Applying joint theoretical experimental research to aptamer modeling : научное издание


Тип публикации: статья из журнала

Год издания: 2021

Идентификатор DOI: 10.20333/2500136-2021-2-105-106

Ключевые слова: 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. Obtaining 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-Показать полностью18 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 methods. It could be very helpful in designing more efficient aptamers based on results obtained from molecular simulations.

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Журнал: Сибирское медицинское обозрение

Выпуск журнала: 2

Номера страниц: 105-106

ISSN журнала: 18199496

Место издания: Красноярск

Издатель: Красноярский государственный медицинский университет им. проф. В.Ф. Войно-Ясенецкого


  • Shchugoreva Irina A. (Siberian Federal University)
  • Artyushenko Polina V. (Siberian Federal University)
  • Tomilin Felix N. (Siberian Federal University)
  • Morozov Dmitry I. (University of Jyvaskyla)
  • Mironov Vladimir A. (Lomonosov Moscow State University)
  • Moryachkov Roman V. (Kirensky Institute of Physics)
  • Kichkailo Anna.S. (Federal Research Center "Krasnoyarsk Science Center SB RAS”)

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