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Вид документа : Статья из сборника (однотомник)
Шифр издания :
Автор(ы) : Шустин, Максим Сергеевич, Морячков, Роман Владимирович, Заблуда, Владимир Николаевич, Щугорева, Ирина Андреевна, Артюшенко, Полина Владимировна, Кичкайло, Анна Сергеевна, Спиридонова В. А., Берлина А. Н., Соколов, Алексей Эдуардович
Заглавие : Низкоэнергетическая модель спин-поляризованной сверхпроводящей нанопроволоки в режиме сильных электронных корреляций
Коллективы : Сибирский семинар по высокотемпературной сверхпроводимости и физике наноструктур, Институт неорганической химии им. А.В. Николаева Сибирского отделения РАН, Новосибирский государственный университет, Новосибирский государственный технический университет, Сибирский федеральный университет, Институт физики им. Л.В. Киренского Сибирского отделения РАН, Омский государственный университет им. Ф.М. Достоевского, Научный совет РАН по физике низких температур
Место публикации : XIII Cибирский семинар по высокотемпературной сверхпроводимости и физике наноструктур (ОКНО-2021): сб. тезисов докладов/ сопредс., чл. прогр. ком. С. Г. Овчинников и др. - 2021. - С. 49. - ISBN 978-5-90168-835-9
Примечания : Библиогр.: 4. - Работа выполнена при поддержке РФФИ (проект No 19-02-00348), Правительства Красноярского края, Красноярского краевого фонда науки в рамках научного проекта «Спиновые флуктуации и магнитный порядок в проблеме реализации майорановских мод в низкоразмерных системах» (No 20-42-243001)
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Вид документа : Статья из сборника (однотомник)
Шифр издания :
Автор(ы) : Морячков, Роман Владимирович, Заблуда, Владимир Николаевич, Щугорева, Ирина Андреевна, Артюшенко, Полина Владимировна, Кичкайло, Анна Сергеевна, Спиридонова В. А., Берлина А. Н., Соколов, Алексей Эдуардович
Заглавие : Исследование пространственной структуры бионаноконъюгатов на основе ДНК-аптамеров синхротронными методами
Коллективы : Сибирский семинар по высокотемпературной сверхпроводимости и физике наноструктур, Институт неорганической химии им. А.В. Николаева Сибирского отделения РАН, Новосибирский государственный университет, Новосибирский государственный технический университет, Сибирский федеральный университет, Институт физики им. Л.В. Киренского Сибирского отделения РАН, Омский государственный университет им. Ф.М. Достоевского, Научный совет РАН по физике низких температур
Место публикации : XIII Cибирский семинар по высокотемпературной сверхпроводимости и физике наноструктур (ОКНО-2021): сб. тезисов докладов/ сопредс., чл. прогр. ком. С. Г. Овчинников и др. - 2021. - С. 50. - ISBN 978-5-90168-835-9
Примечания : Библиогр.: 1
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Вид документа : Статья из сборника (однотомник)
Шифр издания :
Автор(ы) : Moryachkov R. V., Morozov D., Mironov V., Shchugoreva I., Artyushenko P. V., Zamay G. S., Molodenskiy D. S., Zabluda V. N., Kichkailo A.S., Sokolov A. Е.
Заглавие : The role of small-angle X-ray scattering and molecular simulations in 3D structure elucidation of a DNA aptamer-cancer cells magnetic separation agent
Коллективы : International Baltic Conference on Magnetism: focus on nanobiomedicine and smart materials, Балтийский федеральный университет им. И. Канта
Место публикации : 4th International Baltic Conference on Magnetism (IBCM 2021): Book of abstracts. - 2021. - P.168
Примечания : Cited References: 2. - The reported study was funded by RFBR, project number 19-32-90266
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Morozov D., Mironov V., Moryachkov R. V., Shchugoreva I. A., Artyushenko P. V., Zamay G. S., Kolovskaya O. S., Zamay T. N., Krat A. V., Molodenskiy D. S., Zabluda V. N., Veprintsev D. V., Sokolov A. Е., Zukov R. A., Berezovski M. V., Tomilin F. N., Fedorov D. G., Alexeev Y., Kichkailo A. S.
