слова (ненормированные):
MT: Oligonucleotides: Diagnostics and Biosensors -- COVID-19 diagnosis -- SARS-CoV-2 nucleocapsid detection -- label-free optical aptasensor -- aptamer selection -- biolayer interferometry -- binding motif identification
Аннотация: The spread of COVID-19 has affected billions of people across the globe, and the diagnosis of viral infection still needs improvement. Because of high immunogenicity and abundant expression during viral infection, SARS-CoV-2 nucleocapsid (N) protein could be an important diagnostic marker. This study aimed to develop a label-free optical aptasensor fabricated with a novel single-stranded DNA aptamer to detect the N protein. The N-binding aptamers selected using asymmetric-emulsion PCR-SELEX and their binding affinity and cross-reactivity were characterized by biolayer interferometry. The tNSP3 aptamer (44 nt) was identified to bind the N protein of wild type and Delta and Omicron variants with high affinity (KD in the range of 0.6–3.5 nM). Utilizing tNSP3 to detect the N protein spiked in human saliva evinced the potential of this aptamer with a limit of detection of 4.5 nM. Mass spectrometry analysis was performed along with molecular dynamics simulation to obtain an insight into how tNSP3 binds to the N protein. The identified epitope peptides are localized within the RNA-binding domain and C terminus of the N protein. Hence, we confirmed the performance of this aptamer as an analytical tool for COVID-19 diagnosis.

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Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada
Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk 660036, Russia
Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
Department of Chemistry, Siberian Federal University, Krasnoyarsk 660041, Russia
Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, Krasnoyarsk 660036, Russia

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Poolsup, S.; Zaripov, E.; Huttmann, N.; Minic, Z.; Artyushenko, P. V.; Shchugoreva, I. A.; Tomilin, F. N.; Томилин, Феликс Николаевич; Kichkailo, A. S.; Berezovski, M. V.
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Four steps for revealing and adjusting the 3D structure of aptamers in solution by small-angle X-ray scattering and computer simulation / F. N. Tomilin [et al.] // Anal. Bioanal. Chem. - 2019. - Vol. 411, Is. 25. - P. 6723-6732, DOI 10.1007/s00216-019-02045-0. - Cited References: 51. - Authors are grateful to Ana Gargaun for English grammar correction. This work was funded in parts by the Ministry of Science and Higher Education of the Russian Federation; project 0287-2019-0007 the Council of the President of the Russian Federation for Support of Young Scientists and Leading Scientific Schools (project no. SP-938.2015.5) and the grant of KSAI “Krasnoyarsk Regional Fund of Supporting Scientific and Technological Activities” for M.P., the internship “The study of the stacking of the secondary structure of DNA aptamers to thrombin” for R.M. . - ISSN 1618-2642
Кл.слова (ненормированные):
Aptamer -- Thrombin -- Three-dimensional structure -- Small-angle X-ray scattering -- Molecular modeling
Аннотация: Nucleic acid (NA) aptamers bind to their targets with high affinity and selectivity. The three-dimensional (3D) structures of aptamers play a major role in these non-covalent interactions. Here, we use a four-step approach to determine a true 3D structure of aptamers in solution using small-angle X-ray scattering (SAXS) and molecular structure restoration (MSR). The approach consists of (i) acquiring SAXS experimental data of an aptamer in solution, (ii) building a spatial distribution of the molecule’s electron density using SAXS results, (iii) constructing a 3D model of the aptamer from its nucleotide primary sequence and secondary structure, and (iv) comparing and refining the modeled 3D structures with the experimental SAXS model. In the proof-of-principle we analyzed the 3D structure of RE31 aptamer to thrombin in a native free state at different temperatures and validated it by circular dichroism (CD). The resulting 3D structure of RE31 has the most energetically favorable conformation and the same elements such as a B-form duplex, non-complementary region, and two G-quartets which were previously reported by X-ray diffraction (XRD) from a single crystal. More broadly, this study demonstrates the complementary approach for constructing and adjusting the 3D structures of aptamers, DNAzymes, and ribozymes in solution, and could supply new opportunities for developing functional nucleic acids. [Figure not available: see fulltext.]. © 2019, Springer-Verlag GmbH Germany, part of Springer Nature.

