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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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Держатели документа:
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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A key role of tensile strain and surface termination in formation and properties of La0.7Sr0.3MnO3 composites with carbon nanotubes / E. A. Kovaleva [et al.] // Comput. Mater. Sci. - 2017. - Vol. 139. - P. 125-131, DOI 10.1016/j.commatsci.2017.07.021. - Cited References: 39. - This work was supported by National Research Foundation of Republic of Korea under Grant No. NRF-2017R1A2B4004440 and the government contract of the Ministry of Education and Science of the Russian Federation to Siberian Federal University (Grant No. 16.1455.2017/PCh). The authors would like to thank Joint Supercomputer Center of RAS, Moscow; Center of Equipment for Joint Use of Siberian Federal University, Krasnoyarsk; and Information Technology Centre, Novosibirsk State University for providing the access to their supercomputers. P.B.S gratefully acknowledges the financial supports of the Ministry of Education and Science of the Russian Federation in the framework of Increase Competitiveness Program of NUST «MISiS» (No. К2-2017-001) and RFBR, according to the research project No. 16-32-60138 mol_a_dk. E.A. Kovaleva would also like to acknowledge the program of the President of Russian Federation for Leading Scientific Schools Support (Grant No. 2016 NSh-7559.2016.2). . - ISSN 0927-0256
Кл.слова (ненормированные):
Carbon nanotubes -- LSMO -- Interface -- Spin polarization
Аннотация: Atomic and electronic structure of LSMO-based composites with carbon nanotubes were studied by means of density functional theory with respect to the termination of LSMO surface. The deformation of the tubes caused by the lattice mismatch with the substrate leads to a major change in their electronic structure. The surface terminated with Mn-O layer provides much stronger interaction with carbon nanotubes than Sr-O terminated one does. The interaction with transition metal atoms is essential for spin polarization of the nanotube while no spin injection was observed for Sr-O-supported tubes. © 2017 Elsevier B.V.

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Держатели документа:
Siberian Federal University, 79 Svobodny pr., Krasnoyarsk, Russian Federation
L.V. Kirensky Institute of Physics, 50 Akademgorodok, Krasnoyarsk, Russian Federation
Kyungpook National University, 80 Daehakro, Bukgu, Daegu, South Korea
National University of Science and Technology MISiS, 4 Leninskiy prospekt, Moscow, Russian Federation

Доп.точки доступа:
Kovaleva, E. A.; Kuzubov, A. A.; Кузубов, Александр Александрович; Avramov, P. V.; Kholtobina, A. S.; Kuklin, A. V.; Куклин, Артем Валентинович; Tomilin, F. N.; Томилин, Феликс Николаевич; Sorokin, P. B.
}
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A quantum chemical study of the formation of 2-hydroperoxy-coelenterazine in the Ca2+-regulated photoprotein obelin / L. Y. Antipina [et al.] // Journal of Structural Chemistry. - 2011. - Т. 52, № 5. - P870-875 . - ISSN 0022-4766. - ISSN 1573-8779

РИНЦ
Держатели документа:
Institute of Biophysics,Siberian Division,Russian Academy of Sciences
L. V. Kirensky Institute of Physics,Siberian Division,Russian Academy of Sciences
M. F. Reshetnev Siberian State Aerospace University

Доп.точки доступа:
Antipina, L.Y.; Tomilin, F. N.; Томилин, Феликс Николаевич; Ovchinnikov, S.G.; Vysotskii, E.S.
}
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A quantum chemical study of the formation of 2-hydroperoxy-coelenterazine in the Сa2+-regulated photoprotein obelin / L. Y. Antipina [et al.] // J. Struct. Chem. - 2011. - Vol. 52, Is. 5. - P. 870-875. - Cited References: 19. - The work was supported by RFBR (07-04-00930-a), the "Molecular and Cell Biology" Program of the Presidium of the Russian Academy of Sciences, and the Program of the Siberian Division of the Russian Academy of Sciences (project No. 2) within the implementation of the Federal Targeted Program "Scientific and Scientific Pedagogical Personnel of Innovative Russia, 2010" (P333 and P213). . - ISSN 0022-4766