Заглавие : The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer
Место публикации : Mol. Ther. Nucl. Acids. - 2021. - Vol. 25. - P.316-327. - ISSN 21622531 (ISSN), DOI 10.1016/j.omtn.2021.07.015
Примечания : Cited References: 84. - The research was performed using equipment of the Shared Core Facilities of Molecular and Cell Technologies at Krasnoyarsk State Medical University. The synchrotron SAXS data were collected at beamline P12 operated by EMBL Hamburg at the PETRA III storage ring (DESY, Hamburg, Germany). A.S.K. is grateful to Aptamerlab LLC for the assistance in aptamer design and 3D structure analyses. We thank Ivan Lapin for his help with microscopic analyses. Microscopic analyses using Carl Zeiss LSM 800 were carried out at the Center for Bioassay, Nanotechnology and Nanomaterials Safety (“Biotest-Nano”) (Multiple-Access Center, Tomsk State University, Tomsk, Russia). D.M. also thanks the CSC-IT Center in Espoo, Finland, for providing computational resources. The study was supported by a grant from the Russian Science Foundation (project number 21-73-20240) for A.S.K. R.V.M aknowledges Russian Foundation for Basic Research (project number 19-32-90266) for funding. D.G.F. acknowledges financial support by JSPS KAKENHI, grant number 19H02682. D.S.M. acknowledges financial support by BMBF grant number 16QK10A (SAS-BSOFT). Y.A.’s work at Argonne National Laboratory was supported by the US Department of Energy, Office of Science, under contract DE-AC02-06CH11357. D.M. received funding as a part of BioExcel CoE (https://bioexcel.eu/), a project funded by the European Union contracts H2020-INFRAEDI-02-2018-823830 and H2020-EINFRA-2015-1-675728. V.M. thanks Russian Foundation for Basic Research (project number 19-03-00043) for funding
Аннотация: Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity. Here, we present a general optimization procedure for finding the most populated atomistic structures of DNA aptamers. Based on the existed aptamer LC-18 for lung adenocarcinoma, a new truncated LC-18 (LC-18t) aptamer LC-18t was developed. A three-dimensional (3D) shape of LC-18t was reported based on small-angle X-ray scattering (SAXS) experiments and molecular modeling by fragment molecular orbital or molecular dynamic methods. Molecular simulations revealed an ensemble of possible aptamer conformations in solution that were in close agreement with measured SAXS data. The aptamer LC-18t had stronger binding to cancerous cells in lung tumor tissues and shared the binding site with the original larger aptamer. The suggested approach reveals 3D shapes of aptamers and helps in designing better affinity probes.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Mironov, Vladimir, Shchugoreva I. A., Artyushenko P. V., Morozov D. I., Borbone N., Oliviero G., Zamay T. N., Moryachkov R. V., Kolovskaya, ., Lukyanenko K. A., Song Y. L., Merkuleva I. A., Zabluda V. N., Peters G., Koroleva L. S., Veprintsev D. V., Glazyrin Y. E., Volosnikova E. A., Belenkaya S. V., Esina T. I., Isaeva A. A., Nesmeyanova, ., Shanshin D. V., Berlina A. N., Komova N. S., Svetlichnyi V. A., Silnikov V. N., Shcherbakov D. N., Zamay G. S., Zamay S. S., Smolyarova T. E., Tikhonova E. P., Chen U. S., Jeng G., Condorelli V., Franciscis G., Groenhof C. Y., Yang A. A., Moskovsky D. G., Fedorov F. N., Tomilin F. N., Tan Y., Alexeev M. V., Berezovski A. S., Kichkailo A.S.
Заглавие : Structure- and interaction-based design of anti-SARS-CoV-2 Aptamers
Коллективы : Aptamerlab LCC; U.S. Department of Energy, Office of ScienceUnited States Department of Energy (DOE) [DE-AC02-06CH11357]; European UnionEuropean Commission [H2020-INFRAEDI-02-2018-823830, H2020-EINFRA-2015-1-675728, 872391, PRISAR2 872860]; CSC-IT center in Espoo, Finland; PRACE; Russian Foundation for Basic ResearchRussian Foundation for Basic Research (RFBR) [19-03-00043]; Ministry of Science and Higher Education of Russian Federation (state assignment of the Research Center of Biotechnology RAS); Italian Ministry of Education and ResearchMinistry of Education, Universities and Research (MIUR) [FISR2020 _00177]; Canadian Institutes of Health ResearchCanadian Institutes of Health Research (CIHR) [OV1-170353]; Russian Science FoundationRussian Science Foundation (RSF) [21-73-20240]
Место публикации : Chem. - Eur. J. - 2022. - Vol. 28, Is. 12. - Ст.e202104481. - ISSN 0947-6539, DOI 10.1002/chem.202104481. - ISSN 1521-3765(eISSN)
