B1 Non-refereed journal articles
Applying joint theoretical experimental research to aptamer modeling (2021)


Shchugoreva, I. A., Artyushenko, P. V., Tomilin, F. N., Morozov, D., Mironov, V., Moryachkov, R. V., & Kichkailo, A. S. (2021). Applying joint theoretical experimental research to aptamer modeling. Sibirskoe Medicinskoe Obozrenie, 2021(2), 105-106. https://doi.org/10.20333/2500136-2021-2-105-106


JYU authors or editors


Publication details

All authors or editors: Shchugoreva, I. A.; Artyushenko, P. V.; Tomilin, F. N.; Morozov, Dmitry; Mironov, Vladimir; Moryachkov, R. V.; Kichkailo, A. S.

Journal or series: Sibirskoe Medicinskoe Obozrenie

ISSN: 1819-9496

eISSN: 2500-0136

Publication year: 2021

Volume: 2021

Issue number: 2

Pages range: 105-106

Publisher: Krasnoyarsk State Medical University

Publication country: Russian Federation

Publication language: English

DOI: https://doi.org/10.20333/2500136-2021-2-105-106

Persistent website address: https://smr.krasgmu.ru/journal/2103_24_shchugoreva.pdf

Publication open access: Openly available

Publication channel open access: Open Access channel

Additional information: Conference materials. 5th International Seminar "Digital Medicines at the Junction of Sciences."


Abstract

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-18 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 meth-ods. It could be very helpful in designing more efficient aptamers based on results obtained from molecular simulations.


Keywords: cancer cells; adenocarcinoma; oligonucleotides; DNA; molecular dynamics; quantum chemistry; computational chemistry

Free keywords: DFTB3; DNA aptamer; LC-18; Lung adenocarcinoma; SAXS


Contributing organizations


Ministry reporting: Yes


Last updated on 2021-29-07 at 09:05