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Applying jointtheoreticalexperimental researchto aptamer modeling :научное издание Shchugoreva I.A.Artyushenko P.V.Tomilin F.N.2021 год

Applying joint theoretical experimental research to aptamer modeling : научное издание
статья из журнала

Дополнительные ссылки: eLibrary
База данных: Каталог библиотеки СФУ
Библиографическое описание: Applying joint theoretical experimental research to aptamer modeling : научное издание / I. A. Shchugoreva [и др.]. - Текст : непосредственный // Сибирское медицинское обозрение. - 2021. - №2. - С. 105-106. - ISSN 1819-9496. - ISSN 2500-0136, DOI 10.20333/25000136-2021-2-105-106.
Аннотация: <jats:p>The aim of the research. In this work we studied the structure of LC-18 DNA aptamer, which exhibits specifi c binding to lung adenocarcinoma cells. Obtaining the 3D structure of the aptamer is necessary for understanding the mechanism of binding of the aptamer to the target. Th erefore, 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. Th e secondary structure of the LC-18 aptamer was predicted by using OligoAnalyzer and MFold online soft ware under the conditions typical small-angle X-ray scattering (SAXS) experiment. Th e 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 fi elds. 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. Th is study demonstrates the approach for modeling 3D structures of DNA-aptamers in solution using both experimental and theoretical methods. It could be very helpful in designing more effi cient aptamers based on results obtained from molecular simulations.</jats:p>
Год издания: 2021
Авторы: Shchugoreva I.A., Artyushenko P.V., Tomilin F.N., Morozov D.I., Mironov V.A., Moryachkov R.V., Kichkailo A.S.
Издательство: Красноярский государственный медицинский университет им. проф. В.Ф. Войно-Ясенецкого, Красноярск
Источник: Сибирское медицинское обозрение
Выпуск: №2
Номера страниц: 105-106
Количество экземпляров:
Твёрдая копия издания отсутствует в фонде библиотеки

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