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Kirensky Institute of Physics, Federal Research Center KSC Siberian Branch Russian Academy of Sciences, 50/38 Akademgorodok, Krasnoyarsk, 660036, Russian Federation
Siberian Federal University, 79 Svobodny pr., Krasnoyarsk, 660041, Russian Federation
Federal Research Center “Krasnoyarsk Science Center” Siberian Branch of the Russian Academy of Sciences, 50 Akademgorodok, Krasnoyarsk, 660036, Russian Federation
NRC Kurchatov Institute, 1, Academic Kurchatov Square, Moscow, 123182, Russian Federation
A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1/40 Leninskie Gory, Moscow, 119992, Russian Federation
Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk, 660022, Russian Federation
Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N6N5, Canada

Доп.точки доступа:
Tomilin, F. N.; Томилин, Феликс Николаевич; Moryachkov, R.; Морячков, Роман Владимирович; Shchugoreva, I.; Zabluda, V. N.; Заблуда, Владимир Николаевич; Peters, G.; Platunov, M. S.; Платунов, Михаил Сергеевич; Spiridonova, V.; Melnichuk, A.; Atrokhova, A.; Zamay, S. S.; Замай, С. С.; Ovchinnikov, S. G.; Овчинников, Сергей Геннадьевич; Zamay, G. S.; Замай, Галина Сергеевна; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Zamay, T. N.; Замай, Т. Н.; Berezovski, M. V.; Kichkailo, A. S.
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10.

In vivo cancer cells elimination guided by aptamer-functionalized gold-coated magnetic nanoparticles and controlled with low frequency alternating magnetic field / I. V. Belyanina [et al.] // Theranostics. - 2017. - Vol. 7, Is. 13. - P. 3326-3337, DOI 10.7150/thno.17089. - Cited References:35. - The authors are grateful to George Y. Vorogeikin, Yuri I. Vorogeikin and "OKB ART". Andrey Barinov and "OPTEC Group" for help with 3D laser scanning imaging. Microscopic analyses using Carl Zeiss LSM 800 were done in the "Center for bioassay, nanotechnology and nanomaterials safety" ("Biotest-Nano") (Multiple-Access Center, Tomsk State University, Tomsk, Russia). Toxicity studies have been performed in Multiple-Access Center, Central Scientific Research Laboratory in Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecky. This work was supported by the Russian Scientific Fund (grant #14-15-00805). . - ISSN 1838-7640

РУБ Medicine, Research & Experimental
Рубрики:
PHOTOTHERMAL THERAPY
   INTEGRIN ACTIVATION
   FIBRONECTIN
   STIMULATION
Кл.слова (ненормированные):
cancer therapy -- gold coated magnetic nanoparticles -- DNA aptamers -- low -- frequency alternating magnetic field -- fibronectin -- integrin -- apoptosis -- necrosis
Аннотация: Biomedical applications of magnetic nanoparticles under the influence of a magnetic field have been proved useful beyond expectations in cancer therapy. Magnetic nanoparticles are effective heat mediators, drug nanocarriers, and contrast agents; various strategies have been suggested to selectively target tumor cancer cells. Our study presents magnetodynamic nanotherapy using DNA aptamer-functionalized 50 nm gold-coated magnetic nanoparticles exposed to a low frequency alternating magnetic field for selective elimination of tumor cells in vivo. The cell specific DNA aptamer AS-14 binds to the fibronectin protein in Ehrlich carcinoma hence helps deliver the gold-coated magnetic nanoparticles to the mouse tumor. Applying an alternating magnetic field of 50 Hz at the tumor site causes the nanoparticles to oscillate and pull the fibronectin proteins and integrins to the surface of the cell membrane. This results in apoptosis followed by necrosis of tumor cells without heating the tumor, adjacent healthy cells and tissues. The aptamer-guided nanoparticles and the low frequency alternating magnetic field demonstrates a unique non-invasive nanoscalpel technology for precise cancer surgery at the single cell level.

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Держатели документа:
Krasnoyarsk State Med Univ, Krasnoyarsk, Russia.
Russian Acad Sci, KSC Siberian Branch, Fed Res Ctr, Krasnoyarsk, Russia.
Siberian Fed Univ, Krasnoyarsk, Russia.
Univ Ottawa, Dept Chem & Biomol Sci, Ottawa, ON, Canada.
Inst Computat Modeling RAS SB, Krasnoyarsk, Russia.

Доп.точки доступа:
Belyanina, I. V.; Zamay, T. N.; Замай Т. Н.; Zamay, G. S.; Замай, Галина Сергеевна; Zamay, S. S.; Замай С. С.; Kolovskaya, Olga S.; Ivanchenko, Tatiana I.; Denisenko, Valery V.; Kirichenko, Andrey K.; Glazyrin, Yury E.; Garanzha, Irina V.; Grigorieva, Valentina V.; Shabanov, A. V.; Шабанов, Александр Васильевич; Veprintsev, Dmitry V.; Sokolov, A. E.; Соколов, Алексей Эдуардович; Sadovskii, Vladimir M.; Gargaun, Ana; Berezovski, M. V.; Kichkailo, Anna S.; Russian Scientific Fund [14-15-00805]
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