B1 Kirjoitus tieteellisessä aikakauslehdessä
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-tekijät tai -toimittajat
Julkaisun tiedot
Julkaisun kaikki tekijät tai toimittajat: Shchugoreva, I. A.; Artyushenko, P. V.; Tomilin, F. N.; Morozov, Dmitry; Mironov, Vladimir; Moryachkov, R. V.; Kichkailo, A. S.
Lehti tai sarja: Sibirskoe Medicinskoe Obozrenie
ISSN: 1819-9496
eISSN: 2500-0136
Julkaisuvuosi: 2021
Volyymi: 2021
Lehden numero: 2
Artikkelin sivunumerot: 105-106
Kustantaja: Krasnoyarsk State Medical University
Julkaisumaa: Venäjä
Julkaisun kieli: englanti
DOI: https://doi.org/10.20333/2500136-2021-2-105-106
Pysyvä verkko-osoite: https://smr.krasgmu.ru/journal/2103_24_shchugoreva.pdf
Julkaisun avoin saatavuus: Avoimesti saatavilla
Julkaisukanavan avoin saatavuus: Kokonaan avoin julkaisukanava
Lisätietoja: Conference materials. 5th International Seminar "Digital Medicines at the Junction of Sciences."
Tiivistelmä
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.
YSO-asiasanat: syöpäsolut; adenokarsinooma; oligonukleotidit; DNA; molekyylidynamiikka; kvanttikemia; laskennallinen kemia
Vapaat asiasanat: DFTB3; DNA aptamer; LC-18; Lung adenocarcinoma; SAXS
Liittyvät organisaatiot
OKM-raportointi: Kyllä
Raportointivuosi: 2021