Примечания : Cited References: 85. - The authors are grateful to JCSS Joint Super Computer Center of the Russian Academy of Sciences – Branch of Federal State Institution “Scientific Research Institute for System Analysis of the Russian Academy of Sciences” for providing supercomputers for computer simulations. The authors thank the RSC Group (www.rscgroup.ru) and personally Mr. Oleg Gorbachev for the constant support and establishment of “The Good Hope Net Project” (www.thegoodhope.net) multifunctional non-profit anti-CoVID research project. The authors also thank the Helicon Company (www.helicon.ru) and personally Olesya Kucenko, Alexander Kolobov, Leonid Klimov for instrumental support and help with conducting fluorescence polarization assays, which were performed on a demo instrument Clariostar Plus microplate reader (BMG LABTECH, Germany). We thank Dr. Yong-Zhen Zhang for providing the genome sequence of 2019-nCoV and Dr. Xinquan Wang for providing the crystal structure of the binding domain of the SARS-2 Spike protein. The authors are grateful to Aptamerlab LCC financial support (www.aptamerlab.com). Y.A.’s work at Argonne National Laboratory was supported by the U.S. Department of Energy, Office of Science, under contract DE-AC02-06CH11357. The work of D.M. and G.G. has been done as part of the BioExcel CoE (www.bioexcel.eu), a project funded by the European Union contracts H2020-INFRAEDI-02-2018-823830 and H2020-EINFRA-2015-1-675728. D.M. and G.G. also thank the CSC-IT center in Espoo, Finland, as well as PRACE for awarding access to resource Curie-Rome based in France at GENCI. V.M. thanks Russian Foundation for Basic Research (project number 19-03-00043). A.B.’s and N.K.’s work was supported by the Ministry of Science and Higher Education of Russian Federation (state assignment of the Research Center of Biotechnology RAS). V. deF. G.C., N.B and G.O. are grateful to FISR2020 _00177 Shield, Italian Ministry of Education and Research, for funding. GC is grateful to the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement: cONCReTE 872391; PRISAR2 872860. Use of the 13 A BioSAXS beamtime at the Taiwan Photon Source is acknowledged. The work of M.V.B was funded by the Canadian Institutes of Health Research grant OV1-170353. SAXS measurements and PIEDA analyses were funded by the Russian Science Foundation (project No 21-73-20240 for A.S.K.)
Предметные рубрики: BIOLOGICAL MACROMOLECULES
SOLUTION SCATTERING
BINDING
SPIKE
Аннотация: Aptamer selection against novel infections is a complicated and time-consuming approach. Synergy can be achieved by using computational methods together with experimental procedures. This study aims to develop a reliable methodology for a rational aptamer in silico et vitro design. The new approach combines multiple steps: (1) Molecular design, based on screening in a DNA aptamer library and directed mutagenesis to fit the protein tertiary structure; (2) 3D molecular modeling of the target; (3) Molecular docking of an aptamer with the protein; (4) Molecular dynamics (MD) simulations of the complexes; (5) Quantum-mechanical (QM) evaluation of the interactions between aptamer and target with further analysis; (6) Experimental verification at each cycle for structure and binding affinity by using small-angle X-ray scattering, cytometry, and fluorescence polarization. By using a new iterative design procedure, structure- and interaction-based drug design (SIBDD), a highly specific aptamer to the receptor-binding domain of the SARS-CoV-2 spike protein, was developed and validated. The SIBDD approach enhances speed of the high-affinity aptamers development from scratch, using a target protein structure. The method could be used to improve existing aptamers for stronger binding. This approach brings to an advanced level the development of novel affinity probes, functional nucleic acids. It offers a blueprint for the straightforward design of targeting molecules for new pathogen agents and emerging variants.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Moryachkov R. V., Nikolaeva P. A., Spiridonova V. A.
Заглавие : Structure approaches to study of DNA aptamers in solution
Место публикации : Sib. Med. Rev. - 2021. - Vol. 2021, Is. 2. - P.76-78. - ISSN 18199496 (ISSN), DOI 10.20333/2500136-2021-2-76-78; Сиб. мед. обозрение
Примечания : Cited References: 5. - The reported study was funded by RFBR, project number 19-32-90266
Аннотация: The high potential of aptamers – specific molecular agents based on short single-stranded nucleic acids – makes high demands on the molecules under development for the efficiency of interaction with target biomolecules. In this work, approaches are considered for studying the spatial structure of DNA aptamers in solution using various complementary methods, which make it possible to obtain a more complete picture of the formation of the structure and conformational changes, to track the interaction with the target protein, the tendency to oligomerization, and to characterize the spatial structure of both individual molecules and complexes.
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Nikolaeva P. A., Moryachkov R. V., Raldugina V. N., Naumova Iu. O., Novikova T. M., Spiridonova V. A.
