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

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

Доп.точки доступа:
Tomilin, F. N.; Томилин, Феликс Николаевич; Moryachkov, R.; Морячков, Роман Владимирович; Shchugoreva, I.; Zabluda, V. N.; Заблуда, Владимир Николаевич; Peters, G.; Platunov, M. S.; Платунов, Михаил Сергеевич; Spiridonova, V.; Melnichuk, A.; Atrokhova, A.; Zamay, S. S.; Замай, С. С.; Ovchinnikov, S. G.; Овчинников, Сергей Геннадьевич; Zamay, G. S.; Замай, Галина Сергеевна; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Zamay, T. N.; Замай, Т. Н.; Berezovski, M. V.; Kichkailo, A. S.
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Structural analysis of thrombin-binding G-aptamers in presence of bivalent ions / P. A. Nikolaeva, R. V. Moryachkov, V. N. Raldugina [et al.] // Sib. Med. Rev. - 2022. - Is. 5. - P. 111-113 ; Сиб. мед. обозрение, DOI 10.20333/25000136-2022-5-111-113. - Cited References: 4. - The study was supported by a grant from the Russian Science Foundation (project number 21-73-20240) . - ISSN 1819-9496
Кл.слова (ненормированные):
3D structures -- DNA aptamers -- thrombin inhibitors -- G-quadruplexes
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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Держатели документа:
Department bioimformatics and bioengineery, Lomonosov Moscow State University, Moscow, 119992, Russian Federation
Federal Research Center «Krasnoyarsk Science Center SB RAS», Krasnoyarsk, 660036, Russian Federation
Kirensky Institute of Physics, Krasnoyarsk, 660036, Russian Federation
Belozersky Institute of physical chemical biology, Lomonosov Moscow State University, Moscow, 119992, Russian Federation

Доп.точки доступа:
Nikolaeva, P. A.; Moryachkov, R. V.; Морячков, Роман Владимирович; Raldugina, V. N.; Naumova, Iu. O.; Novikova, T. M.; Spiridonova, V. A.

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