РУБ Chemistry, Inorganic & Nuclear + Chemistry, Physical
Рубрики:
CALCIUM-DISCHARGED OBELIN
   SEMIEMPIRICAL METHODS
   1.7 ANGSTROM
   OPTIMIZATION
   PARAMETERS
   MECHANISM
   FLUORESCENCE
   ELEMENTS
   PROTEIN
   EMITTER
Кл.слова (ненормированные):
coelenterazine -- 2-hydroperoxy-coelenterazine -- Obelia longissima -- Renilla muelleri
Аннотация: The Ca2+-regulated photoprotein obelin determines the luminescence of the marine hydroid Obelia longissima. Bioluminescence is initiated by calcium and appears as a result of the oxidative decarboxylation related to the coelenterazine substrate. The luciferase of the luminescent marine coral Renilla muelleri (RM) also uses coelenterazine as a substrate. However, three proteins are involved in the in vivo bioluminescence of these animals: luciferase, green fluorescent protein, and Ca2+-regulated coelenterazine-binding protein (CBP). In fact, CBP that contains one strongly bound coelenterazine molecule is the RM luciferase substrate in the in vivo bioluminescent reaction. Coelenterazine becomes available for oxygen and the reaction with luciferase only after binding CBP with calcium ions. Unlike Ca2+-regulated photoproteins, the coelenterazine molecule is not activated by oxygen in the CBP molecule. In this work, by means of quantum chemical methods the behavior of substrates in these proteins is analyzed. It is shown that coelenterazine can form different tautomers: CLZ(2H) and CLZ(7H). The formation of 2-hydroperoxy-coelenterazine is studied. According to the obtained data, these proteins use different forms of the substrates for the reaction. In obelin, the substrate is in the CLZ(2H) form that affords hydrogen peroxide. In RM, coelenterazine is in the CLZ(7H) form, and therefore, CBP is not activated by oxygen.

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Держатели документа:
Russian Acad Sci, LV Kirensky Phys Inst, Siberian Div, Krasnoyarsk, Russia
Russian Acad Sci, Inst Biophys, Siberian Div, Krasnoyarsk, Russia
MF Reshetnev Siberian State Aerosp Univ, Krasnoyarsk, Russia

Доп.точки доступа:
Antipina, L. Yu.; Tomilin, F. N.; Томилин, Феликс Николаевич; Vysotski, E. S.; Высоцкий, Евгений Степанович; Ovchinnikov, S. G.; Овчинников, Сергей Геннадьевич
}
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Action of the atomic and electronic structure of pheromone molecules on the effectiveness of communication in xylophagous insects / P. V. Artyushenko [et al.] // J. Struct. Chem. - 2016. - Vol. 57, Is. 2. - P. 287-293, DOI 10.1134/S0022476616020074. - Cited References:27. - This work was supported by RFBR projects Nos. 13-04-00375 and16-04-00132. . - ISSN 0022-4766. - ISSN 1573-8779

РУБ Chemistry, Inorganic & Nuclear + Chemistry, Physical
Рубрики:
Monochamus-galloprovincialis coleoptera
   Density-functional theories
   Beetle Ips-typographus
   Pine sawyer beetle
   Aggregation pheromone
   Cerambycidae
   Attraction
   Components
   Attack
   Set
Кл.слова (ненормированные):
atomic and electronic structure -- functional density methods -- absorption -- spectra -- excited states -- xylophages -- pheromones
Аннотация: The B3LYD /6-31(p,d) density functional method is applied to pheromones of the forest xylophagous insects Ips typographus L., Monochamus urussovi Fisch., and Monochamus galloprovincialis Oliv. to calculate the absorption spectra and find excited states. The calculated results are used to assess the possible activity of the molecules when they are affected by solar radiation.

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Публикация на русском языке Влияние атомной и электронной структуры молекул феромонов на эффективность коммуникации насекомых-ксилофагов [Текст] / П. В. Артюшенко [и др.] // Журн. структ. химии. - 2016. - Т. 57 № 2. - С. 304-310

Держатели документа:
Russian Acad Sci, Kirensky Inst Phys, Siberian Branch, Krasnoyarsk, Russia.
Siberian Fed Univ, Krasnoyarsk, Russia.
Russian Acad Sci, Siberian Branch, KSC Presidium, Int Res Ctr Studies Extreme States Organism, Krasnoyarsk, Russia.
Russian Acad Sci, Siberian Branch, Sukachev Inst Forest, Krasnoyarsk, Russia.

