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
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
Reporting Year: 2021