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    Small-angle scattering applications to the analysis of aptamer structure and conformational changes / R. V. Moryachkov, V. N. Zabluda, A. N. Berlina [et al.] // AIP Conference Proceedings : book of abstracts. - 2020. - Vol. 2299. - Ст. 040002 ; Synchrotron and free electron laser radiation: generation and application (SFR-2020). - Novosibirsk. - P. 45-46, DOI 10.1063/5.0030394. - 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
   Перевод заглавия: Использование малоуглового рассеяния для анализа структуры и конформационных изменений аптамеров
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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Держатели документа:
Kirensky Institute of Physics, Akademgorodok 50, bld. 38, Krasnoyarsk, 660012, Russian Federation
Federal Research Center "Krasnoyarsk Science Center SB RAS", Akademgorodok 50, Krasnoyarsk, 660012, Russian Federation
A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky pr. 33, Moscow, 119071, Russian Federation
National Research Center “Kurchatov Institute”, Akademika Kurchatova pl. 1, Moscow, 123182, Russian Federation

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Moryachkov, R. V.; Морячков, Роман Владимирович; Zabluda, V. N.; Заблуда, Владимир Николаевич; Berlina, A. N.; Peters, G. S.; Kichkailo, A. S.; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Internetional Conference on Synchrotron and Free Electron Laser Radiation: Generation and Application(2020 ; 13-16 July ; Novosibirsk)

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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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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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Molecular structure restoration of aptamers by small angle X-ray scattering and computer simulation / F. N. Tomilin, R. V. Moryachkov, I. A. Shchugoreva [et al.] // 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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Tomilin, F. N.; Томилин, Феликс Николаевич; Moryachkov, R. V.; Морячков, Роман Владимирович; Shchugoreva, I. A.; Kaufman, E.; Drevolsky, A.; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Aptamers in Russia, international conference(1 ; 2019 ; Aug. 27-30 ; Krasnoyarsk)
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Small-Angle scattering applications to the analysis of aptamer structure and conformational changes / R. V. Moryachkov, V. N. Zabluda, A. Е. Sokolov [et al.] // 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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Moryachkov, R. V.; Морячков, Роман Владимирович; Zabluda, V. N.; Заблуда, Владимир Николаевич; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Shchugoreva, I. A.; Tomilin, F. N.; Томилин, Феликс Николаевич; Peters, G.; Петерс Георгий; Spiridonova, V. A.; Спиридонова В. А.; Aptamers in Russia, international conference(1 ; 2019 ; Aug. 27-30 ; Krasnoyarsk)
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Moryachkov, R. V.
Structure approaches to study of DNA aptamers in solution / R. V. Moryachkov, P. A. Nikolaeva, V. A. Spiridonova // Sib. Med. Rev. - 2021. - Vol. 2021, Is. 2. - P. 76-78 ; Сиб. мед. обозрение, DOI 10.20333/2500136-2021-2-76-78. - Cited References: 5. - The reported study was funded by RFBR, project number 19-32-90266 . - ISSN 1819-9496
Кл.слова (ненормированные):
biomolecules in solution -- tertiary structure -- small-angle X-ray scattering (SAXS) -- structure analysis
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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Держатели документа:
Federal Research Center “Krasnoyarsk Science Center SB RAS”, 50, Akademgorodok St., Krasnoyarsk, 660036, Russian Federation
Kirensky Institute of Physics, Bld. 38, 50, Akademgorodok St., Krasnoyarsk, 660036, Russian Federation
Lomonosov Moscow State University, 1, Leninskie Gory St., Moscow, 119992, Russian Federation
A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Bld. 40, 1, Leninskie Gory St., Moscow, 119992, Russian Federation

Доп.точки доступа:
Nikolaeva, P. A.; Spiridonova, V. A.; Морячков, Роман Владимирович