Доп.точки доступа:
Artyushenko, P. V.; Артюшенко, Полина Владимировна; Tomilin, F. N.; Томилин, Феликс Николаевич; Kuzubov, A. A.; Кузубов, Александр Александрович; Ovchinnikov, S. G.; Овчинников, Сергей Геннадьевич; Tsikalova, P. E.; Ovchinnikova, T. M.; Soukhovolsky, V. G.; RFBR [13-04-00375, 16-04-00132]
}
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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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Atomic and electronic structure of MAX-phase Cr2AlC studied by DFT calculations / D. Ivanova, N. Fedorova, V. Kozak [et al.] // International workshop on the properties of functional MAX-materials (2nd FunMax) : book of abstracts / org. com. M. Farle [et al.]. - 2021. - P. 37

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Доп.точки доступа:
Farle, M. \org. com.\; Ovchinnikov, S. G. \org. com.\; Овчинников, Сергей Геннадьевич; Tarasov, A. S. \org. com.\; Тарасов, Антон Сергеевич; Smolyarova, T. E. \org. com.\; Смолярова, Татьяна Евгеньевна; Ivanova, D.; Fedorova, N.; Kozak, V.; Shubin, A.; Tomilin, F. N.; Томилин, Феликс Николаевич; International workshop on functional MAX-materials(2 ; 2021 ; Sept. 14-17 ; Krasnoyarsk (on-line)); Kirensky Institute of Physics; Siberian Federal Univercity
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Ca2+-triggered coelenterazine-binding protein Renilla: Expected and unexpected features / A. N. Kudryavtsev, V. V. Krasitskaya, M. K. Efremov [et al.] // Int. J. Mol. Sci. - 2023. - Vol. 24, Is. 3. - Ст. 2144, DOI 10.3390/ijms24032144. - Cited References: 24. - This research was supported by the state budget allocated to the fundamental research at the Russian Academy of Sciences, project No. 0287-2022-0002 and the Interagency Supercomputer Center of the Russian Academy of Sciences, MVS-100K and MVS-10P . - ISSN 1661-6596. - ISSN 1422-0067
Кл.слова (ненормированные):
Ca2+-triggered coelenterazine-binding protein -- coelenterazine -- furimazine -- luciferase NanoLuc -- B3LYP -- TDDFT -- fragmented molecular orbitals method -- DFTB3
Аннотация: Ca2+-triggered coelenterazine-binding protein (CBP) is a natural form of the luciferase substrate involved in the Renilla bioluminescence reaction. It is a stable complex of coelenterazine and apoprotein that, unlike coelenterazine, is soluble and stable in an aquatic environment and yields a significantly higher bioluminescent signal. This makes CBP a convenient substrate for luciferase-based in vitro assay. In search of a similar substrate form for the luciferase NanoLuc, a furimazine-apoCBP complex was prepared and verified against furimazine, coelenterazine, and CBP. Furimazine-apoCBP is relatively stable in solution and in a frozen or lyophilized state, but as distinct from CBP, its bioluminescence reaction with NanoLuc is independent of Ca2+. NanoLuc turned out to utilize all the four substrates under consideration. The pairs of CBP-NanoLuc and coelenterazine-NanoLuc generate bioluminescence with close efficiency. As for furimazine-apoCBP-NanoLuc pair, the efficiency with which it generates bioluminescence is almost twice lower than that of the furimazine-NanoLuc. The integral signal of the CBP-NanoLuc pair is only 22% lower than that of furimazine-NanoLuc. Thus, along with furimazine as the most effective NanoLuc substrate, CBP can also be recommended as a substrate for in vitro analytical application in view of its water solubility, stability, and Ca2+-triggering “character”.

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Держатели документа:
Institute of Biophysics, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia
School of Fundamental Biology and Biotechnology, School of Non-Ferrous Metals and Material Science, Siberian Federal University, pr. Svobodny 79, 660041 Krasnoyarsk, Russia
Kirensky Institute of Physics, Federal Research Center “Krasnoyarsk Science Center SB”, 660036 Krasnoyarsk, Russia

Доп.точки доступа:
Kudryavtsev, Alexander N.; Krasitskaya, Vasilisa V.; Efremov, Maxim K.; Zangeeva, Sayana V.; Rogova, A. V.; Рогова, Анастасия Владимировна; Tomilin, F. N.; Томилин, Феликс Николаевич; Frank, Ludmila A.
}
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Calculating the energy of vacancies and adatoms in a hexagonal SiC monolayer / A. A. Kuzubov [et al.] // Russ. J. Phys. Chem. A. - 2012. - Vol. 86, Is. 7. - P. 1091-1095, DOI 10.1134/S0036024412070138. - Cited References: 21 . - ISSN 0036-0244

