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Вид документа : Статья из журнала
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Автор(ы) : Tomilin F. N., Moryachkov R., Shchugoreva I., Zabluda V. N., Peters G., Platunov M. S., Spiridonova V., Melnichuk A., Atrokhova A., Zamay S. S., Ovchinnikov S. G., Zamay G. S., Sokolov A. Е., Zamay T. N., Berezovski M. V., Kichkailo A. S.
Заглавие : Four steps for revealing and adjusting the 3D structure of aptamers in solution by small-angle X-ray scattering and computer simulation
Место публикации : Anal. Bioanal. Chem. - 2019. - Vol. 411, Is. 25. - P.6723-6732. - ISSN 16182642 (ISSN), DOI 10.1007/s00216-019-02045-0
Примечания : 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.
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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Вид документа : Статья из журнала
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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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