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Applying joint theoretical experimental research to aptamer modeling / I. A. Shchugoreva, P. V. Artyushenko, F. N. Tomilin [et al.] // Sib. Med. Rev. - 2021. - Vol. 2021, Is. 2. - P. 105-106 ; Сиб. мед. обозрение, DOI 10.20333/2500136-2021-2-105-106. - Cited References: 4 . - ISSN 1819-9496
Кл.слова (ненормированные):
LC-18 -- DNA aptamer -- lung adenocarcinoma -- SAXS -- DFTB3
Аннотация: The aim of the research. In this work we studied the structure of LC-18 DNA aptamer, which exhibits specific binding to lung adenocarcinoma cells. Obtain-ing the 3D structure of the aptamer is necessary for understanding the mechanism of binding of the aptamer to the target. Therefore, the aim of the research was modeling of the LC-18 aptamer spatial structure using combination of theoretical methods: DNA folding tools, quantum-chemical calculations and molecular dynamic simulations. Material and methods. The secondary structure of the LC-18 aptamer was predicted by using OligoAnalyzer and MFold online software under the conditions typical small-angle X-ray scattering (SAXS) experiment. The molecular modeling of the aptamer was carried out using the Avogadro program. For prediction of the structure two computational methods were used: quantum-mechanical method with third-order density-functional tight-binding (DFTB3) and molecular dynamics (MD) with force fields. Results. In this paper it was shown that molecular simulations can predict structures from the SAXS experiments. OligoAnalyzer and MFold web servers have been used to generate a set of several likely models. However, more accurate calculations have showed that these models do not predict the relative importance of isomers. Meanwhile, application of quantum-chemical and molecular dynamics calculations have showed reliable molecular structures which have a small deviations from the experimental SAXS curves. Conclusion. This study demonstrates the approach for modeling 3D structures of DNA-aptamers in solution using both experimental and theoretical meth-ods. It could be very helpful in designing more efficient aptamers based on results obtained from molecular simulations.

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Держатели документа:
Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Science Center SB RAS”, Krasnoyarsk, 660036, Russian Federation
Department of Chemistry, Siberian Federal University, Krasnoyarsk, 660041, Russian Federation
Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, Krasnoyarsk, 660012, Russian Federation
Nanoscience Center and Department of Chemistry, University of Jyvaskyla, Jyvaskyla, 40014, Finland
Department of Chemistry, Lomonosov Moscow State University, Moscow, 119234, Russian Federation

Доп.точки доступа:
Shchugoreva, I. A.; Artyushenko, P. V.; Tomilin, F. N.; Morozov, D. I.; Mironov, V. A.; Moryachkov, R. V.; Морячков, Роман Владимирович; Kichkailo, A. S.

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    The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer / D. Morozov, V. Mironov, R. V. Moryachkov [et al.] // Mol. Ther. Nucl. Acids. - 2021. - Vol. 25. - P. 316-327, DOI 10.1016/j.omtn.2021.07.015. - 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 . - ISSN 2162-2531
   Перевод заглавия: Роль малоуглового рентгеновского рассеяния и молекулярного моделирования в выснении трёхмерной структуры ДНК аптамера против рака лёгкого
Кл.слова (ненормированные):
aptamer -- oligonucleotide -- tertiary structure -- spatial structure -- lung adenocarcinoma -- small-angle X-ray scattering -- SAXS -- molecular dynamics -- fragment molecular orbital -- molecular simulations
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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Держатели документа:
Nanoscience Center and Department of Chemistry, University of Jyvaskyla, P.O. Box 35, Jyvaskyla, 40014, Finland
Department of Chemistry, Lomonosov Moscow State University, Moscow, Russian Federation
Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk, 660036, Russian Federation
Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk, 660036, Russian Federation
Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk, 660022, Russian Federation
Department of Chemistry, Siberian Federal University, 79 Svobodny pr., Krasnoyarsk, 660041, Russian Federation
European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, Hamburg, 22603, Germany
Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5, Canada
Research Center for Computational Design of Advanced Functional Materials, National Institute of Advanced Industrial Science and Technology, Tsukuba, 305-8568, Japan
Computational Science Division, Argonne National Laboratory, Lemont, IL, United States