РУБ Chemistry, Physical
Рубрики:
INITIO MOLECULAR-DYNAMICS
ELECTRONIC-PROPERTIES
ABSORPTION-SPECTRA
Кл.слова (ненормированные):
silicon carbide -- defects -- adatoms -- density functional method
Аннотация: It is noted that the development of semiconductor SiC-electronics is prevented by a low quality of grown silicon carbide single crystals. It is found that structural defects of a substrate penetrating into an epitaxial layer upon subsequent homoepitaxial growth can considerably degrade a device's characteristics. We investigate the effect of the deformation of a hexagonal SiC monolayer on vacancy stability and material properties, and study the processes of silicon and carbon adatom migration over a surface of SiC.

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Публикация на русском языке Расчет энергии вакансий и адатомов в монослое гексагонального SiC [Текст] / А. А. Кузубов [и др.] // Журн. физ. химии. - 2012. - Т. 86 № 7. - С. 1207-1211

Держатели документа:
[Kuzubov, A. A.
Eliseeva, N. S.
Tomilin, F. N.
Tolstaya, A. V.] Siberian Fed Univ, Krasnoyarsk 660041, Russia
[Kuzubov, A. A.
Krasnov, P. O.
Tomilin, F. N.
Fedorov, A. S.] Russian Acad Sci, LV Kirensky Phys Inst, Siberian Branch, Krasnoyarsk 660036, Russia
[Kuzubov, A. A.
Krasnov, P. O.] Siberian State Technol Univ, Krasnoyarsk 660049, Russia

Доп.точки доступа:
Kuzubov, A. A.; Кузубов, Александр Александрович; Eliseeva, N. S.; Krasnov, P. O.; Краснов, Павел Олегович; Tomilin, F. N.; Томилин, Феликс Николаевич; Fedorov, A. S.; Федоров, Александр Семенович; Tolstaya, A. V.
}
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10.

Characterizing aptamer interaction with the oncolytic virus VV-GMCSF-Lact / M. A. Dymova, D. O. Malysheva, V. K. Popova [et al.] // Molecules. - 2024. - Vol. 29, Is. 4. - Ст. 848, DOI 10.3390/molecules29040848. - Cited References: 46. - This study was supported by the Russian Science Foundation grant No. 22-64-00041, available online: https://rscf.ru/en/project/22-64-00041/ (accessed on 6 February 2024). This work was supported by the Russian state-funded project for ICBFM SB RAS (grant number 121030200173-6) . - ISSN 1420-3049
Кл.слова (ненормированные):
aptamer -- oncolytic virus -- glioma -- dynamic light scattering -- microscale thermophoresis
Аннотация: Aptamers are currently being investigated for their potential to improve virotherapy. They offer several advantages, including the ability to prevent the aggregation of viral particles, enhance target specificity, and protect against the neutralizing effects of antibodies. The purpose of this study was to comprehensively investigate an aptamer capable of enhancing virotherapy. This involved characterizing the previously selected aptamer for vaccinia virus (VACV), evaluating the aggregation and molecular interaction of the optimized aptamers with the recombinant oncolytic virus VV-GMCSF-Lact, and estimating their immunoshielding properties in the presence of human blood serum. We chose one optimized aptamer, NV14t_56, with the highest affinity to the virus from the pool of several truncated aptamers and built its 3D model. The NV14t_56 remained stable in human blood serum for 1 h and bound to VV-GMCSF-Lact in the micromolar range (Kd ≈ 0.35 μM). Based on dynamic light scattering data, it has been demonstrated that aptamers surround viral particles and inhibit aggregate formation. In the presence of serum, the hydrodynamic diameter (by intensity) of the aptamer–virus complex did not change. Microscale thermophoresis (MST) experiments showed that NV14t_56 binds with virus (EC50 = 1.487 × 109 PFU/mL). The analysis of the amplitudes of MST curves reveals that the components of the serum bind to the aptamer–virus complex without disrupting it. In vitro experiments demonstrated the efficacy of VV-GMCSF-Lact in conjunction with the aptamer when exposed to human blood serum in the absence of neutralizing antibodies (Nabs). Thus, NV14t_56 has the ability to inhibit virus aggregation, allowing VV-GMCSF-Lact to maintain its effectiveness throughout the storage period and subsequent use. When employing aptamers as protective agents for oncolytic viruses, the presence of neutralizing antibodies should be taken into account.

