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    Aptamer-mediated targeted hyperthermia caused by gold nanoparticles / A. Dubynina [et al.] // 11th Annual Meet. of the Oligonucleotide Therapeutics Soc. (OTS). - 2015. - P. 127
   Перевод заглавия: Аптамер-опосредованная целевая гипертермия наночастицами золота

Доп.точки доступа:
Dubynina, A. V.; Дубынина А. В.; Semina, P. N.; Семина, Полина Николаевна; Sokolov, A. E.; Соколов, Алексей Эдуардович; Zabluda, V. N.; Заблуда, Владимир Николаевич; Aleksandrovskii, A. S.; Александровский, Александр Сергеевич; Karacharov, A.; Zamay, G. S.; Замай, Галина Сергеевна; Kolovskaya, O. S.; Ivanchenko, T.; Govorina, Y.; Zamay, A. S.; Замай, Анна Сергеевна; Zamay, T. S.; Замай Т. С.; Annual Meeting of the Oligonucleotide Therapeutics Society(11 ; 2015 ; Sept. ; 22-24 ; Leinden, the Netherlands)
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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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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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