Доп.точки доступа:
Morozov, D.; Mironov, V.; Moryachkov, R. V.; Морячков, Роман Владимирович; Shchugoreva, I. A.; Artyushenko, P. V.; Zamay, G. S.; Kolovskaya, O. S.; Zamay, T. N.; Krat, A. V.; Molodenskiy, D. S.; Zabluda, V. N.; Заблуда, Владимир Николаевич; Veprintsev, D. V.; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Zukov, R. A.; Berezovski, M. V.; Tomilin, F. N.; Томилин, Феликс Николаевич; Fedorov, D. G.; Alexeev, Y.; Kichkailo, A. S.
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The role of small-angle X-ray scattering and molecular simulations in 3D structure elucidation of a DNA aptamer-cancer cells magnetic separation agent / R. V. Moryachkov, D. Morozov, V. Mironov [et al.] // 4th International Baltic Conference on Magnetism (IBCM 2021) : Book of abstracts. - 2021. - P. 168. - Cited References: 2. - The reported study was funded by RFBR, project number 19-32-90266

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Держатели документа:
Kirensky Institute of Physics, Federal Research Center KSC SB RAS

Доп.точки доступа:
Moryachkov, R. V.; Морячков, Роман Владимирович; Morozov, D.; Mironov, V.; Shchugoreva, I.; Artyushenko, P. V.; Артюшенко, Полина Владимировна; Zamay, G. S.; Замай Г. С.; Molodenskiy, D. S.; Zabluda, V. N.; Заблуда, Владимир Николаевич; Kichkailo, A.S.; Кичкайло, Анна Сергеевна; Sokolov, A. Е.; Соколов, Алексей Эдуардович; International Baltic Conference on Magnetism: focus on nanobiomedicine and smart materials(4 ; 2021 ; Aug. 29-Sept. 2 ; Svetlogorsk, Russia); Балтийский федеральный университет им. И. Канта
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Исследование пространственной структуры бионаноконъюгатов на основе ДНК-аптамеров синхротронными методами / Р. В. Морячков, В. Н. Заблуда, И. А. Щугорева [и др.] // 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. - Библиогр.: 1 . - ISBN 978-5-90168-835-9

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Держатели документа:
Институт физики им. Л.В. Киренского СО РАН

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Овчинников, Сергей Геннадьевич \сопредс., прогр. ком.\; Ovchinnikov, S. G.; Морячков, Роман Владимирович; Moryachkov R. V.; Заблуда, Владимир Николаевич; Zabluda, V. N.; Щугорева, Ирина Андреевна; Артюшенко, Полина Владимировна; Artyushenko, P. V.; Кичкайло, Анна Сергеевна; Kichkaylo A.S.; Спиридонова, В. А.; Берлина, А. Н.; Соколов, Алексей Эдуардович; Sokolov, A. E.; Сибирский семинар по высокотемпературной сверхпроводимости и физике наноструктур(13 ; 2021 ; 24-25 мая ; Новосибирск); 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
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10.

Шустин, Максим Сергеевич.
Низкоэнергетическая модель спин-поляризованной сверхпроводящей нанопроволоки в режиме сильных электронных корреляций / М. С. Шустин, Р. В. Морячков, В. Н. Заблуда, И. А. Щугорева [и др.] // 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. - 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) . - ISBN 978-5-90168-835-9

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Держатели документа:
Институт физики им. Л.В. Киренского СО РАН

Доп.точки доступа:
Овчинников, Сергей Геннадьевич \сопредс., прогр. ком.\; Ovchinnikov, S. G.; Морячков, Роман Владимирович; Moryachkov R. V.; Заблуда, Владимир Николаевич; Zabluda, V. N.; Щугорева, Ирина Андреевна; Артюшенко, Полина Владимировна; Artyushenko, P. V.; Кичкайло, Анна Сергеевна; Kichkaylo A.S.; Спиридонова, В. А.; Берлина, А. Н.; Соколов, Алексей Эдуардович; Sokolov, A. E.; Shustin, M. S.; Сибирский семинар по высокотемпературной сверхпроводимости и физике наноструктур(13 ; 2021 ; 24-25 мая ; Новосибирск); 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
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