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Держатели документа:
Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev av. 8, 630090 Novosibirsk, Russia
Department of Natural Sciences, Novosibirsk State University, Pirogova str. 1, 630090 Novosibirsk, Russia
State Research Center of Virology and Biotechnology “Vector”, 630559 Koltsovo, Russia
Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University Named after Prof. V.F. Voyno-Yasenetsky, Partizana Zheleznyaka str. 1, 660022 Krasnoyarsk, Russia
Federal Research Center KSC SB RAS, 50 Akademgorodok, 660036 Krasnoyarsk, Russia
Kirensky Institute of Physics, 50/38 Akademgorodok, 660012 Krasnoyarsk, Russia

Доп.точки доступа:
Dymova, M. A.; Malysheva, D. O.; Popova, V. K.; Dmitrienko, E. V.; Endutkin, A. V.; Drokov, D. V.; Mukhanov, V. S.; Byvakina, A. A.; Kochneva, G. V.; Artyushenko, P. V.; Shchugoreva, I. A.; Rogova, A. V.; Tomilin, F. N.; Томилин, Феликс Николаевич; Kichkailo, A. S.; Richter, V. A.; Kuligina, E. V.
}
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11.

    Charge-transfer plasmons with narrow conductive molecular bridges: A quantum-classical theory / A. S. Fedorov, P. O. Krasnov, M. A. Visotin [et al.] // J. Chem. Phys. - 2019. - Vol. 150, Is. 24. - Ст. 244125, DOI 10.1063/1.5131734. - Cited References: 56. - This study was supported by the Russian Science Foundation, Project No. 18-13-00363. . - ISSN 0021-9606. - ISSN 1089-7690
   Перевод заглавия: Плазмоны с переносом заряда в системах с узкими проводящими молекулярными мостиками: квантово-классическая теория
Аннотация: We analyze a new type of plasmon system arising from small metal nanoparticles linked by narrow conductive molecular bridges. In contrast to the well-known charge-transfer plasmons, the bridge in these systems consists only of a narrow conductive molecule or polymer in which the electrons move in a ballistic mode, showing quantum effects. The plasmonic system is studied by an original hybrid quantum-classical model accounting for the quantum effects, with the main parameters obtained from first-principles density functional theory simulations. We have derived a general analytical expression for the modified frequency of the plasmons and have shown that its frequency lies in the near-infrared (IR) region and strongly depends on the conductivity of the molecule, on the nanoparticle–molecule interface, and on the size of the system. As illustrated, we explored the plasmons in a system consisting of two small gold nanoparticles linked by a conjugated polyacetylene molecule terminated by sulfur atoms. It is argued that applications of this novel type of plasmon may have wide ramifications in the areas of chemical sensing and IR deep tissue imaging.

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Держатели документа:
Kirensky Institute of Physics, Federal Research Center KSC SB RAS, 660036 Krasnoyarsk, Russia
Federal Siberian Research Clinical Center under FMBA of Russia, 660037 Krasnoyarsk, Russia
Siberian Federal University, 660041 Krasnoyarsk, Russia
Reshetnev Siberian State University of Science and Technology, 660037 Krasnoyarsk, Russia
Division of Theoretical Chemistry and Biology, Royal Institute of Technology, SE-100 44 Stockholm, Sweden

Доп.точки доступа:
Fedorov, A. S.; Федоров, Александр Семенович; Krasnov, P. O.; Visotin, M. A.; Высотин, Максим Александрович; Tomilin, F. N.; Томилин, Феликс Николаевич; Polyutov, S. P.; Полютов, Сергей Петрович; Ågren, H.
}
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12.

Choice of the DFT functional for calculation electronic properties of (CrFe)SiC MAX phases / A. Shubin, J. Olshevskaya, A. Kovaleva, F. N. Tomilin // International workshop on the properties of functional MAX-materials (2nd FunMax) : book of abstracts / org. com. M. Farle [et al.]. - 2021. - P. 47

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Farle, M. \org. com.\; Ovchinnikov, S. G. \org. com.\; Овчинников, Сергей Геннадьевич; Tarasov, A. S. \org. com.\; Тарасов, Антон Сергеевич; Smolyarova, T. E. \org. com.\; Смолярова, Татьяна Евгеньевна; Shubin, A.; Olshevskaya, J.; Kovaleva, A.; Tomilin, F. N.; Томилин, Феликс Николаевич; International workshop on functional MAX-materials(2 ; 2021 ; Sept. 14-17 ; Krasnoyarsk (on-line)); Kirensky Institute of Physics; Siberian Federal Univercity
}
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13.