Заглавие : Structural analysis of thrombin-binding G-aptamers in presence of bivalent ions
Место публикации : Sib. Med. Rev. - 2022. - Is. 5. - P.111-113. - ISSN 18199496 (ISSN), DOI 10.20333/25000136-2022-5-111-113; Сиб. мед. обозрение
Примечания : Cited References: 4. - The study was supported by a grant from the Russian Science Foundation (project number 21-73-20240)
Аннотация: The aim of this study was to examine 3D structures of DNA aptamers, thrombin inhibitors. The main objective was to study 3D structure 15TBA, RE31, NU172 aptamers using the small-angle X-ray scattering method. The size of 15TBA was 4.5 nm, which corresponds to a partially unfolded conformation. The CD spectrum of Nu172 in the presence of 50 mM strontium ions indicates the presence of an antiparallel G-quadruplex, the concentration o f which drops at 50°C. NU172 does not have a rigid structure, apparently due to the presence of a guanine residue in the GT loop. The NU172 aptamer does not form a stable conformation in solution either without ions or with Ba2+ and Sr2+ ions. It was shown that there is possibility of aptamers transition from one conformation to another dependently on concentration and temperature confirms that the potassium ion is a unique stabilizing ion of natural molecules containing G-quadruplexes.
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Вид документа : Статья из сборника (выпуск продолж. издания)
Шифр издания :
Автор(ы) : Moryachkov R. V., Zabluda V. N., Berlina A. N., Peters G. S., Kichkailo A. S., Sokolov A. Е.
Заглавие : Small-angle scattering applications to the analysis of aptamer structure and conformational changes
Коллективы : Internetional Conference on Synchrotron and Free Electron Laser Radiation: Generation and Application
Место публикации : Internetional Conference on Synchrotron and Free Electron Laser Radiation: Generation and Application (2020 ; 13-16 July ; Novosibirsk). AIP Conference Proceedings: book of abstracts. - 2020. - Vol. 2299. - Ст.040002. - , DOI 10.1063/5.0030394; \b Synchrotron and free electron laser radiation: generation and application (SFR-2020). - Novosibirsk. - P.45-46
Примечания : Cited References: 40. - The reported study was funded by RFBR, project number 19-32-90266 (investigation of the structure changes). This work was financially supported by Russian Science Foundation (project # 19-44-02020, obtaining of the complexes of aptamer and lead ions). We acknowledge the European Synchrotron Radiation Facility for provision of synchrotron radiation facilities (experiment #MX-2039) and we would like to thank Bart Van Laer for assistance in using beamline BM29
Аннотация: Aptamers, structured single-chain oligonucleotides, are promising tools for detection of a wide variety of compounds, from high to low molecular weight, and affecting on them. The aptamers that are most affine for a detectable compound are selected from the libraries of random sequences by the SELEX method (Systematic evolution of ligands by exponential enrichment). The reason why aptamers deserve a special consideration lies in the specific features of their structure and the mechanism of binding to their target. Aptamers can be exploited for metal-ion sensing, biosensing, drug delivery and other functions. To apply the oligonucleotides in the medicine, ecology, food production, agriculture, etc., we need to know how the aptamers bind to their targets, how they change their conformation upon specific binding and how the environment influences on the affinity of aptamers. Small-Angle X-ray scattering showed that the interaction of aptamers with heavy metal and other divalent ions proceeds according to different mechanisms, and the aptamers used undergo different conformational changes.
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Вид документа : Статья из сборника (однотомник)
Шифр издания :
Автор(ы) : Moryachkov R. V., Zabluda V. N., Sokolov A. Е., Shchugoreva I. A., Tomilin F. N., Peters G., Spiridonova V. A.
Заглавие : Small-Angle scattering applications to the analysis of aptamer structure and conformational changes
Коллективы : Aptamers in Russia, international conference
Место публикации : Aptamers in Russia, international conference (1 ; 2019 ; Aug. 27-30 ; Krasnoyarsk). Molecular Therapy - Nucleic Acids: book of abstracts of the 1st Int. conf. "Aptamers in Russia 2019". - 2019. - Vol. 17, Suppl. 1. - P.4
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10.

Вид документа : Статья из сборника (однотомник)
Шифр издания :
Автор(ы) : Tomilin F. N., Moryachkov R. V., Shchugoreva I. A., Kaufman E., Drevolsky A., Sokolov A. Е.
Заглавие : Molecular structure restoration of aptamers by small angle X-ray scattering and computer simulation
Коллективы : Aptamers in Russia, international conference
Место публикации : Aptamers in Russia, international conference (1 ; 2019 ; Aug. 27-30 ; Krasnoyarsk). Molecular Therapy - Nucleic Acids: book of abstracts of the 1st Int. conf. "Aptamers in Russia 2019". - 2019. - Vol. 17, Suppl. 1. - P.4
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