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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14.

Contact-induced spin polarization in BNNT(CNT)/TM (TM=Co, Ni) nanocomposites / A. A. Kuzubov [et al.] // J. Appl. Phys. - 2014. - Vol. 116, Is. 8. - Ст. 084309, DOI 10.1063/1.4894157. - Cited References: 21. - This work was supported by the Russian Scientific Fund, Project No. 14-13-00139. The authors would like to thank Institute of Computational Modelling of SB RAS, Krasnoyarsk; Joint Supercomputer Center of RAS, Moscow; the HPC Research Department and Center of Equipment for Joint Use of Siberian Federal University, Krasnoyarsk; Siberian Supercomputer Center (SSCC) of SB RAS, Novosibirsk; and Laboratory of Parallel Information Technologies 21 of Research Computing Center of Moscow State University (the SKIF MSU "Chebyshev" system) for providing the access to their supercomputers. . - ISSN 0021-8979. - ISSN 1089-7550

РУБ Physics, Applied
Рубрики:
TOTAL-ENERGY CALCULATIONS
   HEXAGONAL BORON-NITRIDE
   WAVE BASIS-SET
   AB-INITIO
   PSEUDOPOTENTIALS
   DISPERSION
   NANOTUBE
   NI(111)
Аннотация: The interaction between carbon and BN nanotubes (NT) and transition metal Co and Ni supports was studied using electronic structure calculations. Several configurations of interfaces were considered, and the most stable ones were used for electronic structure analysis. All NT/Co interfaces were found to be more energetically favorable than NT/Ni, and conductive carbon nanotubes demonstrate slightly stronger bonding than semiconducting ones. The presence of contact-induced spin polarization was established for all nanocomposites. It was found that the contact-induced polarization of BNNT leads to the appearance of local conductivity in the vicinity of the interface while the rest of the nanotube lattice remains to be insulating. (c) 2014 AIP Publishing LLC.

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Держатели документа:
Siberian Fed Univ, Krasnoyarsk 660041, Russia
LV Kirensky Inst Phys SB RAS, Krasnoyarsk 660036, Russia
Siberian State Technol Univ, Krasnoyarsk 660049, Russia
Japan Atom Energy Agcy, Adv Sci Res Ctr, Tokai, Ibaraki 3191195, Japan

Доп.точки доступа:
Kuzubov, A. A.; Кузубов, Александр Александрович; Kovaleva, E. A.; Ковалева, Евгения Андреевна; Avramov, P. V.; Аврамов, Павел Вениаминович; Kuklin, A. V.; Куклин, Артем Валентинович; Mikhaleva, N. S.; Михалева, Наталья Сергеевна; Tomilin, F. N.; Томилин, Феликс Николаевич; Sakai, S.; Entani, S.; Matsumoto, Y.; Naramoto, H.; Russian Scientific Fund [14-13-00139]
}
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15.

Correlation of the chemical properties of carbon nanotubes with their atomic and electronic structures / F. N. Tomilin [et al.] ; Translated by N. Korovin // Phys. Solid State. - 2004. - Vol. 46, Is. 6. - P. 1179-1182, DOI 10.1134/1.1767264. - Cited References: 16. - This work was performed at the “Quantum-Chemical Calculations of Nanoclusters” Collective Use Center of the Krasnoyarsk Center of Science and Education in High Technology, which is supported by the Russian State Federal Program “Integration of Higher Education and Fundamental Science” (projects nos. 31 and 69) and the 6th Competition of Research Projects of Young Scientists of the Russian Academy of Sciences (project no. 155) . - ISSN 1063-7834

РУБ Physics, Condensed Matter

Аннотация: The nature of chemical bonding in carbon nanoclusters is investigated by the PM3 semiempirical quantum-chemical method. The influence of the atomic structure on the electronic characteristics and chemical properties of nanoclusters is analyzed. A sigma-pi model is proposed for the chemical bonding in nanotubes. It is shown that, in the framework of the proposed model, nanotubes are objects characterized by a small contribution of pi states to the valence band top. (C) 2004 MAIK "Nauka/Interperiodica".

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Публикация на русском языке Связь химических свойств углеродных нанотрубок с их атомной и электронной структурами [Текст] / Ф. Н. Томилин [и др.] // Физ. тверд. тела. - 2004. - Т. 46 Вып. 6. - С. 1143-1146

Держатели документа:
Russian Acad Sci, Siberian Div, Inst Chem & Chem Technol, Krasnoyarsk 660041, Russia
Russian Acad Sci, Siberian Div, LV Kirensky Phys Inst, Krasnoyarsk 660036, Russia
Siberian State Technol Univ, Krasnoyarsk 660041, Russia
Krasnoyarsk State Univ, Krasnoyarsk 660079, Russia
ИФ СО РАН
ИХХТ СО РАН
Inst. of Chem./Chemical Technology, Siberian Division, Russian Academy of Sciences, Krasnoyarsk, 660041, Russian Federation
Kirensky Institute of Physics, Siberian Division, Russian Academy of Sciences, Akademgorodok, Krasnoyarsk, 660036, Russian Federation
Siberian Stt. Technol. University, Krasnoyarsk, 660041, Russian Federation
Krasnoyarsk State University, Krasnoyarsk, 660079, Russian Federation

Доп.точки доступа:
Tomilin, F. N.; Томилин, Феликс Николаевич; Avramov, P. V.; Аврамов, Павел Вениаминович; Kuzubov, A. A.; Кузубов, Александр Александрович; Ovchinnikov, S. G.; Овчинников, Сергей Геннадьевич; Pashkov, G. L.; Пашков, Геннадий Леонидович; Korovin, N. \пер.\
}
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16.

Density-functional theory study of the electronic structure of thin Si/SiO2 quantum nanodots and nanowires / P. V. Avramov [et al.] // Phys. Rev. B. - 2007. - Vol. 75, Is. 20. - Ст. 205427, DOI 10.1103/PhysRevB.75.205427. - Cited References: 63 . - ISSN 1098-0121

РУБ Physics, Condensed Matter
Рубрики:
ERBIUM ION LUMINESCENCE
   TOTAL-ENERGY CALCULATIONS
   WAVE BASIS-SET
   POROUS SILICON
   OPTICAL-PROPERTIES
   OXIDIZED SI
   SEMICONDUCTOR NANOWIRES
   PHASE-TRANSFORMATIONS
   NANOCRYSTALS
   CONFINEMENT
Аннотация: The atomic and electronic structures of a set of proposed pentagonal thin (1.6 nm in diameter) silicon/silica quantum nanodots (QDs) and nanowires (NWs) with narrow interface, as well as parent metastable silicon structures (1.2 nm in diameter), were studied using cluster B3LYP/6-31G(*) and periodic boundary condition (PBC) plane-wave (PW) pseudopotential (PP) local-density approximation methods. The total density of states (TDOS) of the smallest quasispherical QD (Si-85) corresponds well to the PBC PW PP LDA TDOS of the crystalline silicon. The elongated SiQDs and SiNWs demonstrate the metallic nature of the electronic structure. The surface oxidized layer opens the band gap in the TDOS of the Si/SiO2 species. The top of the valence band and the bottom of conduction band of the particles are formed by the silicon core derived states. The theoretical band gap width is determined by the length of the Si/SiO2 clusters and describes the size confinement effect in the experimental photoluminescence spectra of the silica embedded nanocrystalline silicon with high accuracy.

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Держатели документа:
Japan Atom Energy Agcy, Adv Sci Res Ctr, Takasaki Branch, Takasaki, Gumma 3701292, Japan
Russian Acad Sci, LV Kirensky Phys Inst, SB, Krasnoyarsk 660036, Russia
Russian Acad Sci, NM Emanuel Inst Biochem Phys, Moscow 119334, Russia
Kyoto Univ, Dept Energy Sci & Technol, Kyoto 6068501, Japan
ИФ СО РАН

Доп.точки доступа:
Avramov, P. V.; Аврамов, Павел Вениаминович; Kuzubov, A. A.; Кузубов, Александр Александрович; Fedorov, A. S.; Федоров, Александр Семенович; Sorokin, P. B.; Tomilin, F. N.; Томилин, Феликс Николаевич; Maeda, Y.
}
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17.

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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18.

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

Доп.точки доступа:
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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19.

Effect of complexation with closo-decaborate anion on photophysical properties of copolyfluorenes containing dicyanophenanthrene units in the main chain / A. A. Yakimanskiy, K. I. Kaskevich, T. G. Chulkova [et al.] // Micro. - 2023. - Vol. 3, Is. 4. - P. 930-940, DOI 10.3390/micro3040063. - Cited References: 23. - This work was supported by the Russian Science Foundation, grant no. 23-43-00060 . - ISSN 2673-8023
Кл.слова (ненормированные):
CAM-B3LYP -- charge transfer -- copolyfluorene -- energy transfer -- hole-electron distribution -- nitrilium derivatives of closo-decaborate anions -- lambda-diagnostic -- luminescence -- phenanthrene-9,10-dicarbonitrile -- TD-DFT
Аннотация: The functionalization of copolyfluorenes containing dicyanophenanthrene units by closo-decaborate anion is described. Target copolyfluorenes were analyzed using SEM, UV-vis, luminescence, NMR, and Fourier-transform infrared (FTIR) spectroscopy. The effect of complexation with the closo-decaborate anion on the photophysical properties was studied both experimentally and theoretically. The PL data indicate an efficient charge transfer from fluorene to the dicyanophenanthrene units coordinated to the closo-decaborate. The coordination of closo-decaborate clusters to the nitrile groups of copolyfluorenes provides an important route to new materials for sensors and light-emitting devices while, at the same time, serving as a platform for further study of the nature of boron clusters.

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Держатели документа:
Institute of Macromolecular Compounds, RAS, Bolshoi Prospect of Vasilyevsky Island 31, Saint Petersburg 199004, Russia
Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
Kurnakov Institute of General and Inorganic Chemistry, RAS, Moscow 119991, Russia
Kirensky Institute of Physics, Federal Research Center KSC SB RAS, Krasnoyarsk 660036, Russia
Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center KSC SB RAS, Krasnoyarsk 660041, Russia

Доп.точки доступа:
Yakimanskiy, Anton A.; Kaskevich, Ksenia I.; Chulkova, Tatiana G.; Krasnopeeva, Elena L.; Savilov, Serguei V.; Voinova, Vera V.; Neumolotov, Nikolay K.; Zhdanov, Andrey P.; Rogova, Anastasia V.; Рогова, Анастасия Владимировна; Tomilin, F. N.; Томилин, Феликс Николаевич; Zhizhin, Konstantin Yu.; Yakimansky, Alexander V.
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20.

Effect of electron correlations on the structure of photoprotein substrates / S. G. Ovchinnikov [et al.] // JETP Letters. - 2010. - Vol. 91, Is. 9. - P. 490-493, DOI 10.1134/S0021364010090122. - Cited References: 14. - This work was supported by the Russian Foundation for Basic Research (project no. 07-04-00930-a), by the Presidium of the Russian Academy of Sciences (program "Molecular and Cellular Biology"), and by the Siberian Branch, Russian Academy of Sciences (project no. 2). . - ISSN 0021-3640

РУБ Physics, Multidisciplinary
Рубрики:
ANGSTROM RESOLUTION
   CRYSTAL-STRUCTURE
   AEQUORIN
   ENERGY
   OBELIN
   GAS
Аннотация: The electronic structure and total energy of various isomeric forms of coelenterazine and coelenteramide have been calculated by quantum chemistry methods both in the single-electron approximation and taking into account correlation effects. It has been shown that the inclusion of electron correlations makes it possible to obtain the structure of the coelenteramide close to the experimentally determined structure, as well as to choose the structure of the coelenterazine CLZ(1H) as the most probable isomeric form.

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Держатели документа:
[Ovchinnikov, S. G.
Tomilin, F. N.] Russian Acad Sci, LV Kirensky Phys Inst, Siberian Branch, Krasnoyarsk 660036, Russia
[Ovchinnikov, S. G.
Antipina, L. Yu.
Tomilin, F. N.
Kuzubov, A. A.] Siberian Fed Univ, Krasnoyarsk 660041, Russia
ИФ СО РАН
Kirensky Institute of Physics, Siberian Branch, Russian Academy of Sciences, Akademgorodok, Krasnoyarsk 660036, Russian Federation
Siberian Federal University, Krasnoyarsk 660041, Russian Federation

Доп.точки доступа:
Ovchinnikov, S. G.; Овчинников, Сергей Геннадьевич; Antipina, L. Yu.; Tomilin, F. N.; Томилин, Феликс Николаевич; Kuzubov, A. A.; Кузубов, Александр Александрович
}
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